void close() {
try {
if (mySelector != null) mySelector.close();
} catch (IOException e) {
}
mySelector = null;
// run down open connections and sockets.
Iterator<ServerSocketChannel> i = Acceptors.values().iterator();
while (i.hasNext()) {
try {
i.next().close();
} catch (IOException e) {
}
}
// 29Sep09: We create an ArrayList of the existing connections, then iterate over
// that to call unbind on them. This is because an unbind can trigger a reconnect,
// which will add to the Connections HashMap, causing a ConcurrentModificationException.
// XXX: The correct behavior here would be to latch the various reactor methods to return
// immediately if the reactor is shutting down.
ArrayList<EventableChannel> conns = new ArrayList<EventableChannel>();
Iterator<EventableChannel> i2 = Connections.values().iterator();
while (i2.hasNext()) {
EventableChannel ec = i2.next();
if (ec != null) {
conns.add(ec);
}
}
Connections.clear();
ListIterator<EventableChannel> i3 = conns.listIterator(0);
while (i3.hasNext()) {
EventableChannel ec = i3.next();
eventCallback(ec.getBinding(), EM_CONNECTION_UNBOUND, null);
ec.close();
EventableSocketChannel sc = (EventableSocketChannel) ec;
if (sc != null && sc.isAttached()) DetachedConnections.add(sc);
}
ListIterator<EventableSocketChannel> i4 = DetachedConnections.listIterator(0);
while (i4.hasNext()) {
EventableSocketChannel ec = i4.next();
ec.cleanup();
}
DetachedConnections.clear();
}
/** listIterator only returns those elements after the given index */
public void testListIterator2() {
List full = populatedArray(3);
ListIterator i = full.listIterator(1);
int j;
for (j = 0; i.hasNext(); j++) assertEquals(j + 1, ((Integer) i.next()).intValue());
assertEquals(2, j);
}
public static void maxFlow(ListGraph g) {
ListGraph residualG = g.residualGraph();
LinkedList<DirEdge> path = residualG.getFlowPath();
while (path != null) {
// System.out.println("Got path");
int minCapacity = ListGraph.minCapacityInPath(path);
assert minCapacity > 0;
// augment every edge on the path in the original graph
int head = g.getSource();
ListIterator it = path.listIterator();
while (it.hasNext()) {
DirEdge rEdge = (DirEdge) it.next();
int tail = rEdge.end;
DirEdge e = g.getEdge(head, tail);
e.flow += minCapacity;
// System.out.println("Augmenting (" + head + "," + tail + ") to be " + e.flow);
head = tail;
}
residualG = g.residualGraph();
// System.out.println("g:");
// g.print();
// System.out.println("Residual graph:");
// residualG.print();
path = residualG.getFlowPath();
}
}
/** Sorts the static LinkedList mainlineLinks in the order they appear on the freeway */
private LinkedList<Link> recursiveLinkSort(LinkedList<Link> links2) {
if (links2.size() == 1) {
return links2;
} else {
boolean swapMade = false;
ListIterator<Link> itr1 = links2.listIterator();
while (itr1.hasNext()) {
Link temp = itr1.next();
int tempindex = itr1.nextIndex();
// if this loop makes any switches, set the flag to true
if (links2.getFirst().getUpNode().getNodeID() == temp.getDownNode().getNodeID()) {
swapMade = true;
links2.addFirst(temp);
links2.remove(tempindex);
return this.recursiveLinkSort(links2);
}
}
if (!swapMade) {
// assign last n-1 links to links3
LinkedList<Link> links3 = new LinkedList<Link>();
Link temp = links2.getFirst();
links2.removeFirst();
links3 = this.recursiveLinkSort(links2);
links3.addFirst(temp);
return links3;
} else {
return links2;
}
}
}
/**
* Reads an array of strings from the TIFF file.
*
* @param count Number of strings to read
* @param value Offset from which to read
*/
protected String[] readASCIIArray(long count, long value) throws IOException {
_raf.seek(value);
int nstrs = 0;
List list = new LinkedList();
byte[] buf = new byte[(int) count];
_raf.read(buf);
StringBuffer strbuf = new StringBuffer();
for (int i = 0; i < count; i++) {
int b = buf[i];
if (b == 0) {
list.add(strbuf.toString());
strbuf.setLength(0);
} else {
strbuf.append((char) b);
}
}
/* We can't use ArrayList.toArray because that returns an
Object[], not a String[] ... sigh. */
String[] strs = new String[nstrs];
ListIterator iter = list.listIterator();
for (int i = 0; i < nstrs; i++) {
strs[i] = (String) iter.next();
}
return strs;
}
public String hasSameContent(JarFile2 file, JarEntry entry) throws IOException {
String thisName = null;
Long crcL = new Long(entry.getCrc());
// check if this jar contains files with the passed in entry's crc
if (_crcToEntryMap.containsKey(crcL)) {
// get the Linked List with files with the crc
LinkedList ll = (LinkedList) _crcToEntryMap.get(crcL);
// go through the list and check for content match
ListIterator li = ll.listIterator(0);
if (li != null) {
while (li.hasNext()) {
JarEntry thisEntry = (JarEntry) li.next();
// check for content match
InputStream oldIS = getJarFile().getInputStream(thisEntry);
InputStream newIS = file.getJarFile().getInputStream(entry);
if (!differs(oldIS, newIS)) {
thisName = thisEntry.getName();
return thisName;
}
}
}
}
return thisName;
}
public DirEdge getEdge(int i, int j) {
ListIterator it = edges.get(i).listIterator();
while (it.hasNext()) {
DirEdge edge = (DirEdge) it.next();
if (edge.end == j) {
return edge;
}
}
return null;
}
/*
* Print the action sequence (Probably) to the printer
*/
public void actionPrint(PrintWriter ps) {
int i = 0;
ps.println("Stepper - action sequence");
ps.println("Task ID - " + curTask);
ps.println();
ListIterator li = actionSequence.listIterator();
while (li.hasNext()) {
i++;
oclPredicate pred = (oclPredicate) li.next();
ps.println(i + ": " + pred.toString());
}
}
public static String writeGridOfRateCoeffs(ReactionModel p_reactionModel) {
StringBuilder result = new StringBuilder();
LinkedList pDepList = new LinkedList();
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) {
PDepNetwork pdn = (PDepNetwork) iter.next();
for (ListIterator pdniter = pdn.getNetReactions().listIterator(); pdniter.hasNext(); ) {
PDepReaction rxn = (PDepReaction) pdniter.next();
if (cerm.categorizeReaction(rxn) != 1) continue;
// check if this reaction is not already in the list and also check if this reaction has a
// reverse reaction
// which is already present in the list.
if (rxn.getReverseReaction() == null) rxn.generateReverseReaction();
if (!rxn.reactantEqualsProduct()
&& !pDepList.contains(rxn)
&& !pDepList.contains(rxn.getReverseReaction())) {
pDepList.add(rxn);
}
}
}
Temperature[] tempsUsedInFame = PDepRateConstant.getTemperatures();
int numTemps = tempsUsedInFame.length;
Pressure[] pressUsedInFame = PDepRateConstant.getPressures();
int numPress = pressUsedInFame.length;
for (int i = 0; i < numTemps; i++) {
for (int j = 0; j < numPress; j++) {
result.append(
"T=" + tempsUsedInFame[i].getK() + "K,P=" + pressUsedInFame[j].getBar() + "bar\t");
}
result.append("\n");
}
result.append("\n");
for (Iterator iter = pDepList.iterator(); iter.hasNext(); ) {
PDepReaction r = (PDepReaction) iter.next();
result.append(r.toString() + "\n");
double[][] rates = new double[numTemps][numPress];
rates = r.getPDepRate().getRateConstants();
for (int i = 0; i < numTemps; i++) {
for (int j = 0; j < numPress; j++) {
result.append(rates[i][j] + "\t");
}
result.append("\n");
}
result.append("\n");
}
return result.toString();
}
public double getBalance() {
double totalBal = 0.0;
if (cardCount() == 0) return 0.0;
else {
ListIterator iter = cards.dataIterator();
while (iter.hasNext()) {
CreditCard tmp = (CreditCard) iter.next();
totalBal += tmp.getCredit();
}
}
return totalBal;
}
public static int minCapacityInPath(LinkedList<DirEdge> path) {
int minCapacity = Integer.MAX_VALUE;
ListIterator it = path.listIterator();
while (it.hasNext()) {
DirEdge e = (DirEdge) it.next();
if (e.capacity < minCapacity) {
minCapacity = e.capacity;
}
}
return minCapacity;
}
public void print() {
for (int i = 0; i < v; i++) {
ListIterator it = edges.get(i).listIterator();
while (it.hasNext()) {
DirEdge edge = (DirEdge) it.next();
System.out.print("->" + edge.end + "(" + edge.flow + "/" + edge.capacity + ")");
}
System.out.println();
}
}
void addNewConnections() {
ListIterator<EventableSocketChannel> iter = DetachedConnections.listIterator(0);
while (iter.hasNext()) {
EventableSocketChannel ec = iter.next();
ec.cleanup();
}
DetachedConnections.clear();
ListIterator<Long> iter2 = NewConnections.listIterator(0);
while (iter2.hasNext()) {
long b = iter2.next();
EventableChannel ec = Connections.get(b);
if (ec != null) {
try {
ec.register();
} catch (ClosedChannelException e) {
UnboundConnections.add(ec.getBinding());
}
}
}
NewConnections.clear();
}
private void relabelToFront() {
assert (!V.isEmpty()) : "No vertices";
ListIterator<Vertex> iter = V.listIterator();
while (iter.hasNext()) {
Vertex v = iter.next();
// System.out.println("Considering vertex: " + v);
int oldHeight = v.getHeight();
discharge(v);
if (v.getHeight() > oldHeight) {
iter.remove();
V.addFirst(v);
iter = V.listIterator(1);
}
}
}
/**
* Insert the list of <code>newPasses</code> into <code>passes</code> immediately after the pass
* named <code>id</code>.
*/
public void afterPass(List passes, Pass.ID id, List newPasses) {
for (ListIterator i = passes.listIterator(); i.hasNext(); ) {
Pass p = (Pass) i.next();
if (p.id() == id) {
for (Iterator j = newPasses.iterator(); j.hasNext(); ) {
i.add(j.next());
}
return;
}
}
throw new InternalCompilerError("Pass " + id + " not found.");
}
void removeUnboundConnections() {
ListIterator<Long> iter = UnboundConnections.listIterator(0);
while (iter.hasNext()) {
long b = iter.next();
EventableChannel ec = Connections.remove(b);
if (ec != null) {
eventCallback(b, EM_CONNECTION_UNBOUND, null);
ec.close();
EventableSocketChannel sc = (EventableSocketChannel) ec;
if (sc != null && sc.isAttached()) DetachedConnections.add(sc);
}
}
UnboundConnections.clear();
}
void runTimers() {
long now = new Date().getTime();
while (!Timers.isEmpty()) {
long k = Timers.firstKey();
if (k > now) break;
ArrayList<Long> callbacks = Timers.get(k);
Timers.remove(k);
// Fire all timers at this timestamp
ListIterator<Long> iter = callbacks.listIterator(0);
while (iter.hasNext()) {
eventCallback(0, EM_TIMER_FIRED, null, iter.next().longValue());
}
}
}
/** Remove the pass named <code>id</code> from <code>passes</code>. */
public void removePass(List passes, Pass.ID id) {
for (ListIterator i = passes.listIterator(); i.hasNext(); ) {
Pass p = (Pass) i.next();
if (p.id() == id) {
if (p instanceof BarrierPass) {
throw new InternalCompilerError("Cannot remove a barrier pass.");
}
i.remove();
return;
}
}
throw new InternalCompilerError("Pass " + id + " not found.");
}
public void configureCar(Automotive car) {
System.out.println("Configure the Car-\nPlease enter option choice.");
Scanner read = new Scanner(System.in);
ListIterator<String> it = car.getOptionSetNamesIterator();
while (it.hasNext()) {
String optionSetName = it.next().toString();
System.out.println(optionSetName + ":");
try {
car.setOptionChoice(optionSetName, read.nextLine());
} catch (InvalidOptionException e) {
e.fixException();
}
}
car.calculateFinalPrice();
System.out.println("\nFinal Configuration-");
car.printFinalConfig();
}
/**
* Brings the specified entities to the front, keeping their layer. The order of the specified
* entities in the map is unchanged.
*
* @param entities the entities to move
*/
public void bringToFront(List<MapEntity> entities) {
List<MapEntity> sortedEntities = getSortedEntities(entities);
// bring to front each entity from sortedEntities
ListIterator<MapEntity> iterator = sortedEntities.listIterator(0);
while (iterator.hasNext()) {
MapEntity entity = iterator.next();
Layer layer = entity.getLayer();
allEntities[layer.getId()].remove(entity);
allEntities[layer.getId()].addLast(entity);
}
setChanged();
notifyObservers();
}
public ListGraph residualGraph() {
ListGraph residualG = new ListGraph(getNumNodes(), this.source, this.sink);
for (int i = 0; i < v; i++) {
ListIterator it = edges.get(i).listIterator();
while (it.hasNext()) {
DirEdge edge = (DirEdge) it.next();
int leftCapacity = edge.capacity - edge.flow;
if (leftCapacity > 0) residualG.addEdge(i, edge.end, leftCapacity);
if (edge.flow > 0)
residualG.addEdge(edge.end, i, edge.flow); // add the reverse direction capacity
}
}
return residualG;
}
/**
* Insert the list of <code>newPasses</code> into <code>passes</code> immediately before the pass
* named <code>id</code>.
*/
public void beforePass(List passes, Pass.ID id, List newPasses) {
for (ListIterator i = passes.listIterator(); i.hasNext(); ) {
Pass p = (Pass) i.next();
if (p.id() == id) {
// Backup one position.
i.previous();
for (Iterator j = newPasses.iterator(); j.hasNext(); ) {
i.add(j.next());
}
return;
}
}
throw new InternalCompilerError("Pass " + id + " not found.");
}
public static void dumpcode(final MethodEditor m) {
final PrintWriter out = new PrintWriter(System.out, true);
final StackHeightCounter shc = new StackHeightCounter(m);
out.println("Code for method " + m.name() + m.type());
final List instructions = m.code();
final ListIterator iter = instructions.listIterator();
while (iter.hasNext()) {
final Object obj = iter.next();
if (obj instanceof Label) {
shc.handle((Label) obj);
} else if (obj instanceof Instruction) {
shc.handle((Instruction) obj);
}
System.out.println(" " + obj + " (sh: " + shc.height() + ")");
}
}
public LinkedList<DirEdge> getFlowPath() {
// do a depth first search to see if there is path from source to the sink
boolean[] visited = new boolean[v];
Arrays.fill(visited, false);
Stack<Integer> tobeVisited = new Stack<Integer>();
tobeVisited.push(source);
int[] predecessor = new int[v];
Arrays.fill(predecessor, -1);
while (!tobeVisited.isEmpty()) {
int vertex = tobeVisited.pop();
if (!visited[vertex]) {
// System.out.println("Visiting " + vertex);
visited[vertex] = true;
// put vertex's next hop nodes into the stack
ListIterator it = edges.get(vertex).listIterator();
while (it.hasNext()) {
DirEdge e = (DirEdge) it.next();
if (predecessor[e.end] == -1) {
predecessor[e.end] = vertex;
}
if (e.end == sink) {
return constructPath(predecessor);
}
if (!visited[e.end]) {
tobeVisited.push(e.end);
}
}
}
}
return null; // we cannot find an augment path
}
// ---------------------------------------------------------------------------
private BuildAction addToBuildQueue(String target, boolean primaryTarget, int insertPosition)
throws TablesawException {
// The target was already checked and does not need to be built
if (m_noBuildCache.contains(target)) return (null);
Debug.print("addToBuildQueue(" + target + ", " + primaryTarget + ", " + insertPosition + ")");
Debug.indent();
Rule trule = findTargetRule(target);
CachedFile targetFile = null;
BuildAction[] buildDep = null;
BuildAction targetBA = null;
BuildAction depBA = null;
BuildAction ret = null;
if (trule == null) {
targetFile = m_fileManager.locateFile(target);
// TODO: Add the rule that required this target to the error message
if (targetFile == null)
throw new TablesawException("Unable to locate rule for '" + target + "'");
if (m_sourceFiles != null)
m_sourceFiles.add(
new File(
targetFile.getPath())); // Doing this because locateFile will return a CachedFile
// TODO: check file against cache file stamps and if changed return dummy rule
Debug.print("Cache lookup for " + targetFile.getPath());
// Add file to cache for next run
m_newModificationCache.put(targetFile.getPath(), targetFile.lastModified());
Long cacheModTime = m_modificationCache.get(targetFile.getPath());
if (cacheModTime != null) {
Debug.print("Cache hit " + cacheModTime + ":" + targetFile.lastModified());
if (cacheModTime != targetFile.lastModified()) {
Debug.print("returning obj for " + targetFile);
Debug.popIndent();
targetBA =
new BuildAction(
m_fileManager, new ModifiedFileRule(targetFile.getPath()), m_classAnnotations);
m_buildQueue.add(insertPosition, targetBA);
return (targetBA);
}
} else Debug.print("Cache miss");
// System.out.println("File "+targetFile);
m_noBuildCache.add(target);
Debug.print("Target " + target + " is a file with no rule");
Debug.popIndent();
return (null);
}
if ((m_sourceFiles != null) && (trule instanceof SourceFileSet)) {
m_sourceFiles.addAll(((SourceFileSet) trule).getSourceFiles());
}
long targetTime = 0;
boolean tExists = true;
boolean tDir = false;
boolean tPhony = true;
boolean rebuild = false;
targetBA = new BuildAction(m_fileManager, trule, m_classAnnotations);
int index;
if (m_buildQueueCache.containsKey(targetBA)) {
// Get the build action from the queue
targetBA = m_buildQueueCache.get(targetBA);
Debug.print("target: " + trule + " already in build queue.");
// Target has already been added to build queue
Debug.popIndent();
return (targetBA);
}
File f;
trule.preBuild(m_depCache, m_modificationCache);
// NOTE: need to add in dependencies that are individually declared
// NOTE: getPrerequisites is also where dependency parsing happens to include C headers and
// other java classes
// String[] prereqs = getPrerequisites(trule, true);
List<String> prereqs = new ArrayList<String>();
for (String dn : trule.getDependNames()) {
Debug.print("adding depend name " + dn);
prereqs.add(dn);
}
for (Rule r : trule.getDependRules()) {
Debug.print("adding depend rule " + r);
if (r.getName() == null) {
// Generate name for rule
String genRuleName = NAMED_RULE_PREFIX + (m_ruleNameCounter++);
r.setName(genRuleName);
m_nameRuleMap.put(genRuleName, r);
}
prereqs.add(r.getName());
}
Debug.print("rule dependents " + prereqs.size());
if (prereqs.size() > 0) {
ListIterator<String> it = prereqs.listIterator();
while (it.hasNext()) {
String prereq = it.next();
if (prereq.equals(target))
throw new TablesawException("Target " + target + " depends on itself");
/* //See if the prereq is the name of a rule first
Rule nameRule = m_nameRuleMap.get(prereq);
//Add the new rule targets to the prereqs list
// TODO: some kind of check so we dont add the same named rule again and again.
if (nameRule != null)
{
Iterable<String> ruleTargets = nameRule.getTargets();
boolean hasTargets = false;
for (String t : ruleTargets)
{
hasTargets = true;
it.add(t);
it.previous();
}
if (hasTargets)
continue;
} */
// Add dependencies to build queue first.
// f = m_fileManager.getFile(prereq);
if ((depBA = addToBuildQueue(prereq, false, insertPosition)) != null) {
targetBA.addDependency(depBA);
// trule.addNewerDepend(prereq);
if (depBA.isBinding()) {
Debug.print("Rebuild: " + trule + " because rebuild of " + depBA.getTargetRule());
rebuild = true;
}
}
}
}
if (!rebuild) {
rebuild = trule.needToRun();
Debug.print("Rule needToRun() returned " + rebuild);
}
// TODO: change this to get depends from above and check if no depends
if ((!rebuild)
&& (primaryTarget
&& (!trule
.getTargets()
.iterator()
.hasNext()))) { // If target is the primary target and it has no targets
Debug.print("Adding primary target: " + trule + " to build queue.");
rebuild = true;
}
if (rebuild) { // Add target to build queue
m_buildQueue.add(insertPosition, targetBA);
m_buildQueueCache.put(targetBA, targetBA);
Debug.print("Adding " + targetBA + " to build queue at pos " + insertPosition);
// System.out.println("Adding "+targetBA+" to build queue at pos "+insertPosition);
ret = targetBA;
}
// Add target to cache if it does not need to be built
// This is to speed up incremental builds
if (ret == null) m_noBuildCache.add(target);
Debug.popIndent();
return (ret);
}
/**
* Process the specified HTTP request, and create the corresponding HTTP response (or forward to
* another web component that will create it). Return an <code>ActionForward</code> instance
* describing where and how control should be forwarded, or <code>null</code> if the response has
* already been completed.
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @exception Exception if business logic throws an exception
*/
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// Extract attributes we will need
MessageResources messages = getResources(request);
// save errors
ActionMessages errors = new ActionMessages();
// START check for login (security)
if (!SecurityService.getInstance().checkForLogin(request.getSession(false))) {
return (mapping.findForward("welcome"));
}
// END check for login (security)
// START get id of current project from either request, attribute, or cookie
// id of project from request
String projectId = null;
projectId = request.getParameter("projectViewId");
// check attribute in request
if (projectId == null) {
projectId = (String) request.getAttribute("projectViewId");
}
// id of project from cookie
if (projectId == null) {
projectId = StandardCode.getInstance().getCookie("projectViewId", request.getCookies());
}
// default project to last if not in request or cookie
if (projectId == null) {
java.util.List results = ProjectService.getInstance().getProjectList();
ListIterator iterScroll = null;
for (iterScroll = results.listIterator(); iterScroll.hasNext(); iterScroll.next()) {}
iterScroll.previous();
Project p = (Project) iterScroll.next();
projectId = String.valueOf(p.getProjectId());
}
Integer id = Integer.valueOf(projectId);
// END get id of current project from either request, attribute, or cookie
// get project
Project p = ProjectService.getInstance().getSingleProject(id);
// get user (project manager)
User u =
UserService.getInstance()
.getSingleUserRealName(
StandardCode.getInstance().getFirstName(p.getPm()),
StandardCode.getInstance().getLastName(p.getPm()));
// START process pdf
try {
PdfReader reader = new PdfReader("C://templates/CL01_001.pdf"); // the template
// save the pdf in memory
ByteArrayOutputStream pdfStream = new ByteArrayOutputStream();
// the filled-in pdf
PdfStamper stamp = new PdfStamper(reader, pdfStream);
// stamp.setEncryption(true, "pass", "pass", PdfWriter.AllowCopy | PdfWriter.AllowPrinting);
AcroFields form1 = stamp.getAcroFields();
Date cDate = new Date();
Integer month = cDate.getMonth();
Integer day = cDate.getDate();
Integer year = cDate.getYear() + 1900;
String[] monthName = {
"January",
"February",
"March",
"April",
"May",
"June",
"July",
"August",
"September",
"October",
"November",
"December"
};
// set the field values in the pdf form
// form1.setField("", projectId)
form1.setField("currentdate", monthName[month] + " " + day + ", " + year);
form1.setField(
"firstname", StandardCode.getInstance().noNull(p.getContact().getFirst_name()));
form1.setField("pm", p.getPm());
form1.setField("emailpm", u.getWorkEmail1());
if (u.getWorkPhoneEx() != null && u.getWorkPhoneEx().length() > 0) { // ext present
form1.setField(
"phonepm",
StandardCode.getInstance().noNull(u.getWorkPhone())
+ " ext "
+ StandardCode.getInstance().noNull(u.getWorkPhoneEx()));
} else { // no ext present
form1.setField("phonepm", StandardCode.getInstance().noNull(u.getWorkPhone()));
}
form1.setField("faxpm", StandardCode.getInstance().noNull(u.getLocation().getFax_number()));
form1.setField("postalpm", StandardCode.getInstance().printLocation(u.getLocation()));
// START add images
// if(u.getPicture() != null && u.getPicture().length() > 0) {
// PdfContentByte over;
// Image img = Image.getInstance("C:/Program Files (x86)/Apache Software
// Foundation/Tomcat 7.0/webapps/logo/images/" + u.getPicture());
// img.setAbsolutePosition(200, 200);
// over = stamp.getOverContent(1);
// over.addImage(img, 54, 0,0, 65, 47, 493);
// }
// END add images
form1.setField("productname", StandardCode.getInstance().noNull(p.getProduct()));
form1.setField("project", p.getNumber() + p.getCompany().getCompany_code());
form1.setField("description", StandardCode.getInstance().noNull(p.getProductDescription()));
form1.setField("additional", p.getProjectRequirements());
// get sources and targets
StringBuffer sources = new StringBuffer("");
StringBuffer targets = new StringBuffer("");
if (p.getSourceDocs() != null) {
for (Iterator iterSource = p.getSourceDocs().iterator(); iterSource.hasNext(); ) {
SourceDoc sd = (SourceDoc) iterSource.next();
sources.append(sd.getLanguage() + " ");
if (sd.getTargetDocs() != null) {
for (Iterator iterTarget = sd.getTargetDocs().iterator(); iterTarget.hasNext(); ) {
TargetDoc td = (TargetDoc) iterTarget.next();
if (!td.getLanguage().equals("All")) targets.append(td.getLanguage() + " ");
}
}
}
}
form1.setField("source", sources.toString());
form1.setField("target", targets.toString());
form1.setField(
"start",
(p.getStartDate() != null)
? DateFormat.getDateInstance(DateFormat.SHORT).format(p.getStartDate())
: "");
form1.setField(
"due",
(p.getDueDate() != null)
? DateFormat.getDateInstance(DateFormat.SHORT).format(p.getDueDate())
: "");
if (p.getCompany().getCcurrency().equalsIgnoreCase("USD")) {
form1.setField(
"cost",
(p.getProjectAmount() != null)
? "$ " + StandardCode.getInstance().formatDouble(p.getProjectAmount())
: "");
} else {
form1.setField(
"cost",
(p.getProjectAmount() != null)
? "€ "
+ StandardCode.getInstance()
.formatDouble(p.getProjectAmount() / p.getEuroToUsdExchangeRate())
: "");
}
// stamp.setFormFlattening(true);
stamp.close();
// write to client (web browser)
response.setHeader(
"Content-disposition",
"attachment; filename="
+ p.getNumber()
+ p.getCompany().getCompany_code()
+ "-Order-Confirmation"
+ ".pdf");
OutputStream os = response.getOutputStream();
pdfStream.writeTo(os);
os.flush();
} catch (Exception e) {
System.err.println("PDF Exception:" + e.getMessage());
throw new RuntimeException(e);
}
// END process pdf
// Forward control to the specified success URI
return (mapping.findForward("Success"));
}
public void run() {
System.err.println();
Date now = new Date();
if (!done) flout("INTERRUPTED\n");
flout("START: " + start + "\n");
flout("FINISH: " + now + "\n");
flout("N: " + n_files + "\n");
flout("Subject id: " + subject_id + "\n");
flout("Sample id: " + sample_id + "\n");
flout("total files: " + total_files + "\n");
flout("total bytes: " + total_bytes + "\n");
flout("retrieve failures: " + retrieve_failures + "\n");
flout("metadata retrieve failures: " + md_retrieve_failures + "\n");
flout("bad files retrieved: " + bad_file_errors + "\n");
flout("bad metadata retrieved: " + bad_md_errors + "\n");
reportExceptions();
flout("store retries: " + store_retries + "\n");
flout("retrieve retries: " + retrieve_retries + "\n");
flout("md retrieve retries: " + md_retrieve_retries + "\n");
if (md_retrieve_time > 0)
flout("md retrieve rate (ms/record): " + (md_retrieve_time / md_retrieves) + "\n");
if (total_store_time > 0)
flout("total store rate (bytes/sec): " + ((total_bytes * 1000) / total_store_time) + "\n");
if (total_retrieve_time > 0)
flout(
"total retrieve rate (bytes/sec): "
+ ((total_bytes * 1000) / total_retrieve_time)
+ "\n");
if (time_store_30M > 0)
flout("30 MB store (bytes/sec): " + (1000 * bytes_30M / time_store_30M) + "\n");
if (time_retrv_30M > 0)
flout("30 MB retrieve (bytes/sec): " + (1000 * bytes_30M / time_retrv_30M) + "\n");
if (time_store_3M > 0)
flout("3 MB store (bytes/sec): " + (1000 * bytes_30M / time_store_3M) + "\n");
if (time_retrv_3M > 0)
flout("3 MB retrieve (bytes/sec): " + (1000 * bytes_3M / time_retrv_3M) + "\n");
if (time_store_300K > 0)
flout("300 KB store (bytes/sec): " + (1000 * bytes_300K / time_store_300K) + "\n");
if (time_retrv_300K > 0)
flout("300 KB retrieve (bytes/sec): " + (1000 * bytes_300K / time_retrv_300K) + "\n");
if (update) {
flout("update oid query retries: " + query_retries + "\n");
flout("update retries: " + update_retries + "\n");
if (oid_query_time > 0) flout("query-oid's time (ms): " + oid_query_time + "\n");
if (update_time > 0) flout("update time (ms/record): " + (update_time / updates) + "\n");
if (updating && updates != n_files * 3)
flout("files saved: " + (n_files * 3) + " updates: " + updates + "\n");
}
if (failed_rtrv.size() > 0) {
ListIterator li = failed_rtrv.listIterator(0);
while (li.hasNext()) flout("lost data: " + (String) li.next() + "\n");
}
if (failed_md_rtrv.size() > 0) {
ListIterator li = failed_md_rtrv.listIterator(0);
while (li.hasNext()) flout("lost mdata: " + (String) li.next() + "\n");
}
// long deltat = now.getTime() - start.getTime();
// if (deltat > 0)
// flout("total thruput (bytes/sec rdwr): " +
// (2000 * total_bytes / deltat) + "\n");
try {
new File(lastfile).delete();
} catch (Exception e) {
}
}
// ## operation writeChemkinReactions(ReactionModel)
public static String writeChemkinPdepReactions(
ReactionModel p_reactionModel, SystemSnapshot p_beginStatus) {
// #[ operation writeChemkinReactions(ReactionModel)
StringBuilder result = new StringBuilder();
// result.append("REACTIONS KCAL/MOLE\n");
String reactionHeader = "";
String units4Ea = ArrheniusKinetics.getEaUnits();
if (units4Ea.equals("cal/mol")) reactionHeader = "CAL/MOL\t";
else if (units4Ea.equals("kcal/mol")) reactionHeader = "KCAL/MOL\t";
else if (units4Ea.equals("J/mol")) reactionHeader = "JOULES/MOL\t";
else if (units4Ea.equals("kJ/mol")) reactionHeader = "KJOULES/MOL\t";
else if (units4Ea.equals("Kelvins")) reactionHeader = "KELVINS\t";
String units4A = ArrheniusKinetics.getAUnits();
if (units4A.equals("moles")) reactionHeader += "MOLES\n";
else if (units4A.equals("molecules")) reactionHeader += "MOLECULES\n";
result.append("REACTIONS\t" + reactionHeader);
LinkedList pDepList = new LinkedList();
LinkedList nonPDepList = new LinkedList();
LinkedList duplicates = new LinkedList();
CoreEdgeReactionModel cerm = (CoreEdgeReactionModel) p_reactionModel;
// first get troe and thirdbodyreactions
for (Iterator iter = cerm.getReactionSet().iterator(); iter.hasNext(); ) {
Reaction r = (Reaction) iter.next();
/*
* 1Jul2009-MRH:
* Added extra set of parenthesis. Before, if the rxn was reverse but an instance of
* TROEReaction, it would also be added to the pDepList, resulting in RMG reporting
* both rxns (forward and reverse) in the chem.inp file, w/o a DUP tag. Furthermore,
* both rxns were given the same set of Arrhenius parameters. Running this in
* Chemkin-v4.1.1 resulted in an error.
*/
if (r.isForward()
&& (r instanceof ThirdBodyReaction
|| r instanceof TROEReaction
|| r instanceof LindemannReaction)) {
pDepList.add(r);
}
}
for (Iterator iter = PDepNetwork.getNetworks().iterator(); iter.hasNext(); ) {
PDepNetwork pdn = (PDepNetwork) iter.next();
for (ListIterator pdniter = pdn.getNetReactions().listIterator(); pdniter.hasNext(); ) {
PDepReaction rxn = (PDepReaction) pdniter.next();
if (cerm.categorizeReaction(rxn) != 1) continue;
// check if this reaction is not already in the list and also check if this reaction has a
// reverse reaction
// which is already present in the list.
if (rxn.getReverseReaction() == null) rxn.generateReverseReaction();
if (!rxn.reactantEqualsProduct()
&& !pDepList.contains(rxn)
&& !pDepList.contains(rxn.getReverseReaction())) {
pDepList.add(rxn);
}
}
}
LinkedList removeReactions = new LinkedList();
for (Iterator iter = p_reactionModel.getReactionSet().iterator(); iter.hasNext(); ) {
Reaction r = (Reaction) iter.next();
boolean presentInPDep = false;
if (r.isForward()
&& !(r instanceof ThirdBodyReaction)
&& !(r instanceof TROEReaction)
&& !(r instanceof LindemannReaction)) {
Iterator r_iter = pDepList.iterator();
while (r_iter.hasNext()) {
Reaction pDepr = (Reaction) r_iter.next();
if (pDepr.equals(r)) {
// removeReactions.add(pDepr);
// duplicates.add(pDepr);
// if (!r.hasAdditionalKinetics()){
// duplicates.add(r);
// presentInPDep = true;
// }
presentInPDep = true;
nonPDepList.add(r);
}
}
if (!presentInPDep) nonPDepList.add(r);
}
}
for (Iterator iter = removeReactions.iterator(); iter.hasNext(); ) {
Reaction r = (Reaction) iter.next();
pDepList.remove(r);
}
for (Iterator iter = pDepList.iterator(); iter.hasNext(); ) {
Reaction r = (Reaction) iter.next();
// 6Jul2009-MRH:
// Pass both system temperature and pressure to function toChemkinString.
// The only PDepKineticsModel that uses the passed pressure is RATE
result.append(
r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure())
+ "\n"); // 10/26/07 gmagoon: eliminating use of Global.temperature; **** I use
// beginStatus here, which may or may not be appropriate
// result.append(r.toChemkinString(Global.temperature)+"\n");
}
for (Iterator iter = nonPDepList.iterator(); iter.hasNext(); ) {
Reaction r = (Reaction) iter.next();
result.append(
r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure()) + "\n");
// result.append(r.toChemkinString(Global.temperature)+"\n");
}
for (Iterator iter = duplicates.iterator(); iter.hasNext(); ) {
Reaction r = (Reaction) iter.next();
result.append(
r.toChemkinString(p_beginStatus.getTemperature(), p_beginStatus.getPressure())
+ "\n\tDUP\n");
// result.append(r.toChemkinString(Global.temperature)+"\n\tDUP\n");
}
result.append("END\n");
return result.toString();
// #]
}
public static void main(String[] arg) {
Vector<Boolean> containerTypes = new Vector<Boolean>();
Vector<String> environmentTypes = new Vector<String>();
Vector<String> testNames = new Vector<String>();
Vector<Class> argTests = new Vector<Class>();
Class[] tests = {};
for (int i = 0; i < arg.length; i++) {
if (arg[i].startsWith("-")) {
switch (arg[i].charAt(1)) {
case 'c':
String cType = arg[++i];
if (cType.equalsIgnoreCase(NODE)) containerTypes.add(true);
else if (cType.equalsIgnoreCase(WHOLE)) containerTypes.add(false);
else if (cType.equalsIgnoreCase(ALL)) {
containerTypes.add(true);
containerTypes.add(false);
} else usage();
break;
case 'e':
String eType = arg[++i];
if (eType.equalsIgnoreCase(NONE)
|| eType.equalsIgnoreCase(TXN)
|| eType.equalsIgnoreCase(CDS)) environmentTypes.add(eType);
else if (eType.equalsIgnoreCase(ALL)) {
environmentTypes.add(NONE);
environmentTypes.add(TXN);
environmentTypes.add(CDS);
} else usage();
break;
default:
usage();
}
} else testNames.add(arg[i]);
}
if (containerTypes.size() == 0) {
containerTypes.add(true);
containerTypes.add(false);
}
if (environmentTypes.size() == 0) {
environmentTypes.add(NONE);
environmentTypes.add(TXN);
environmentTypes.add(CDS);
}
// Get the tests to run
if (testNames.size() != 0) {
for (int i = 0; i < testNames.size(); i++) {
Class testClass = null;
try {
testClass = Class.forName("dbxmltest." + testNames.get(i));
} catch (ClassNotFoundException e) {
System.out.println("Skipping test " + testClass + ". Test not found.");
}
if (testClass != null) argTests.add(testClass);
}
if (argTests.size() != 0) tests = argTests.toArray(tests);
else tests = allTests;
} else tests = allTests;
// Run the tests
int failureCount = 0;
boolean success = true;
File errorFile = new File(getEnvironmentPath() + "/errorLog.txt");
try {
if (errorFile.exists()) errorFile.delete();
errorFile.createNewFile();
System.setErr(new PrintStream(new FileOutputStream(errorFile)));
} catch (IOException e) {
}
for (int j = 0; j < environmentTypes.size(); j++) {
System.out.println("Testing env type " + environmentTypes.get(j));
for (int i = 0; i < containerTypes.size(); i++) {
System.out.println("\tContainer type " + (containerTypes.get(i) ? "node" : "whole"));
NODE_CONTAINER = containerTypes.get(i);
ENV_TYPE = environmentTypes.get(j);
Result res = org.junit.runner.JUnitCore.runClasses(tests);
if (!res.wasSuccessful()) {
System.err.println(
"Number of failures for environment type "
+ ENV_TYPE
+ " and is node container "
+ NODE_CONTAINER
+ " are "
+ res.getFailureCount());
List<Failure> testFailures = res.getFailures();
ListIterator<Failure> iter = testFailures.listIterator();
while (iter.hasNext()) {
Failure fail = iter.next();
System.err.println(fail.getDescription());
Throwable e = fail.getException();
if (e != null) e.printStackTrace();
else System.err.println(fail.getTrace());
}
failureCount += res.getFailureCount();
success = res.wasSuccessful();
}
}
}
if (success) System.out.println("All tests successful.");
else System.out.println(failureCount + " tests failed.");
System.out.println("Failures printed to " + errorFile.getName());
}
/**
* Inserts residency/update/swizzle checks into a method. Iterates over the bytecodes in the
* method and inserts the appropriate residency opcode.
*
* @param method The method to which to add checks.
* @see MethodEditor#code
*/
private static void transform(final MethodEditor method) {
if (Main.VERBOSE > 1) {
System.out.println("Decorating method " + method);
}
// Optimize initialization of arrays to speed things up.
CompactArrayInitializer.transform(method);
final ListIterator iter = method.code().listIterator();
// Go through the code (Instructions and Labels) in the method
INST:
while (iter.hasNext()) {
final Object ce = iter.next();
if (Main.VERBOSE > 2) {
System.out.println("Examining " + ce);
}
if (ce instanceof Instruction) {
final Instruction inst = (Instruction) ce;
int uctype = Main.NONE; // Type of update check (POINTER or
// SCALAR)
boolean insert_sc = false; // Insert swizzle check (aaload
// only)?
final int opc = inst.opcodeClass();
int depth;
switch (opc) {
case opcx_arraylength:
case opcx_athrow:
case opcx_getfield:
case opcx_instanceof:
{
depth = 0;
break;
}
case opcx_iaload:
case opcx_laload:
case opcx_faload:
case opcx_daload:
case opcx_baload:
case opcx_caload:
case opcx_saload:
{
depth = 1;
break;
}
case opcx_aaload:
{
depth = 1;
insert_sc = true;
break;
}
case opcx_iastore:
case opcx_fastore:
case opcx_aastore:
case opcx_bastore:
case opcx_castore:
case opcx_sastore:
{
depth = 2;
break;
}
case opcx_lastore:
case opcx_dastore:
{
depth = 3;
break;
}
case opcx_putfield:
{
final MemberRef ref = (MemberRef) inst.operand();
depth = ref.type().stackHeight();
if (ref.type().isReference()) {
uctype = Main.POINTER;
} else {
uctype = Main.SCALAR;
}
break;
}
case opcx_invokevirtual:
case opcx_invokespecial:
case opcx_invokeinterface:
{
final MemberRef ref = (MemberRef) inst.operand();
depth = ref.type().stackHeight();
break;
}
case opcx_rc:
{
// Skip any existing residency checks.
iter.remove();
continue INST;
}
case opcx_aupdate:
{
// Skip any existing update checks.
iter.remove();
continue INST;
}
case opcx_supdate:
{
// Skip any existing update checks.
iter.remove();
continue INST;
}
default:
{
continue INST;
}
}
Instruction addInst;
// Insert a residency check...
if (Main.RC) {
Object t;
// //////////////////////////////////
// Before...
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
//
// After...
// +-----+----+------+-----------+
// | ... | RC | inst | afterInst |
// +-----+----+------+-----------+
// ^prev ^next
// //////////////////////////////////
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
t = iter.previous();
Assert.isTrue(t == inst, t + " != " + inst);
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
addInst = new Instruction(Opcode.opcx_rc, new Integer(depth));
iter.add(addInst);
// +-----+----+------+-----------+
// | ... | RC | inst | afterInst |
// +-----+----+------+-----------+
// ^prev ^next
t = iter.previous();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+----+------+-----------+
// | ... | RC | inst | afterInst |
// +-----+----+------+-----------+
// ^prev ^next
t = iter.next();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+----+------+-----------+
// | ... | RC | inst | afterInst |
// +-----+----+------+-----------+
// ^prev ^next
t = iter.next();
Assert.isTrue(t == inst, t + " != " + inst);
// +-----+----+------+-----------+
// | ... | RC | inst | afterInst |
// +-----+----+------+-----------+
// ^prev ^next
if (Main.VERBOSE > 2) {
System.out.println("Inserting " + addInst + " before " + inst);
}
} else {
if (Main.VERBOSE > 2) {
System.out.println("Not inserting rc before " + inst);
}
}
// Insert a swizzle check...
if (insert_sc) {
if (Main.SC) {
Object t;
// ////////////////////////////////////////////
// Before...
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
//
// After...
// +-----+------+----------+------+-----------+
// | ... | dup2 | aswizzle | inst | afterInst |
// +-----+------+----------+------+-----------+
// ^prev ^next
// /////////////////////////////////////////////
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
t = iter.previous();
Assert.isTrue(t == inst, t + " != " + inst);
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
addInst = new Instruction(Opcode.opcx_dup2);
iter.add(addInst);
// +-----+------+------+-----------+
// | ... | dup2 | inst | afterInst |
// +-----+------+------+-----------+
// ^prev ^next
t = iter.previous();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+------+------+-----------+
// | ... | dup2 | inst | afterInst |
// +-----+------+------+-----------+
// ^prev ^next
t = iter.next();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+------+------+-----------+
// | ... | dup2 | inst | afterInst |
// +-----+------+------+-----------+
// ^prev ^next
addInst = new Instruction(Opcode.opcx_aswizzle);
iter.add(addInst);
// +-----+------+----------+------+-----------+
// | ... | dup2 | aswizzle | inst | afterInst |
// +-----+------+----------+------+-----------+
// ^prev ^next
t = iter.previous();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+------+----------+------+-----------+
// | ... | dup2 | aswizzle | inst | afterInst |
// +-----+------+----------+------+-----------+
// ^prev ^next
t = iter.next();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+------+----------+------+-----------+
// | ... | dup2 | aswizzle | inst | afterInst |
// +-----+------+----------+------+-----------+
// ^prev ^next
t = iter.next();
Assert.isTrue(t == inst, t + " != " + inst);
// +-----+------+----------+------+-----------+
// | ... | dup2 | aswizzle | inst | afterInst |
// +-----+------+----------+------+-----------+
// ^prev ^next
if (Main.VERBOSE > 2) {
System.out.println("Inserting dup2,aswizzle before " + inst);
}
} else {
if (Main.VERBOSE > 2) {
System.out.println("Not inserting aswizzle before " + inst);
}
}
}
// Insert an update check...
if (uctype != Main.NONE) {
if (Main.UC) {
Object t;
// ////////////////////////////////////////////
// Before...
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
//
// After...
// +-----+---------+------+-----------+
// | ... | aupdate | inst | afterInst |
// +-----+---------+------+-----------+
// ^prev ^next
// /////////////////////////////////////////////
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
t = iter.previous();
Assert.isTrue(t == inst, t + " != " + inst);
// +-----+------+-----------+
// | ... | inst | afterInst |
// +-----+------+-----------+
// ^prev ^next
addInst = new Instruction(Opcode.opcx_aupdate, new Integer(depth));
/*
* if (uctype == POINTER) { addInst = new
* Instruction(opcx_aupdate, new Integer(depth)); } else {
* addInst = new Instruction(opcx_supdate, new
* Integer(depth)); }
*/
iter.add(addInst);
// +-----+---------+------+-----------+
// | ... | aupdate | inst | afterInst |
// +-----+---------+------+-----------+
// ^prev ^next
t = iter.previous();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+---------+------+-----------+
// | ... | aupdate | inst | afterInst |
// +-----+---------+------+-----------+
// ^prev ^next
t = iter.next();
Assert.isTrue(t == addInst, t + " != " + addInst);
// +-----+---------+------+-----------+
// | ... | aupdate | inst | afterInst |
// +-----+---------+------+-----------+
// ^prev ^next
t = iter.next();
Assert.isTrue(t == inst, t + " != " + inst);
// +-----+---------+------+-----------+
// | ... | aupdate | inst | afterInst |
// +-----+---------+------+-----------+
// ^prev ^next
if (Main.VERBOSE > 2) {
System.out.println("Inserting " + addInst + " before " + inst);
}
} else if (Main.VERBOSE > 2) {
System.out.println("Not inserting uc before " + inst);
}
}
}
}
}
