/*
* Obtain device names configured in the WebUI (ReGa)
*/
private static void fetchDeviceNamesFromReGa() {
lastFetch = System.currentTimeMillis();
L.info("Obtaining ReGa device and channel names");
String r =
TCLRegaHandler.sendHMScript(
"string id;"
+ "foreach(id, root.Channels ().EnumUsedIDs())"
+ " {"
+ " var ch=dom.GetObject(id);"
+ " WriteLine(ch.Address()+\"\t\"+ch.Name());"
+ " }"
+ "foreach(id, root.Devices().EnumUsedIDs())"
+ " {"
+ " var d=dom.GetObject(id);"
+ " WriteLine(d.Address()+\":0\t\"+d.Name());"
+ " }");
if (r == null) return;
String lines[] = r.split("\n");
for (String l : lines) {
String p[] = l.split("\t");
synchronized (nameCache) {
if (p.length == 2) nameCache.put(p[0], p[1]);
}
}
couldFetchOnce = true;
DeviceInfo.resolveNames();
}
public void summaryAction(HttpServletRequest req, HttpServletResponse res) {
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<String, Object>();
DocumentManager docMan = new DocumentManager();
try {
if (req.getParameter("documentId") != null) {
// Get the document ID
int docId = Integer.parseInt(req.getParameter("documentId"));
// Get the document using document id
Document document = docMan.get(docId);
// Set title to name of the document
viewData.put("title", document.getDocumentName());
// Create List of access records
List<AccessRecord> accessRecords = new LinkedList<AccessRecord>();
// Add access records for document to the list
accessRecords = docMan.getAccessRecords(docId);
viewData.put("accessRecords", accessRecords);
} else {
// Go back to thread page.
}
} catch (Exception e) {
Logger.getLogger("").log(Level.SEVERE, "An error occurred when getting profile user", e);
}
view(req, res, "/views/group/Document.jsp", viewData);
}
/**
* Displays a Discussion Thread page
*
* <p>- Requires a cookie for the session user - Requires a threadId request parameter for the
* HTTP GET
*
* @param req The HTTP Request
* @param res The HTTP Response
*/
public void discussionAction(HttpServletRequest req, HttpServletResponse res) {
// Ensure there is a cookie for the session user
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<>();
if (req.getMethod() == HttpMethod.Get) {
// Get the thread
GroupManager gm = new GroupManager();
int threadId = Integer.parseInt(req.getParameter("threadId"));
DiscussionManager discussionManager = new DiscussionManager();
DiscussionThread thread = discussionManager.getThread(threadId);
thread.setGroup(gm.get(thread.getGroupId()));
thread.setPosts(discussionManager.getPosts(threadId));
// get documents for the thread
DocumentManager docMan = new DocumentManager();
viewData.put("documents", docMan.getDocumentsForThread(threadId));
viewData.put("thread", thread);
viewData.put("title", "Discussion: " + thread.getThreadName());
view(req, res, "/views/group/DiscussionThread.jsp", viewData);
} else {
httpNotFound(req, res);
}
}
/**
* Displays a page showing details for all groups in RGMS
*
* @param req The HTTP Request
* @param res The HTTP Response
*/
public void showgroupsAction(HttpServletRequest req, HttpServletResponse res) {
// Ensure there is a cookie for the session user
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<String, Object>();
viewData.put("title", "RGMS Groups");
// Get all groups in the RGMS database
GroupManager groupMan = new GroupManager();
List<Group> groups = groupMan.getEveryGroup();
viewData.put("allGroups", groups);
view(req, res, "/views/group/ShowGroups.jsp", viewData);
}
public void addSelection(Point p) {
ExprPoint ep = null;
int minDist = -1;
for (ExprPoint ex : points) {
int sd = ex.screenDist(p);
if (ep == null || sd < minDist) {
ep = ex;
minDist = sd;
}
}
if (ep != null) {
Set<Point> remove = new HashSet<Point>();
for (Point rp : selections.keySet()) {
if (selections.get(rp).equals(ep)) {
remove.add(rp);
}
}
selections.put(p, ep);
for (Point rp : remove) {
selections.remove(rp);
}
}
}
/**
* Stores the value for the given field associated to last inserted symbol. If no symbol has been
* inserted yet, an exception occurs.
*/
public void putValue(final Field field, final double val) {
final String symbol = symbols.get(symbols.size() - 1);
Map<Field, Double> vs = values.get(symbol);
if (vs == null) vs = new HashMap<Field, Double>();
vs.put(field, val);
this.values.put(symbol, vs);
}
/** @param aProperties the updated properties. */
@SuppressWarnings("rawtypes")
final void setProperties(final Dictionary aProperties) {
final Map<String, String> newProps = new HashMap<String, String>();
Enumeration keys = aProperties.keys();
while (keys.hasMoreElements()) {
final String key = (String) keys.nextElement();
if (!KNOWN_KEYS.contains(key) && !IGNORED_KEYS.contains(key)) {
LOG.log(Level.WARNING, "Unknown/unsupported profile key: " + key);
continue;
}
final String value = aProperties.get(key).toString();
newProps.put(key, value.trim());
}
// Verify whether all known keys are defined...
final List<String> checkedKeys = new ArrayList<String>(KNOWN_KEYS);
checkedKeys.removeAll(newProps.keySet());
if (!checkedKeys.isEmpty()) {
throw new IllegalArgumentException(
"Profile settings not complete! Missing keys are: " + checkedKeys.toString());
}
this.properties.putAll(newProps);
LOG.log(
Level.INFO,
"New device profile settings applied for {1} ({0}) ...", //
new Object[] {getType(), getDescription()});
}
public void addEdge(TreeEdge e) {
if (e.start() == e.string.length() - 1) {
int key = e.string.getIndex();
if (terminalEdges.containsKey(key)) {
throw new IllegalArgumentException();
}
e.headNode = this;
terminalEdges.put(key, e);
} else {
char key = e.getChar(0);
if (childEdges.containsKey(key)) {
throw new IllegalArgumentException();
}
e.headNode = this;
childEdges.put(key, e);
}
}
/**
* Sends a specific <tt>Request</tt> to the STUN server associated with this
* <tt>StunCandidateHarvest</tt>.
*
* @param request the <tt>Request</tt> to send to the STUN server associated with this
* <tt>StunCandidateHarvest</tt>
* @param firstRequest <tt>true</tt> if the specified <tt>request</tt> should be sent as the first
* request in the terms of STUN; otherwise, <tt>false</tt>
* @return the <tt>TransactionID</tt> of the STUN client transaction through which the specified
* <tt>Request</tt> has been sent to the STUN server associated with this
* <tt>StunCandidateHarvest</tt>
* @param transactionID the <tt>TransactionID</tt> of <tt>request</tt> because <tt>request</tt>
* only has it as a <tt>byte</tt> array and <tt>TransactionID</tt> is required for the
* <tt>applicationData</tt> property value
* @throws StunException if anything goes wrong while sending the specified <tt>Request</tt> to
* the STUN server associated with this <tt>StunCandidateHarvest</tt>
*/
protected TransactionID sendRequest(
Request request, boolean firstRequest, TransactionID transactionID) throws StunException {
if (!firstRequest && (longTermCredentialSession != null))
longTermCredentialSession.addAttributes(request);
StunStack stunStack = harvester.getStunStack();
TransportAddress stunServer = harvester.stunServer;
TransportAddress hostCandidateTransportAddress = hostCandidate.getTransportAddress();
if (transactionID == null) {
byte[] transactionIDAsBytes = request.getTransactionID();
transactionID =
(transactionIDAsBytes == null)
? TransactionID.createNewTransactionID()
: TransactionID.createTransactionID(harvester.getStunStack(), transactionIDAsBytes);
}
synchronized (requests) {
try {
transactionID =
stunStack.sendRequest(
request, stunServer, hostCandidateTransportAddress, this, transactionID);
} catch (IllegalArgumentException iaex) {
if (logger.isLoggable(Level.INFO)) {
logger.log(
Level.INFO,
"Failed to send "
+ request
+ " through "
+ hostCandidateTransportAddress
+ " to "
+ stunServer,
iaex);
}
throw new StunException(StunException.ILLEGAL_ARGUMENT, iaex.getMessage(), iaex);
} catch (IOException ioex) {
if (logger.isLoggable(Level.INFO)) {
logger.log(
Level.INFO,
"Failed to send "
+ request
+ " through "
+ hostCandidateTransportAddress
+ " to "
+ stunServer,
ioex);
}
throw new StunException(StunException.NETWORK_ERROR, ioex.getMessage(), ioex);
}
requests.put(transactionID, request);
}
return transactionID;
}
public void loadNetwork() throws IOException {
logger.log(Level.INFO, "Loading metabolism network...");
File file = props.getNetworkFile();
Mapper<String, MetabolicEntry> entryMapper = new MetabolicEntry.MetabolicMapper();
Parser<MetabolicEntry> parser = new Parser<MetabolicEntry>(file, entryMapper);
while (parser.hasNext()) {
MetabolicEntry entry = parser.next();
entries.add(entry);
Rxn rxn =
new Rxn(
props,
entry.getReaction(),
entry.getAbbreviation(),
entry.getReactionName(),
entry.getORF());
reactions.put(entry.getAbbreviation(), rxn);
locations.add(rxn.getLocation());
LogicalORFTree lot = new LogicalORFTree(entry.getORF());
ORFSet os = new ORFSet(entry.getORF());
totalORFs.addAll(os.getORFs());
orfSets.put(entry.getAbbreviation(), lot);
}
logger.log(Level.FINE, String.format("Loaded %d entries.", entries.size()));
abbrevs = new MetabolismAbbreviations(props);
abbrevs.loadAbbreviations();
logger.log(Level.FINEST, "Loaded abbrevations.");
}
/**
* Stores the value for the given field associated to given symbol. Be careful: If symbol has not
* been previously inserted, object will become incoherent.
*/
public void putValue(final String symbol, final Field field, final double val) {
Map<Field, Double> vs = values.get(symbol);
if (vs == null) vs = new HashMap<Field, Double>();
vs.put(field, val);
this.values.put(symbol, vs);
// Consistency check.
for (int i = 0; i < this.symbols.size(); i++) {
if (this.symbols.get(i).equals(symbol)) return;
}
log.severe(
"Danger: inconsistent usage of ParseResult object. "
+ "'putValue' function should be called AFTER 'addSymbol'. "
+ "Read documentation");
}
/**
* Load the application information from the properties file specified by the application adaptor.
* The resource bundle information is stored in a Map for convenient access.
*
* @param path Path to the source information.
* @return The map containing the application information
*/
private Map loadApplicationInfo(final String path) {
Map infoMap;
try {
infoMap = Util.loadResourceBundle(path);
} catch (MissingResourceException exception) {
final String message = "No application \"About Box\" information resource found at: " + path;
Logger.getLogger("global").log(Level.WARNING, message, exception);
System.err.println(message);
// substitute with default information
infoMap = new HashMap();
infoMap.put("name", Application.getAdaptor().getClass().getName());
}
return infoMap;
}
/*
* Obtain device names from a JSON table (e.g. from hm-manager)
*/
private static void fetchDeviceNamesFromNameTable(String filename) {
lastFetch = System.currentTimeMillis();
try (FileReader f = new FileReader(filename)) {
JsonObject table = Json.parse(f).asObject();
int cnt = 0;
synchronized (nameCache) {
for (Member m : table) {
nameCache.put(m.getName(), m.getValue().asString());
cnt++;
}
}
L.log(Level.INFO, "Read " + cnt + " entries from name table " + filename);
couldFetchOnce = true;
DeviceInfo.resolveNames();
} catch (Exception e) {
L.log(Level.WARNING, "Error reading device name table " + filename, e);
}
}
private void remember(Object tv) { // remember where allocated
synchronized (undisposed) {
java.io.StringWriter sw = new java.io.StringWriter();
java.io.PrintWriter pw = new java.io.PrintWriter(sw);
new Exception("This vector was never disposed").printStackTrace(pw);
pw.flush();
undisposed.put(tv, sw.toString());
// LOG.info("**********************************************");
// LOG.info(sw.toString());
max = Math.max(max, undisposed.size());
total += 1;
if (undisposed.size() > 12 && !printedUndisposed) {
LOG.severe("**********************************************");
LOG.severe(getTraces());
LOG.severe("**********************************************");
printedUndisposed = true;
}
}
}
/** Clones result COPYING all data into new variables. */
public Object clone() {
final ParseResult cloned = new ParseResult();
for (int i = 0; i < this.symbols.size(); i++) {
cloned.symbols.add(this.symbols.get(i));
}
for (final Map.Entry<String, Map<Field, Double>> entry1 : this.values.entrySet()) {
final Map<Field, Double> vals = new HashMap<Field, Double>();
for (final Map.Entry<Field, Double> entry2 : entry1.getValue().entrySet()) {
vals.put(entry2.getKey(), entry2.getValue());
}
cloned.values.put(entry1.getKey(), vals);
}
for (final Calendar c : this.calendars) {
cloned.calendars.add((Calendar) c.clone());
}
return cloned;
}
/**
* Displays a given Research Group page for a HTTP Get, or creates a new Group for a HTTP Post
*
* <p>- Requires a cookie for the session user - Requires a groupId request parameter for a GET -
* Requires a groupName, description, createdByUserId request parameters for a POST
*
* @param req The HTTP Request
* @param res The HTTP Response
*/
public void researchgroupAction(HttpServletRequest req, HttpServletResponse res) {
// Ensure there is a cookie for the session user
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<String, Object>();
viewData.put("title", "Research Group");
if (req.getMethod() == HttpMethod.Get) {
// Load group data into Map
GroupManager gm = new GroupManager();
int groupId = Integer.parseInt(req.getParameter("groupId"));
Group group = gm.get(groupId);
if (group != null) {
// Load Group into map
viewData.put("group", group);
// Load group members into Map
List<String> groupMembers = gm.getGroupMembers(groupId);
viewData.put("groupMembers", groupMembers);
// Load meetings into map
MeetingManager meetMan = new MeetingManager();
List<Meeting> groupMeetings = meetMan.getGroupMeetings(groupId);
viewData.put("groupMeetings", groupMeetings);
// Load Document Data into Map
DocumentManager docMan = new DocumentManager();
List<Document> groupDocuments = docMan.getGroupDocuments(groupId);
viewData.put("groupDocuments", groupDocuments);
// Load discussion threads
DiscussionManager dm = new DiscussionManager();
viewData.put("groupDiscussions", dm.getThreads(groupId));
// Check if the user is a member
boolean isMember = false;
HttpSession session = req.getSession();
Session userSession = (Session) session.getAttribute("userSession");
User user = userSession.getUser();
for (Group g : gm.getAllGroups(user.getId())) {
if (g.getId() == group.getId()) {
isMember = true;
break;
}
}
viewData.put("notMember", !isMember);
// View group page.
view(req, res, "/views/group/ResearchGroup.jsp", viewData);
} else {
httpNotFound(req, res);
}
} else if (req.getMethod() == HttpMethod.Post) {
// Create Group
// Get data from parameters
String groupName = req.getParameter("groupName");
String description = req.getParameter("description");
int adminId = Integer.parseInt(req.getParameter("createdByUserId"));
// Create the Group
GroupManager groupMan = new GroupManager();
Group group = new Group();
group.setGroupName(groupName);
group.setDescription(description);
group.setCoordinatorId(adminId);
// Create the mapping
groupMan.createGroup(group);
int groupId = groupMan.getIdFor(group);
groupMan.createMapping(groupId, adminId);
group.setId(groupId);
// Update the User Session to show new group
HttpSession session = req.getSession();
Session userSession = (Session) session.getAttribute("userSession");
User admin = userSession.getUser();
admin.getGroups().add(group);
// Show the Group Page
viewData.put("groupName", group.getGroupName());
List<String> groupMembers = groupMan.getGroupMembers(groupId);
viewData.put("groupMembers", groupMembers);
view(req, res, "/views/group/ResearchGroup.jsp", viewData);
}
}
public ConsoleManager(GlowServer server) {
this.server = server;
// install Ansi code handler, which makes colors work on Windows
AnsiConsole.systemInstall();
for (Handler h : logger.getHandlers()) {
logger.removeHandler(h);
}
// add log handler which writes to console
logger.addHandler(new FancyConsoleHandler());
// reader must be initialized before standard streams are changed
try {
reader = new ConsoleReader();
} catch (IOException ex) {
logger.log(Level.SEVERE, "Exception initializing console reader", ex);
}
reader.addCompleter(new CommandCompleter());
// set system output streams
System.setOut(new PrintStream(new LoggerOutputStream(Level.INFO), true));
System.setErr(new PrintStream(new LoggerOutputStream(Level.WARNING), true));
// set up colorization replacements
replacements.put(
ChatColor.BLACK,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLACK).boldOff().toString());
replacements.put(
ChatColor.DARK_BLUE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLUE).boldOff().toString());
replacements.put(
ChatColor.DARK_GREEN,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.GREEN).boldOff().toString());
replacements.put(
ChatColor.DARK_AQUA,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.CYAN).boldOff().toString());
replacements.put(
ChatColor.DARK_RED,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.RED).boldOff().toString());
replacements.put(
ChatColor.DARK_PURPLE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.MAGENTA).boldOff().toString());
replacements.put(
ChatColor.GOLD,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.YELLOW).boldOff().toString());
replacements.put(
ChatColor.GRAY,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.WHITE).boldOff().toString());
replacements.put(
ChatColor.DARK_GRAY,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLACK).bold().toString());
replacements.put(
ChatColor.BLUE, Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLUE).bold().toString());
replacements.put(
ChatColor.GREEN,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.GREEN).bold().toString());
replacements.put(
ChatColor.AQUA, Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.CYAN).bold().toString());
replacements.put(
ChatColor.RED, Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.RED).bold().toString());
replacements.put(
ChatColor.LIGHT_PURPLE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.MAGENTA).bold().toString());
replacements.put(
ChatColor.YELLOW,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.YELLOW).bold().toString());
replacements.put(
ChatColor.WHITE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.WHITE).bold().toString());
replacements.put(ChatColor.MAGIC, Ansi.ansi().a(Ansi.Attribute.BLINK_SLOW).toString());
replacements.put(ChatColor.BOLD, Ansi.ansi().a(Ansi.Attribute.UNDERLINE_DOUBLE).toString());
replacements.put(
ChatColor.STRIKETHROUGH, Ansi.ansi().a(Ansi.Attribute.STRIKETHROUGH_ON).toString());
replacements.put(ChatColor.UNDERLINE, Ansi.ansi().a(Ansi.Attribute.UNDERLINE).toString());
replacements.put(ChatColor.ITALIC, Ansi.ansi().a(Ansi.Attribute.ITALIC).toString());
replacements.put(ChatColor.RESET, Ansi.ansi().a(Ansi.Attribute.RESET).toString());
}
/**
* Displays a given Meeting page for a HTTP Get, or creates a new Meeting for a HTTP Post
*
* <p>- Requires a cookie for the session user - Requires a meetingId request parameter for a GET
* - Requires description, createdByUserId, datepicker, meetingTime, groupId request parameters
* for a POST
*
* @param req The HTTP Request
* @param res The HTTP Response
*/
public void meetingAction(HttpServletRequest req, HttpServletResponse res) {
// Ensure there is a cookie for the session user
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<String, Object>();
viewData.put("title", "Meeting");
// Initialise Manager connections
MeetingManager meetingMan = new MeetingManager();
GroupManager groupMan = new GroupManager();
if (req.getMethod() == HttpMethod.Get) {
// Get request parameter
int meetingId = Integer.parseInt(req.getParameter("meetingId"));
Meeting meeting = meetingMan.get(meetingId);
if (meeting != null) {
List<User> meetingUsers = groupMan.getGroupUsers(meeting.getGroupId());
viewData.put("meetingUsers", meetingUsers);
viewData.put("meeting", meeting);
view(req, res, "/views/group/Meeting.jsp", viewData);
} else {
httpNotFound(req, res);
}
} else if (req.getMethod() == HttpMethod.Post) {
// Get details from request
String description = req.getParameter("description");
int createdByUserId = Integer.parseInt(req.getParameter("createdByUserId"));
Date dateCreated = new Date();
String meetingDate = req.getParameter("datepicker");
String meetingTime = req.getParameter("meetingTime");
// Parse meeting date time details
DateFormat format = new SimpleDateFormat("MM/dd/yyyy HH:mm");
Date dateDue = new Date();
try {
dateDue = format.parse(meetingDate + " " + meetingTime);
} catch (ParseException e) {
// Unable to parse date. This shouldn't happen since we are
// performing javascript validation.
}
int groupId = Integer.parseInt(req.getParameter("groupId"));
// Create a Meeting
Meeting meeting = new Meeting();
meeting.setDescription(description);
meeting.setCreatedByUserId(createdByUserId);
meeting.setDateCreated(dateCreated);
meeting.setDateDue(dateDue);
meeting.setGroupId(groupId);
meetingMan.createMeeting(meeting);
int meetingId = meetingMan.getIdFor(meeting);
meeting.setId(meetingId);
UserManager userMan = new UserManager();
User createdByUser = userMan.get(createdByUserId);
// Create a notification for all users in group
NotificationManager notificationMan = new NotificationManager();
List<User> users = groupMan.getGroupUsers(groupId);
for (User u : users) {
Notification notification =
new Notification(
u.getId(),
u,
groupId,
null,
"Meeting " + description + " was created by " + createdByUser.getFullName(),
"/group/meeting?meetingId=" + meetingId);
notificationMan.createNotification(notification);
}
// Update the User Session to show new meeting
HttpSession session = req.getSession();
Session userSession = (Session) session.getAttribute("userSession");
User admin = userSession.getUser();
admin.getMeetings().add(meeting);
// Show meeting page
viewData.put("meetingUsers", users);
viewData.put("meeting", meeting);
view(req, res, "/views/group/Meeting.jsp", viewData);
}
}
/**
* Displays the Create Discussion page for a HTTP Get, or creates a Discussion Thread for a HTTP
* Post
*
* <p>- Requires a cookie for the session user - Requires a groupId request parameter for a GET -
* Requires a groupId and threadName request parameter for a POST - Requires a document request
* part for a POST
*
* @param req The HTTP Request
* @param res The HTTP Response
*/
public void createDiscussionAction(HttpServletRequest req, HttpServletResponse res) {
// Ensure there is a cookie for the session user
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<>();
if (req.getMethod() == HttpMethod.Get) {
viewData.put("title", "Create Discussion");
viewData.put("groupId", req.getParameter("groupId"));
view(req, res, "/views/group/CreateDiscussion.jsp", viewData);
return;
} else if (req.getMethod() == HttpMethod.Post) {
// save discussion
GroupManager groupMan = new GroupManager();
DiscussionThread thread = new DiscussionThread();
int groupId = Integer.parseInt(req.getParameter("groupId"));
thread.setGroupId(groupId);
thread.setGroup(groupMan.get(groupId));
thread.setThreadName(req.getParameter("threadName"));
DiscussionManager dm = new DiscussionManager();
dm.createDiscussion(thread);
try {
Part documentPart = req.getPart("document");
// if we have a document to upload
if (documentPart.getSize() > 0) {
String uuid = DocumentController.saveDocument(this.getServletContext(), documentPart);
Document doc = new Document();
doc.setDocumentName(getFileName(documentPart));
doc.setDocumentPath(uuid);
doc.setVersionNumber(1);
doc.setThreadId(thread.getId());
doc.setGroupId(thread.getGroupId());
DocumentManager docMan = new DocumentManager();
docMan.createDocument(doc);
// Get uploading User
HttpSession session = req.getSession();
Session userSession = (Session) session.getAttribute("userSession");
User uploader = userSession.getUser();
// Create a notification to all in the group
NotificationManager notificationMan = new NotificationManager();
groupMan = new GroupManager();
List<User> groupUsers = groupMan.getGroupUsers(groupId);
for (User u : groupUsers) {
Notification notification =
new Notification(
u.getId(),
u,
groupId,
null,
"User " + uploader.getFullName() + " has uploaded a document",
"/document/document?documentId=" + doc.getId());
notificationMan.createNotification(notification);
}
}
} catch (Exception e) {
logger.log(Level.SEVERE, "Document save error", e);
}
redirectToLocal(req, res, "/group/discussion/?threadId=" + thread.getId());
return;
}
httpNotFound(req, res);
}
public void testStatelessSearch()
throws org.jzkit.configuration.api.ConfigurationException, org.jzkit.search.SearchException,
org.jzkit.search.util.ResultSet.IRResultSetException,
org.jzkit.search.util.QueryModel.InvalidQueryException {
Logger log = Logger.getLogger(TestService.class.getName());
log.info("Starting jzkit2 server...");
RecordFormatSpecification request_spec = new ArchetypeRecordFormatSpecification("F");
ExplicitRecordFormatSpecification display_spec =
new ExplicitRecordFormatSpecification("text:html:F");
ApplicationContext app_context =
new ClassPathXmlApplicationContext("TestApplicationContext.xml");
log.info("JZKit server startup completed");
Vector collection_ids = new Vector();
collection_ids.add("LC/BOOKS");
QueryModel qm = new PrefixString("@attrset bib-1 @attr 1=4 Science");
System.err.println("Processing search......");
try {
Map additional_properties = new HashMap();
additional_properties.put("base_dir", "/a/b/c/d");
StatelessQueryService stateless_query_service =
(StatelessQueryService) app_context.getBean("StatelessQueryService");
org.jzkit.search.landscape.SimpleLandscapeSpecification landscape =
new org.jzkit.search.landscape.SimpleLandscapeSpecification(collection_ids);
// Test 1 - Kick off a search
StatelessSearchResultsPageDTO rp =
stateless_query_service.getResultsPageFor(
null, qm, landscape, 1, 5, request_spec, display_spec, additional_properties);
if (rp != null) {
System.err.println(
"Result Set Size....."
+ rp.total_hit_count
+ " records - result contains "
+ rp.number_of_records
+ " records");
System.err.println("Result Set ID : " + rp.result_set_id);
} else {
System.err.println("Results page was null");
}
if (rp.records != null) {
for (int i = 0; ((i < rp.records.length) && (i < 25)); i++) {
System.err.println(
"Getting next record (" + i + " out of " + rp.number_of_records + ").....");
InformationFragment frag = rp.records[i];
System.err.println(frag);
}
}
// Test 2 - use the result set ID to get a page of requests
rp =
stateless_query_service.getResultsPageFor(
rp.result_set_id,
qm,
landscape,
6,
5,
request_spec,
display_spec,
additional_properties);
if (rp.records != null) {
for (int i = 0; ((i < rp.records.length) && (i < 25)); i++) {
System.err.println(
"Getting next record (" + i + " out of " + rp.number_of_records + ").....");
InformationFragment frag = rp.records[i];
System.err.println(frag);
}
}
// Test 3 - Use the query to get a cache hit
rp =
stateless_query_service.getResultsPageFor(
null, qm, landscape, 6, 5, request_spec, display_spec, additional_properties);
if (rp.records != null) {
for (int i = 0; ((i < rp.records.length) && (i < 25)); i++) {
System.err.println(
"Getting next record (" + i + " out of " + rp.number_of_records + ").....");
InformationFragment frag = rp.records[i];
System.err.println(frag);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
public void doProcess(HttpServletRequest req, HttpServletResponse res, boolean isPost) {
StringBuffer bodyContent = null;
OutputStream out = null;
PrintWriter writer = null;
String serviceKey = null;
try {
BufferedReader in = req.getReader();
String line = null;
while ((line = in.readLine()) != null) {
if (bodyContent == null) bodyContent = new StringBuffer();
bodyContent.append(line);
}
} catch (Exception e) {
}
try {
if (requireSession) {
// check to see if there was a session created for this request
// if not assume it was from another domain and blow up
// Wrap this to prevent Portlet exeptions
HttpSession session = req.getSession(false);
if (session == null) {
res.setStatus(HttpServletResponse.SC_FORBIDDEN);
return;
}
}
serviceKey = req.getParameter("id");
// only to preven regressions - Remove before 1.0
if (serviceKey == null) serviceKey = req.getParameter("key");
// check if the services have been loaded or if they need to be reloaded
if (services == null || configUpdated()) {
getServices(res);
}
String urlString = null;
String xslURLString = null;
String userName = null;
String password = null;
String format = "json";
String callback = req.getParameter("callback");
String urlParams = req.getParameter("urlparams");
String countString = req.getParameter("count");
// encode the url to prevent spaces from being passed along
if (urlParams != null) {
urlParams = urlParams.replace(' ', '+');
}
try {
if (services.has(serviceKey)) {
JSONObject service = services.getJSONObject(serviceKey);
// default to the service default if no url parameters are specified
if (urlParams == null && service.has("defaultURLParams")) {
urlParams = service.getString("defaultURLParams");
}
String serviceURL = service.getString("url");
// build the URL
if (urlParams != null && serviceURL.indexOf("?") == -1) {
serviceURL += "?";
} else if (urlParams != null) {
serviceURL += "&";
}
String apikey = "";
if (service.has("username")) userName = service.getString("username");
if (service.has("password")) password = service.getString("password");
if (service.has("apikey")) apikey = service.getString("apikey");
urlString = serviceURL + apikey;
if (urlParams != null) urlString += "&" + urlParams;
if (service.has("xslStyleSheet")) {
xslURLString = service.getString("xslStyleSheet");
}
}
// code for passing the url directly through instead of using configuration file
else if (req.getParameter("url") != null) {
String serviceURL = req.getParameter("url");
// build the URL
if (urlParams != null && serviceURL.indexOf("?") == -1) {
serviceURL += "?";
} else if (urlParams != null) {
serviceURL += "&";
}
urlString = serviceURL;
if (urlParams != null) urlString += urlParams;
} else {
writer = res.getWriter();
if (serviceKey == null)
writer.write("XmlHttpProxyServlet Error: id parameter specifying serivce required.");
else
writer.write(
"XmlHttpProxyServlet Error : service for id '" + serviceKey + "' not found.");
writer.flush();
return;
}
} catch (Exception ex) {
getLogger().severe("XmlHttpProxyServlet Error loading service: " + ex);
}
Map paramsMap = new HashMap();
paramsMap.put("format", format);
// do not allow for xdomain unless the context level setting is enabled.
if (callback != null && allowXDomain) {
paramsMap.put("callback", callback);
}
if (countString != null) {
paramsMap.put("count", countString);
}
InputStream xslInputStream = null;
if (urlString == null) {
writer = res.getWriter();
writer.write(
"XmlHttpProxyServlet parameters: id[Required] urlparams[Optional] format[Optional] callback[Optional]");
writer.flush();
return;
}
// default to JSON
res.setContentType(responseContentType);
out = res.getOutputStream();
// get the stream for the xsl stylesheet
if (xslURLString != null) {
// check the web root for the resource
URL xslURL = null;
xslURL = ctx.getResource(resourcesDir + "xsl/" + xslURLString);
// if not in the web root check the classpath
if (xslURL == null) {
xslURL =
XmlHttpProxyServlet.class.getResource(classpathResourcesDir + "xsl/" + xslURLString);
}
if (xslURL != null) {
xslInputStream = xslURL.openStream();
} else {
String message =
"Could not locate the XSL stylesheet provided for service id "
+ serviceKey
+ ". Please check the XMLHttpProxy configuration.";
getLogger().severe(message);
try {
out.write(message.getBytes());
out.flush();
return;
} catch (java.io.IOException iox) {
}
}
}
if (!isPost) {
xhp.doGet(urlString, out, xslInputStream, paramsMap, userName, password);
} else {
if (bodyContent == null)
getLogger()
.info(
"XmlHttpProxyServlet attempting to post to url "
+ urlString
+ " with no body content");
xhp.doPost(
urlString,
out,
xslInputStream,
paramsMap,
bodyContent.toString(),
req.getContentType(),
userName,
password);
}
} catch (Exception iox) {
iox.printStackTrace();
getLogger().severe("XmlHttpProxyServlet: caught " + iox);
try {
writer = res.getWriter();
writer.write(iox.toString());
writer.flush();
} catch (java.io.IOException ix) {
ix.printStackTrace();
}
return;
} finally {
try {
if (out != null) out.close();
if (writer != null) writer.close();
} catch (java.io.IOException iox) {
}
}
}
/** Receive notification of the end of an element. */
@Override
public void endElement(String uri, String l, String q) {
/*
* 1. If current element is a String, update its value from the string buffer.
* 2. Add the element to parent.
*/
ElementInfo element = _stack.remove(_stack.size() - 1);
_logger.fine("endElement " + element);
if (element.type == null) {
_logger.warning("Element " + element.name + " not created ");
return;
} else if (_chars.length() > 0) {
try {
injectProperty(element.data, String.class, _chars.toString(), null, null);
} catch (Exception x) {
if (!_lenient) {
throw new BeanAssemblyException(
"Failed to set characters to object " + element.type.getName(), x);
} else {
_logger.warning("Failed to set characters to parent " + element.data);
}
}
}
_chars.setLength(0);
_logger.fine(
"<<ElementInfo: "
+ element.type.getName()
+ " in "
+ element
+ "\n @as is "
+ element.inst.get("@as")
+ "\n @id is "
+ element.inst.get("@id"));
if (List.class.isAssignableFrom(element.data.getClass()) && element.name.endsWith("...")) {
List<?> list = (List<?>) element.data;
Object array = Array.newInstance(element.type, list.size());
for (int i = 0; i < list.size(); ++i) {
Array.set(array, i, list.get(i));
}
element.data = array;
}
String id = element.inst.get("@id");
if (id != null) {
// locally stored object - not added to the parent
_local.put(id, element);
} else if (!_stack.isEmpty()) {
// inject into the parent as a property
ElementInfo parent = _stack.get(_stack.size() - 1);
_logger.fine("Parent is " + parent.data.getClass().getName());
try {
String as = element.inst.get("@as");
if (as != null) {
injectProperty(
parent.data,
element.type,
element.data,
Strings.toCamelCase(as, '-', false),
element.args.complete());
} else {
injectProperty(parent.data, element.type, element.data, null, element.args.complete());
}
} catch (Exception x) {
if (!_lenient) {
throw new BeanAssemblyException(
"Failed to set value " + element.data + " to parent " + parent.data, x);
} else {
_logger.log(
Level.WARNING,
"Failed to set value " + element.data + " to parent " + parent.data,
x);
}
}
}
_top = element.data;
}
