/*
* 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 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);
}
}
}
// Walks the tree, checking to make sure that we haven't violated any
// logical constraints. This is a method for debugging.
public boolean check() {
String path = pathLabel();
if (suffixLink != null) {
String suffixPath = suffixLink.pathLabel();
if (!path.substring(1, path.length()).equals(suffixPath)) {
logger.log(
Level.SEVERE,
String.format("Suffix Link for node (%s) didn't match: %s", path, suffixPath));
return false;
}
}
for (char c : childEdges.keySet()) {
TreeEdge e = childEdges.get(c);
if (!e.check()) {
return false;
}
}
for (int k : terminalEdges.keySet()) {
TreeEdge e = terminalEdges.get(k);
if (!e.check()) {
return false;
}
}
return true;
}
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);
}
}
/**
* 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()});
}
private void showExternalDownloadItems() {
final Map<String, FcpPersistentGet> items = persistentQueue.getDownloadRequests();
for (final FcpPersistentGet downloadRequest : items.values()) {
if (!downloadModelItems.containsKey(downloadRequest.getIdentifier())) {
addExternalItem(downloadRequest);
}
}
}
public void collectSuffixes(Set<StringSuffix> suffices) {
suffices.addAll(suffixes);
for (char key : childEdges.keySet()) {
childEdges.get(key).tailNode.collectSuffixes(suffices);
}
for (int key : terminalEdges.keySet()) {
terminalEdges.get(key).tailNode.collectSuffixes(suffices);
}
}
public Map<String, Rxn> getReactions(String compartment) {
TreeMap<String, Rxn> crxns = new TreeMap<String, Rxn>();
for (String rn : reactions.keySet()) {
Rxn r = reactions.get(rn);
if (r.getLocation().equals(compartment)) {
crxns.put(rn, r);
}
}
return crxns;
}
public Set<String> getOutputReactions(Rxn r) {
TreeSet<String> rxns = new TreeSet<String>();
for (String rn : reactions.keySet()) {
Rxn rxn = reactions.get(rn);
if (r.connects(rxn)) {
rxns.add(rn);
}
}
return rxns;
}
private String calculateViewId(FacesContext context) {
Map map = context.getExternalContext().getRequestMap();
String viewId = (String) map.get(RequestDispatcher.INCLUDE_PATH_INFO);
if (viewId == null) viewId = context.getExternalContext().getRequestPathInfo();
if (viewId == null) viewId = (String) map.get(RequestDispatcher.INCLUDE_SERVLET_PATH);
if (viewId == null) viewId = context.getExternalContext().getRequestServletPath();
return viewId;
}
/**
* 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);
}
/**
* 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");
}
/**
* Notifies this <tt>ResponseCollector</tt> that a transaction described by the specified
* <tt>BaseStunMessageEvent</tt> has failed. The possible reasons for the failure include
* timeouts, unreachable destination, etc.
*
* @param event the <tt>BaseStunMessageEvent</tt> which describes the failed transaction and the
* runtime type of which specifies the failure reason
* @see AbstractResponseCollector#processFailure(BaseStunMessageEvent)
*/
@Override
protected void processFailure(BaseStunMessageEvent event) {
TransactionID transactionID = event.getTransactionID();
logger.finest("A transaction expired: tranid=" + transactionID);
logger.finest("localAddr=" + hostCandidate);
/*
* Clean up for the purposes of the workaround which determines the STUN
* Request to which a STUN Response responds.
*/
Request request;
synchronized (requests) {
request = requests.remove(transactionID);
}
if (request == null) {
Message message = event.getMessage();
if (message instanceof Request) request = (Request) message;
}
boolean completedResolvingCandidate = true;
try {
if (processErrorOrFailure(null, request, transactionID)) completedResolvingCandidate = false;
} finally {
if (completedResolvingCandidate) completedResolvingCandidate(request, null);
}
}
@Override
public void dispose() {
synchronized (undisposed) {
super.dispose();
undisposed.remove(this);
}
}
/**
* Get the information associated with the specified key from the application information map.
*
* @param key The key corresponding to the piece of information requested
* @param appInfo The map containing keyed application information
* @return The information
*/
private String getValue(final String key, final Map appInfo) {
String value = (String) appInfo.get(key);
if (value == null) {
value = "Unspecified";
}
return value;
}
/**
* 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;
}
private String colorize(String string) {
if (string.indexOf(ChatColor.COLOR_CHAR) < 0) {
return string; // no colors in the message
} else if (!jLine || !reader.getTerminal().isAnsiSupported()) {
return ChatColor.stripColor(string); // color not supported
} else {
// colorize or strip all colors
for (ChatColor color : colors) {
if (replacements.containsKey(color)) {
string = string.replaceAll("(?i)" + color.toString(), replacements.get(color));
} else {
string = string.replaceAll("(?i)" + color.toString(), "");
}
}
return string + Ansi.ansi().reset().toString();
}
}
/**
* View traces for debugging
*
* @return printable version of traces
*/
public static String getTraces() {
StringBuilder sb = new StringBuilder();
for (String s : undisposed.values()) {
sb.append(s);
sb.append("\n");
}
return sb.toString();
}
public void print(int indent, PrintStream ps) {
if (isLeaf()) {
printSuffixes(ps);
ps.println();
} else {
int i = 0;
for (char c : childEdges.keySet()) {
TreeEdge edge = childEdges.get(c);
edge.print(indent, i != 0, ps);
i++;
}
for (int k : terminalEdges.keySet()) {
TreeEdge edge = terminalEdges.get(k);
edge.print(indent, i != 0, ps);
i++;
}
}
}
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);
}
}
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;
}
}
}
/**
* 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;
}
/** 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;
}
public DvnCitationFileWriter(Map<String, String> resultInfo) {
this.offlineCitation = resultInfo.get("offlineCitation");
this.subsetUNF = resultInfo.get("fileUNF");
this.variableList = resultInfo.get("variableList");
this.requestType = resultInfo.get("option");
if ((resultInfo.containsKey("subsettingCriteria"))
&& (resultInfo.get("subsettingCriteria") != null)) {
this.subsettingCriteria = resultInfo.get("subsettingCriteria");
} else {
this.subsettingCriteria = "";
}
}
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.");
}
public void doLayout() {
selections.clear();
if (points == null) {
points = new Vector<ExprPoint>();
}
points.clear();
for (Pair<Integer, Double> p : watsonProbes) {
ExprPoint ep = new ExprPoint(p.getFirst(), p.getLast(), '+');
points.add(ep);
}
for (Pair<Integer, Double> p : crickProbes) {
ExprPoint ep = new ExprPoint(p.getFirst(), p.getLast(), '-');
points.add(ep);
}
}
/*
* 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);
}
}
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) {
}
}
}