/** Compares our trees, and triggers repairs for any ranges that mismatch. */
public void run() {
InetAddress local = FBUtilities.getLocalAddress();
// restore partitioners (in case we were serialized)
if (ltree.partitioner() == null) ltree.partitioner(StorageService.getPartitioner());
if (rtree.partitioner() == null) rtree.partitioner(StorageService.getPartitioner());
// compare trees, and collect differences
differences.addAll(MerkleTree.difference(ltree, rtree));
// choose a repair method based on the significance of the difference
String format =
"Endpoints " + local + " and " + remote + " %s for " + cfname + " on " + range;
if (differences.isEmpty()) {
logger.info(String.format(format, "are consistent"));
completed(remote, cfname);
return;
}
// non-0 difference: perform streaming repair
logger.info(String.format(format, "have " + differences.size() + " range(s) out of sync"));
try {
performStreamingRepair();
} catch (IOException e) {
throw new RuntimeException(e);
}
}
public static boolean testCommand(
final Context context,
final String command,
final String contains,
final List<String> arguments) {
try {
final List<String> commandAndArgs = new ArrayList<String>();
commandAndArgs.add(command);
commandAndArgs.addAll(arguments);
final ProcessBuilder pb = new ProcessBuilder(commandAndArgs);
logCommand(context, pb);
final Process compilation = pb.start();
final ConsumeStream result = ConsumeStream.start(compilation.getInputStream(), null);
final ConsumeStream error = ConsumeStream.start(compilation.getErrorStream(), null);
compilation.waitFor();
result.join();
error.join();
return error.output.toString().contains(contains)
|| result.output.toString().contains(contains);
} catch (IOException ex) {
context.log(ex.getMessage());
return false;
} catch (InterruptedException ex) {
context.log(ex.getMessage());
return false;
}
}
// Deze method maakt alle types activities aan
public void makeActivities() {
for (Course course : courses) {
activities.addAll(createActivity(course, course.numberLectures, 0, "Hoorcollege", true));
activities.addAll(
createActivity(
course, course.numberWorkGroups, course.maxStudentsGroups, "Werkcollege", false));
activities.addAll(
createActivity(
course, course.numberPracticum, course.maxStudentsPracticum, "Practicum", false));
}
/*
//Print alle Activities met bijbehorende studentnummers van studenten
for (int i = 0; i < activities.size(); i++) {
//Stukje code die studentNumber uit lijst van Student extraheert
List studentList = activities.get(i).studentGroup;
List<Integer> studentNumberList = new ArrayList<>();
int studentNumber;
for (int x = 0; x < studentList.size(); x++) {
Student thisStudent = (Student) studentList.get(x);
studentNumber = thisStudent.studentNumber;
studentNumberList.add(studentNumber);
}
System.out.println(activities.get(i).course.name + " | Aantal " + activities.get(i).activity + ": " +
activities.get(i).occurrence + " | Groep: " + activities.get(i).groupNumber + " | Aantal studenten: " + activities.get(i).studentGroup.size() + " | Studentnummers: " +
studentNumberList);
}
*/
// System.out.println("Aantal Activities: " + activities.size());
}
void test(String[] opts, String className) throws Exception {
count++;
System.err.println("Test " + count + " " + Arrays.asList(opts) + " " + className);
Path testSrcDir = Paths.get(System.getProperty("test.src"));
Path testClassesDir = Paths.get(System.getProperty("test.classes"));
Path classes = Paths.get("classes." + count);
classes.createDirectory();
Context ctx = new Context();
PathFileManager fm = new JavacPathFileManager(ctx, true, null);
JavaCompiler compiler = ToolProvider.getSystemJavaCompiler();
List<String> options = new ArrayList<String>();
options.addAll(Arrays.asList(opts));
options.addAll(Arrays.asList("-verbose", "-XDverboseCompilePolicy", "-d", classes.toString()));
Iterable<? extends JavaFileObject> compilationUnits =
fm.getJavaFileObjects(testSrcDir.resolve(className + ".java"));
StringWriter sw = new StringWriter();
PrintWriter out = new PrintWriter(sw);
JavaCompiler.CompilationTask t =
compiler.getTask(out, fm, null, options, null, compilationUnits);
boolean ok = t.call();
System.err.println(sw.toString());
if (!ok) {
throw new Exception("compilation failed");
}
File expect = new File("classes." + count + "/" + className + ".class");
if (!expect.exists()) throw new Exception("expected file not found: " + expect);
long expectedSize = new File(testClassesDir.toString(), className + ".class").length();
long actualSize = expect.length();
if (expectedSize != actualSize)
throw new Exception("wrong size found: " + actualSize + "; expected: " + expectedSize);
}
/**
* Return a List of SA Fields for all the java fields in this class, including all inherited
* fields. This includes hidden fields. Thus the returned list can contain fields with the same
* name. Return an empty list if there are no fields. Only designed for use in a debugging system.
*/
public List getAllFields() {
// Contains a Field for each field in this class, including immediate
// fields and inherited fields.
List allFields = getImmediateFields();
// transitiveInterfaces contains all interfaces implemented
// by this class and its superclass chain with no duplicates.
ObjArray interfaces = getTransitiveInterfaces();
int n = (int) interfaces.getLength();
for (int i = 0; i < n; i++) {
InstanceKlass intf1 = (InstanceKlass) interfaces.getObjAt(i);
if (Assert.ASSERTS_ENABLED) {
Assert.that(intf1.isInterface(), "just checking type");
}
allFields.addAll(intf1.getImmediateFields());
}
// Get all fields in the superclass, recursively. But, don't
// include fields in interfaces implemented by superclasses;
// we already have all those.
if (!isInterface()) {
InstanceKlass supr;
if ((supr = (InstanceKlass) getSuper()) != null) {
allFields.addAll(supr.getImmediateFields());
}
}
return allFields;
}
public static void readExternal(
final Element element,
final List<ShelvedChangeList> changes,
final List<ShelvedChangeList> recycled)
throws InvalidDataException {
changes.addAll(ShelvedChangeList.readChanges(element, false, true));
recycled.addAll(ShelvedChangeList.readChanges(element, true, true));
}
@Override
public List<String> getCandidates(String word) {
List<String> suggestions = new ArrayList<>();
List<List<String>> partList = splitter.getAllSplits(word);
List<String> candidates = new ArrayList<>();
for (List<String> parts : partList) {
candidates.addAll(super.getCandidates(parts));
}
suggestions.addAll(candidates);
return suggestions;
}
@Override
public List<DecompilerBasicBlock> getAllBasicBlocks() {
List<DecompilerBasicBlock> blocks = new ArrayList<>();
blocks.add(head);
for (DecompilerBlock b : thenBranch) {
blocks.addAll(b.getAllBasicBlocks());
}
for (DecompilerBlock b : elseBranch) {
blocks.addAll(b.getAllBasicBlocks());
}
return blocks;
}
public static File[] getDirectoryListing(File dir) {
SortedSet<File> dirSet = new TreeSet<File>();
SortedSet<File> fileSet = new TreeSet<File>();
File[] files = dir.listFiles();
for (int i = 0; i < files.length; i++) {
if (files[i].isDirectory()) dirSet.add(files[i]);
else fileSet.add(files[i]);
}
List<File> fileList = new LinkedList<File>();
fileList.addAll(dirSet);
fileList.addAll(fileSet);
return fileList.toArray(new File[] {});
}
private BundleInfo[] orderingInitialConfig(List setToInitialConfig) {
List notToBeStarted = new LinkedList();
List toBeStarted = new LinkedList();
for (Iterator ite2 = setToInitialConfig.iterator(); ite2.hasNext(); ) {
BundleInfo bInfo = (BundleInfo) ite2.next();
if (bInfo.isMarkedAsStarted()) toBeStarted.add(bInfo);
else notToBeStarted.add(bInfo);
}
setToInitialConfig.clear();
setToInitialConfig.addAll(notToBeStarted);
setToInitialConfig.addAll(toBeStarted);
return Utils.getBundleInfosFromList(setToInitialConfig);
}
private static <T> Pair<List<T>, List<T>> splitData(List<T> original, double splitForSecond) {
List<T> first = new ArrayList<>();
List<T> second = new ArrayList<>();
if (splitForSecond > 0.0) {
Collections.shuffle(original, new Random(0L));
int numFirst = (int) ((1.0 - splitForSecond) * original.size());
first.addAll(original.subList(0, numFirst));
second.addAll(original.subList(numFirst, original.size()));
} else {
first.addAll(original);
// second stays empty
}
return Tuples.pair(first, second);
}
private static List<? extends StaticError> flattenErrors(Iterable<? extends StaticError> ex) {
List<StaticError> result = new LinkedList<StaticError>();
for (StaticError err : ex) {
result.addAll(flattenErrors(err));
}
return result;
}
/**
* Method removes a Spring bean definition from the XML application context file. Bean definition
* is identified by its id or bean name.
*
* @param project
* @param id
*/
public void removeBeanDefinition(File configFile, Project project, String id) {
Source xsltSource;
Source xmlSource;
try {
xsltSource =
new StreamSource(new ClassPathResource("transform/delete-bean.xsl").getInputStream());
xsltSource.setSystemId("delete-bean");
List<File> configFiles = new ArrayList<>();
configFiles.add(configFile);
configFiles.addAll(getConfigImports(configFile, project));
for (File file : configFiles) {
xmlSource = new StringSource(FileUtils.readToString(new FileInputStream(configFile)));
// create transformer
Transformer transformer = transformerFactory.newTransformer(xsltSource);
transformer.setParameter("bean_id", id);
// transform
StringResult result = new StringResult();
transformer.transform(xmlSource, result);
FileUtils.writeToFile(format(result.toString(), project.getSettings().getTabSize()), file);
return;
}
} catch (IOException e) {
throw new ApplicationRuntimeException(UNABLE_TO_READ_TRANSFORMATION_SOURCE, e);
} catch (TransformerException e) {
throw new ApplicationRuntimeException(FAILED_TO_UPDATE_BEAN_DEFINITION, e);
}
}
public String _path(String args[]) {
List<String> list = new ArrayList<String>();
for (int i = 1; i < args.length; i++) {
list.addAll(Processor.split(args[i]));
}
return Processor.join(list, File.pathSeparator);
}
/** Finds the lexical items used to produce the highest scoring parse. */
public List getMaxLexEntries() {
List result = new LinkedList();
for (ParseResult p : bestParses) {
result.addAll(p.getLexEntries());
}
return result;
}
/** Finds the lexical items used to produce the highest scoring parse with semantics sem. */
public List getMaxLexEntriesFor(Exp sem) {
List result = new LinkedList();
for (ParseResult p : findBestParses(allParses, sem)) {
result.addAll(p.getLexEntries());
}
return result;
}
private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
Set<String> keys = new HashSet<String>();
boolean sawGoodGT = false;
boolean sawGoodQual = false;
boolean sawGenotypeFilter = false;
for (Genotype g : vc.getGenotypes().values()) {
keys.addAll(g.getAttributes().keySet());
if (g.isAvailable()) sawGoodGT = true;
if (g.hasNegLog10PError()) sawGoodQual = true;
if (g.isFiltered() && g.isCalled()) sawGenotypeFilter = true;
}
if (sawGoodQual) keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
if (sawGenotypeFilter) keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
// make sure the GT is first
if (sawGoodGT) {
List<String> newList = new ArrayList<String>(sortedList.size() + 1);
newList.add(VCFConstants.GENOTYPE_KEY);
newList.addAll(sortedList);
sortedList = newList;
}
return sortedList;
}
/** Loads streamhost address and ports from the proxies on the local server. */
private void initStreamHosts() {
List<Bytestream.StreamHost> streamHosts = new ArrayList<Bytestream.StreamHost>();
Iterator it = proxies.iterator();
IQ query;
PacketCollector collector;
Bytestream response;
while (it.hasNext()) {
String jid = it.next().toString();
query =
new IQ() {
public String getChildElementXML() {
return "<query xmlns=\"http://jabber.org/protocol/bytestreams\"/>";
}
};
query.setType(IQ.Type.GET);
query.setTo(jid);
collector = connection.createPacketCollector(new PacketIDFilter(query.getPacketID()));
connection.sendPacket(query);
response = (Bytestream) collector.nextResult(SmackConfiguration.getPacketReplyTimeout());
if (response != null) {
streamHosts.addAll(response.getStreamHosts());
}
collector.cancel();
}
this.streamHosts = streamHosts;
}
/**
* Obtain a new Node from a type that matches the given string. It will try to correctly detect
* RealVar and constant nodes. The Node is cloned and initialized, so it can be used separatedly
*
* @param name The type of the requested Node. It must coincide with one of the class names of
* available Nodes, unless it represents a variable or constant terminal
* @param currentGlobalDepth The depth of the requested Node in the Tree
*/
public Node newNode(String name, int currentGlobalDepth) {
System.out.println(name);
Node outNode = null;
if (name.startsWith("X")) {
outNode = new RealVar(Integer.parseInt(name.substring("X".length(), name.length())));
} else if (name.startsWith("angle")) {
outNode = new Angle(Integer.parseInt(name.substring("angle".length(), name.length())));
} else if (name.substring(0, 1).matches("\\d")) {
outNode = new RealConstant(Double.parseDouble(name));
} else if (name.equals("true")) {
outNode = new LogicConstant(1);
} else if (name.equals("false")) {
outNode = new LogicConstant(0);
} else {
List<Node> all = new ArrayList<Node>();
for (int i = 0; i < nodeSets.length; i++) {
all.addAll(nodeSets[i].getAll());
}
for (Node n : all) {
if (name.equals(n.name())) {
try {
outNode = (Node) n.clone();
} catch (CloneNotSupportedException e) {
Logger.log(e);
}
break;
}
}
}
outNode.setCurrentDepth(currentGlobalDepth);
return outNode;
}
public List<TreeNode> getChildren() {
List<TreeNode> lst = new ArrayList<TreeNode>();
for (List<TreeNodeImpl> lst1 : childs.values()) {
lst.addAll(lst1);
}
return lst;
}
ActiveFile(File f, List<Thread> list) {
file = f;
if (list != null) {
threads.addAll(list);
}
threads.add(Thread.currentThread());
}
public static Either<CommandResult> runCommand(
final Context context, final String command, final File path, final List<String> arguments) {
try {
final List<String> commandAndArgs = new ArrayList<String>();
commandAndArgs.add(command);
commandAndArgs.addAll(arguments);
final ProcessBuilder pb = new ProcessBuilder(commandAndArgs);
if (path != null) {
pb.directory(path);
}
logCommand(context, pb);
final Process compilation = pb.start();
final ConsumeStream result = ConsumeStream.start(compilation.getInputStream(), context);
final ConsumeStream error = ConsumeStream.start(compilation.getErrorStream(), context);
final int exitCode = compilation.waitFor();
result.join();
error.join();
if (result.exception != null) {
return Either.fail(result.exception);
}
if (error.exception != null) {
return Either.fail(error.exception);
}
return Either.success(
new CommandResult(result.output.toString(), error.output.toString(), exitCode));
} catch (IOException ex) {
return Either.fail(ex);
} catch (InterruptedException ex) {
return Either.fail(ex);
}
}
public boolean avrdude(Collection params) throws RunnerException {
List commandDownloader = new ArrayList();
commandDownloader.add("avrdude");
// Point avrdude at its config file since it's in a non-standard location.
if (Base.isMacOS()) {
commandDownloader.add("-C" + "hardware/tools/avr/etc/avrdude.conf");
} else if (Base.isWindows()) {
String userdir = System.getProperty("user.dir") + File.separator;
commandDownloader.add("-C" + userdir + "hardware/tools/avr/etc/avrdude.conf");
} else {
// ???: is it better to have Linux users install avrdude themselves, in
// a way that it can find its own configuration file?
commandDownloader.add("-C" + "hardware/tools/avrdude.conf");
}
if (Preferences.getBoolean("upload.verbose")) {
commandDownloader.add("-v");
commandDownloader.add("-v");
commandDownloader.add("-v");
commandDownloader.add("-v");
} else {
commandDownloader.add("-q");
commandDownloader.add("-q");
}
// XXX: quick hack to chop the "atmega" off of "atmega8" and "atmega168",
// then shove an "m" at the beginning. won't work for attiny's, etc.
commandDownloader.add(
"-pm" + Preferences.get("boards." + Preferences.get("board") + ".build.mcu").substring(6));
commandDownloader.addAll(params);
return executeUploadCommand(commandDownloader);
}
private static List<? extends StaticError> flattenErrors(StaticError ex) {
List<StaticError> result = new LinkedList<StaticError>();
if (ex instanceof MultipleStaticError) {
for (StaticError err : (MultipleStaticError) ex) result.addAll(flattenErrors(err));
} else result.add(new WrappedException(ex, Debug.stackTraceOn()));
return result;
}
// Ast0.Block ---
// Ast0.Stmt[] stmts;
//
// AG:
// code: {stmt.c}
//
static List<IR0.Inst> gen(Ast0.Block n) throws Exception {
List<IR0.Inst> code = new ArrayList<IR0.Inst>();
// ... need code ...
for (Ast0.Stmt s : n.stmts) code.addAll(gen(s));
return code;
}
public static List<Library> list(File folder) {
List<Library> libraries = new ArrayList<Library>();
List<File> librariesFolders = new ArrayList<File>();
librariesFolders.addAll(discover(folder));
for (File baseFolder : librariesFolders) {
libraries.add(new Library(baseFolder));
}
// Support libraries inside of one level of subfolders? I believe this was
// the compromise for supporting library groups, but probably a bad idea
// because it's not compatible with the Manager.
String[] folderNames = folder.list(junkFolderFilter);
if (folderNames != null) {
for (String subfolderName : folderNames) {
File subfolder = new File(folder, subfolderName);
if (!librariesFolders.contains(subfolder)) {
List<File> discoveredLibFolders = discover(subfolder);
for (File discoveredFolder : discoveredLibFolders) {
libraries.add(new Library(discoveredFolder, subfolderName));
}
}
}
}
return libraries;
}
// look up and apply coarts for given rels to each sign in result
private void applyCoarts(List<String> coartRels, Collection<Sign> result) {
List<Sign> inputSigns = new ArrayList<Sign>(result);
result.clear();
List<Sign> outputSigns = new ArrayList<Sign>(inputSigns.size());
// for each rel, lookup coarts and apply to input signs, storing results in output signs
for (Iterator<String> it = coartRels.iterator(); it.hasNext(); ) {
String rel = it.next();
Collection<String> preds = (Collection<String>) _coartRelsToPreds.get(rel);
if (preds == null) continue; // not expected
Collection<Sign> coartResult = getSignsFromRelAndPreds(rel, preds);
if (coartResult == null) continue;
for (Iterator<Sign> it2 = coartResult.iterator(); it2.hasNext(); ) {
Sign coartSign = it2.next();
// apply to each input
for (int j = 0; j < inputSigns.size(); j++) {
Sign sign = inputSigns.get(j);
grammar.rules.applyCoart(sign, coartSign, outputSigns);
}
}
// switch output to input for next iteration
inputSigns.clear();
inputSigns.addAll(outputSigns);
outputSigns.clear();
}
// add results back
result.addAll(inputSigns);
}
private void insertAfter(JPegStmt node, JPegStmt after) {
// System.out.println("node: "+node);
// System.out.println("after: "+after);
// System.out.println("succs of node: "+getSuccsOf(node));
// this must be done first because the succs of node will be chanaged lately
List succOfAfter = new ArrayList();
succOfAfter.addAll(getSuccsOf(node));
unitToSuccs.put(after, succOfAfter);
Iterator succsIt = getSuccsOf(node).iterator();
while (succsIt.hasNext()) {
Object succ = succsIt.next();
List pred = getPredsOf(succ);
pred.remove(node);
pred.add(after);
}
List succOfNode = new ArrayList();
succOfNode.add(after);
unitToSuccs.put(node, succOfNode);
List predOfAfter = new ArrayList();
predOfAfter.add(node);
unitToPreds.put(after, predOfAfter);
// buildPredecessor(Chain pegChain);
}
/*
* return 0 is success, otherwise failure
*/
public final int runAdminCommandOnRemoteNode(
Node thisNode, StringBuilder output, List<String> args, List<String> stdinLines)
throws SSHCommandExecutionException, IllegalArgumentException, UnsupportedOperationException {
String humanreadable = null;
try {
this.node = thisNode;
dcomInfo = new DcomInfo(node);
List<String> fullcommand = new ArrayList<String>();
WindowsRemoteAsadmin asadmin = dcomInfo.getAsadmin();
if (stdinLines != null && !stdinLines.isEmpty()) setupAuthTokenFile(fullcommand, stdinLines);
fullcommand.addAll(args);
humanreadable = dcomInfo.getNadminPath() + " " + commandListToString(fullcommand);
// This is where the rubber meets the road...
String out = asadmin.run(fullcommand);
output.append(out);
logger.info(Strings.get("remote.command.summary", humanreadable, out));
return determineStatus(args);
} catch (WindowsException ex) {
throw new SSHCommandExecutionException(
Strings.get("remote.command.error", ex.getMessage(), humanreadable), ex);
} finally {
teardownAuthTokenFile();
}
}
// look up and apply coarts for w to each sign in result
@SuppressWarnings("unchecked")
private void applyCoarts(Word w, SignHash result) throws LexException {
List<Sign> inputSigns = new ArrayList<Sign>(result.asSignSet());
result.clear();
List<Sign> outputSigns = new ArrayList<Sign>(inputSigns.size());
// for each surface attr, lookup coarts and apply to input signs, storing results in output
// signs
for (Iterator<Pair<String, String>> it = w.getSurfaceAttrValPairs(); it.hasNext(); ) {
Pair<String, String> p = it.next();
String attr = (String) p.a;
if (!_indexedCoartAttrs.contains(attr)) continue;
String val = (String) p.b;
Word coartWord = Word.createWord(attr, val);
SignHash coartResult = getSignsFromWord(coartWord, null, null, null);
for (Iterator<Sign> it2 = coartResult.iterator(); it2.hasNext(); ) {
Sign coartSign = it2.next();
// apply to each input
for (int j = 0; j < inputSigns.size(); j++) {
Sign sign = inputSigns.get(j);
grammar.rules.applyCoart(sign, coartSign, outputSigns);
}
}
// switch output to input for next iteration
inputSigns.clear();
inputSigns.addAll(outputSigns);
outputSigns.clear();
}
// add results back
result.addAll(inputSigns);
}