/**
* Is MIME type supported
*
* @param mime MIME-Type
* @return Boolean
*/
public static boolean isMimeTypeSupported(String mime) {
if (mime.equals("*")) { // Changed by Deutsche Telekom AG
return true;
} else {
return mimeTable.containsValue(mime);
}
}
public void add(LogicalClient client) {
if (!table.containsValue(client)) {
table.put(client.getPort(), client);
for (LogicalClientsContainerListener listener : listeners) {
listener.clientAdded(client.getPort());
}
}
}
/**
* get the Enum Value of a stocky code.
*
* @param code
* @return
*/
public SexeValues convertToValue(String code) {
SexeValues result = SexeValues.inconnu;
if (sexeCodification.containsValue(code)) {
for (SexeValues sVal : sexeCodification.keySet()) {
if (sexeCodification.get(sVal).equals(code)) {
result = sVal;
}
}
}
return result;
}
/**
* Returns the SimpleType associated with the given name, or null if no such SimpleType exists.
*
* @return the SimpleType associated with the given name, or null if no such SimpleType exists.
*/
public SimpleType getSimpleType(String name) {
// -- Null?
if (name == null) {
String err = NULL_ARGUMENT + "getSimpleType: ";
err += "'name' cannot be null.";
throw new IllegalArgumentException(err);
}
// -- Namespace prefix?
String canonicalName = name;
String nsPrefix = "";
String ns = null;
int colon = name.indexOf(':');
if (colon >= 0) {
canonicalName = name.substring(colon + 1);
nsPrefix = name.substring(0, colon);
ns = (String) namespaces.get(nsPrefix);
if (ns == null) {
String err = "getSimpleType: ";
err += "Namespace prefix not recognised '" + name + "'";
throw new IllegalArgumentException(err);
}
}
// -- Get SimpleType object
SimpleType result = null;
if (ns == null) {
// -- first try built-in types
result = simpleTypesFactory.getBuiltInType(name);
// if we have a built-in type not declared in the good namespace -> Exception
if ((result != null) && (namespaces.containsValue(DEFAULT_SCHEMA_NS))) {
String err =
"getSimpleType: the simple type '"
+ name
+ "' has not been declared in XML Schema namespace.";
throw new IllegalArgumentException(err);
}
// -- otherwise check user-defined types
if (result == null) result = (SimpleType) simpleTypes.get(name);
} else if (ns.equals(schemaNS)) result = simpleTypesFactory.getBuiltInType(canonicalName);
else if (ns.equals(targetNS)) result = (SimpleType) simpleTypes.get(canonicalName);
else {
Schema schema = getImportedSchema(ns);
if (schema != null) result = schema.getSimpleType(canonicalName);
}
// -- Result could be a deferredSimpleType => getType will resolve it
if (result != null) result = (SimpleType) result.getType();
return result;
} // -- getSimpleType
private int getCategoryide(String type) {
Categories.containsValue(type);
for (Iterator iterator = Categories.entrySet().iterator(); iterator.hasNext(); ) {
Entry<Integer, String> cat = (Entry<Integer, String>) iterator.next();
if (cat.getValue().equals(type)) {
return cat.getKey();
}
}
return -1;
}
/* (non-Javadoc)
* @see SketchMaster.system.Recogniziers.RecognizierSystem#addNewCategory(java.lang.String)
*/
@Override
public void addNewCategory(String Name) {
this.CurrentCategory = Name;
// check if exist
if (Categories.containsValue(Name)) return;
else {
// it does not exist
// get size
int temp = Categories.size();
Categories.put(temp, Name);
}
trained = false;
}
public Hashtable<String, Object> respond(Hashtable<String, Object> req) {
Hashtable<String, String> messageHeader = new Hashtable<String, String>();
if (req.containsValue("GET")) {
resp.put("status-line", ResponseStatusLine.get("200", req.get("HTTP-Version")));
} else if (req.get("Method").equals("OPTIONS")) {
resp.put("status-line", ResponseStatusLine.get("200", req.get("HTTP-Version")));
messageHeader.put("Allow", "HEAD,POST,OPTIONS,PUT,GET");
} else {
resp.put("status-line", ResponseStatusLine.get("404", req.get("HTTP-Version")));
}
messageHeader.put("Content-Type", "text/html");
messageHeader.put("Connection", "close");
resp.put("message-header", messageHeader);
resp.put("message-body", body.getBytes(Charset.forName("utf-8")));
return resp;
}
/**
* Process Query request
*
* @param request
* @return
*/
public Response QueryRequestProcess(Request request) {
ArrayList<String> responseMessage = new ArrayList<String>();
String msg = request.getMessage().get(0).trim();
int key = PeerNode.getAscii(msg) % this.getMaxId();
Hashtable<Integer, String> hashtbl = this.getHashtable();
if (hashtbl.containsValue(msg)) {
return new Response(Settings.Version, "QUERY", "0", "200", "OK", responseMessage);
} else if (getInt(this.getID()) <= key && key < getInt(this.getNextPeerID())
|| getInt(this.getID()) <= key && getInt(this.getID()) > getInt(this.getNextPeerID())
|| getInt(this.getNextPeerID()) > key
&& getInt(this.getID()) > getInt(this.getNextPeerID())) {
return new Response(Settings.Version, "ADD", "0", "201", "NotPresent", responseMessage);
} else {
responseMessage.add(msg);
return new Response(Settings.Version, "ADD", "0", "400", "NotResponsible", responseMessage);
}
}
/* (non-Javadoc)
* @see SketchMaster.system.Recogniziers.RecognizierSystem#deleteCategory(java.lang.String)
*/
@Override
public void deleteCategory(String Name) {
// check if exist
if (Categories.containsValue(Name)) {
Set<Entry<Integer, String>> collection = Categories.entrySet();
for (Iterator iter = collection.iterator(); iter.hasNext(); ) {
Entry element = (Entry) iter.next();
if (element.getValue().equals(Name)) {
iter.remove();
break;
}
}
// now remove all entries of this category from the train set.
trainSet.removeType(Name);
if (Interactive) TrainSetStrokes.removeType(Name);
return;
}
trained = false;
}
private String setValueForClass(String value, JTextComponent component) {
Iterator iter = getAllJavaClasses(component);
ArrayList<String> li = new ArrayList<String>();
Hashtable ht = new Hashtable();
String entry = "";
if (iter != null) {
while (iter.hasNext()) {
entry = (String) iter.next();
if (entry != null) ht.put(entry, getPkgPart(entry));
}
}
if (ht.containsKey(value)) value = getClassPart(value);
if (ht.containsValue(getPkgPart(value))) hasPkg = true;
return value;
}
/**
* Process Add query request
*
* @param request
* @return
*/
public Response AddQueryRequestProcess(Request request) {
ArrayList<String> responseMessage = new ArrayList<String>();
String msg = request.getMessage().get(0).trim();
int key =
PeerNode.getAscii(msg)
% this
.getMaxId(); // get the Ascii value and convert it to the range of ids by modula
// maxId
Hashtable<Integer, String> hashtbl = this.getHashtable();
if (hashtbl.containsValue(msg)) {
return new Response(Settings.Version, "ADD", "0", "202", "duplicate", responseMessage);
} else if (getInt(this.getID()) <= key && key < getInt(this.getNextPeerID())
|| getInt(this.getID()) <= key && getInt(this.getID()) > getInt(this.getNextPeerID())
|| getInt(this.getNextPeerID()) > key
&& getInt(this.getID()) > getInt(this.getNextPeerID())) {
hashtbl.put(key, msg);
return new Response(Settings.Version, "ADD", "0", "200", "ok", responseMessage);
} else {
responseMessage.add(msg);
nextClient(new Request("ADD", Settings.Version, 0, this.getID(), responseMessage).toString());
return new Response(Settings.Version, "ADD", "0", "400", "NotResponsible", responseMessage);
}
}
public boolean containsValue(Object value) {
return m_delegatee.containsValue(value);
}
/** @see Runnable#run() */
public void run() {
if ((mzWeight == 0) && (rtWeight == 0)) {
setStatus(TaskStatus.ERROR);
errorMessage = "Cannot run alignment, all the weight parameters are zero";
return;
}
setStatus(TaskStatus.PROCESSING);
logger.info("Running join aligner");
// Remember how many rows we need to process. Each row will be processed
// twice, first for score calculation, second for actual alignment.
for (int i = 0; i < peakLists.length; i++) {
totalRows += peakLists[i].getNumberOfRows() * 2;
}
// Collect all data files
Vector<RawDataFile> allDataFiles = new Vector<RawDataFile>();
for (PeakList peakList : peakLists) {
for (RawDataFile dataFile : peakList.getRawDataFiles()) {
// Each data file can only have one column in aligned peak list
if (allDataFiles.contains(dataFile)) {
setStatus(TaskStatus.ERROR);
errorMessage =
"Cannot run alignment, because file "
+ dataFile
+ " is present in multiple peak lists";
return;
}
allDataFiles.add(dataFile);
}
}
// Create a new aligned peak list
alignedPeakList = new SimplePeakList(peakListName, allDataFiles.toArray(new RawDataFile[0]));
// Iterate source peak lists
for (PeakList peakList : peakLists) {
// Create a sorted set of scores matching
TreeSet<RowVsRowScore> scoreSet = new TreeSet<RowVsRowScore>();
PeakListRow allRows[] = peakList.getRows();
// Calculate scores for all possible alignments of this row
for (PeakListRow row : allRows) {
if (isCanceled()) return;
// Calculate limits for a row with which the row can be aligned
Range mzRange = mzTolerance.getToleranceRange(row.getAverageMZ());
Range rtRange = rtTolerance.getToleranceRange(row.getAverageRT());
// Get all rows of the aligned peaklist within parameter limits
PeakListRow candidateRows[] = alignedPeakList.getRowsInsideScanAndMZRange(rtRange, mzRange);
// Calculate scores and store them
for (PeakListRow candidate : candidateRows) {
if (sameChargeRequired) {
if (!PeakUtils.compareChargeState(row, candidate)) continue;
}
if (sameIDRequired) {
if (!PeakUtils.compareIdentities(row, candidate)) continue;
}
if (compareIsotopePattern) {
IsotopePattern ip1 = row.getBestIsotopePattern();
IsotopePattern ip2 = candidate.getBestIsotopePattern();
if ((ip1 != null) && (ip2 != null)) {
ParameterSet isotopeParams =
parameters
.getParameter(JoinAlignerParameters.compareIsotopePattern)
.getEmbeddedParameters();
if (!IsotopePatternScoreCalculator.checkMatch(ip1, ip2, isotopeParams)) {
continue;
}
}
}
RowVsRowScore score =
new RowVsRowScore(
row, candidate, mzRange.getSize() / 2, mzWeight, rtRange.getSize() / 2, rtWeight);
scoreSet.add(score);
}
processedRows++;
}
// Create a table of mappings for best scores
Hashtable<PeakListRow, PeakListRow> alignmentMapping =
new Hashtable<PeakListRow, PeakListRow>();
// Iterate scores by descending order
Iterator<RowVsRowScore> scoreIterator = scoreSet.iterator();
while (scoreIterator.hasNext()) {
RowVsRowScore score = scoreIterator.next();
// Check if the row is already mapped
if (alignmentMapping.containsKey(score.getPeakListRow())) continue;
// Check if the aligned row is already filled
if (alignmentMapping.containsValue(score.getAlignedRow())) continue;
alignmentMapping.put(score.getPeakListRow(), score.getAlignedRow());
}
// Align all rows using mapping
for (PeakListRow row : allRows) {
PeakListRow targetRow = alignmentMapping.get(row);
// If we have no mapping for this row, add a new one
if (targetRow == null) {
targetRow = new SimplePeakListRow(newRowID);
newRowID++;
alignedPeakList.addRow(targetRow);
}
// Add all peaks from the original row to the aligned row
for (RawDataFile file : row.getRawDataFiles()) {
targetRow.addPeak(file, row.getPeak(file));
}
// Add all non-existing identities from the original row to the
// aligned row
PeakUtils.copyPeakListRowProperties(row, targetRow);
processedRows++;
}
} // Next peak list
// Add new aligned peak list to the project
MZmineProject currentProject = MZmineCore.getCurrentProject();
currentProject.addPeakList(alignedPeakList);
// Add task description to peakList
alignedPeakList.addDescriptionOfAppliedTask(
new SimplePeakListAppliedMethod("Join aligner", parameters));
logger.info("Finished join aligner");
setStatus(TaskStatus.FINISHED);
}
public static void main(String args[]) {
// Use correct Semantria API credentias here
String key = "f4a9add2-627c-4cd9-bf3d-08dba99cc048";
String secret = "fb17fecf-6919-4c98-994d-a0cee0730c00";
if (args != null && args.length == 2) {
key = args[0];
secret = args[1];
}
Hashtable<String, TaskStatus> docsTracker = new Hashtable<String, TaskStatus>();
List<String> initialTexts = new ArrayList<String>();
System.out.println("Semantria service demo.");
// File file = new File(
// DetailedModeTestApp.class.getProtectionDomain().getCodeSource().getLocation().toString().replace("/target/classes", "/src/main/java/" + DiscoveryModeTestApp.class.getPackage().getName().replace(".","/")).replace("file:/", "")+ "/source.txt");
File file = new File(System.getProperty("user.dir") + "/source.txt");
if (!file.exists()) {
System.out.println("Source file isn't available.");
return;
}
// Reads dataset from the source file
try {
FileInputStream fstream = new FileInputStream(file);
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String strLine;
while ((strLine = br.readLine()) != null) {
if (StringUtils.isEmpty(strLine) || strLine.length() < 3) {
continue;
}
initialTexts.add(strLine);
}
in.close();
} catch (Exception e) {
System.err.println("Error: " + e.getMessage());
}
// Creates JSON serializer instance
// ISerializer jsonSerializer = new JsonSerializer();
// Initializes new session with the serializer object and the keys.
ISerializer serializer = new JsonSerializer();
Session session = Session.createSession(key, secret, serializer, true);
session.setCallbackHandler(new CallbackHandler());
// Obtaining subscription object to get user limits applicable on server side
Subscription subscription = session.getSubscription();
List<Document> outgoingBatch =
new ArrayList<Document>(subscription.getBasicSettings().getBatchLimit());
for (Iterator<String> iterator = initialTexts.iterator(); iterator.hasNext(); ) {
String uid = UUID.randomUUID().toString();
Document doc = new Document(uid, iterator.next());
// System.out.println("doc content = \n\n\n\n\n"+doc.toString()+"\n\n\n\n");
outgoingBatch.add(doc);
docsTracker.put(uid, TaskStatus.QUEUED);
if (outgoingBatch.size() == subscription.getBasicSettings().getBatchLimit()) {
if (session.queueBatch(outgoingBatch) == 202) {
System.out.println("\"" + outgoingBatch.size() + "\" documents queued successfully.");
outgoingBatch.clear();
}
}
}
if (outgoingBatch.size() > 0) {
if (session.queueBatch(outgoingBatch) == 202) {
System.out.println("\"" + outgoingBatch.size() + "\" documents queued successfully.");
outgoingBatch.clear();
}
}
// System.out.println();
try {
List<DocAnalyticData> processed = new ArrayList<DocAnalyticData>();
while (docsTracker.containsValue(TaskStatus.QUEUED)) {
// As Semantria isn't real-time solution you need to wait some time before getting of the
// processed results
// In real application here can be implemented two separate jobs, one for queuing of source
// data another one for retrieving
// Wait half of second while Semantria process queued document
Thread.currentThread().sleep(TIMEOUT_BEFORE_GETTING_RESPONSE);
// Requests processed results from Semantria service
List<DocAnalyticData> temp = session.getProcessedDocuments();
for (Iterator<DocAnalyticData> i = temp.iterator(); i.hasNext(); ) {
DocAnalyticData item = i.next();
if (docsTracker.containsKey(item.getId())) {
processed.add(item);
docsTracker.put(item.getId(), TaskStatus.PROCESSED);
}
}
System.out.println("Retrieving your processed results...");
}
StringBuffer sbr = new StringBuffer();
sbr.append(
"\ndoc_id,doc_sentiment_score,doc_sentiment_polarity,cat_topic,cat_strength_score,theme_title,theme_sentiment_score,theme_sentiment_polarity,entity_title,entity_sentiment_score,entity_sentiment_polarity");
// Output results
for (DocAnalyticData doc : processed) {
// (!"".isEmpty() && null!="") ? return "" : "";
// String str="";
// System.out.println((str.isEmpty() && str.length()>0) ? str : "null");
sbr.append(
"\n"
+ (checkNull(doc.getId())
+ ","
+ checkNull(Float.toString(doc.getSentimentScore()))
+ ","
+ checkNull(doc.getSentimentPolarity())
+ ","));
System.out.println(
"Document:\n\tid: "
+ doc.getId()
+ "\n\tsentiment score: "
+ Float.toString(doc.getSentimentScore())
+ "\n\tsentiment polarity: "
+ doc.getSentimentPolarity());
System.out.println();
if (doc.getAutoCategories() != null) {
System.out.println("\tdocument categories:");
for (DocCategory category : doc.getAutoCategories()) {
System.out.println(
"\t\ttopic: "
+ category.getTitle()
+ " \n\t\tStrength score: "
+ Float.toString(category.getStrengthScore()));
System.out.println();
sbr.append(
checkNull(category.getTitle())
+ ","
+ checkNull(Float.toString(category.getStrengthScore()))
+ ",");
}
} else {
sbr.append("null," + "null,");
}
if (doc.getThemes() != null) {
System.out.println("\tdocument themes:");
for (DocTheme theme : doc.getThemes()) {
System.out.println(
"\t\ttitle: "
+ theme.getTitle()
+ " \n\t\tsentiment: "
+ Float.toString(theme.getSentimentScore())
+ "\n\t\tsentiment polarity: "
+ theme.getSentimentPolarity());
System.out.println();
sbr.append(
checkNull(theme.getTitle())
+ ","
+ checkNull(Float.toString(theme.getStrengthScore()))
+ ","
+ checkNull(theme.getSentimentPolarity())
+ ",");
}
} else {
sbr.append("null," + "null," + "null,");
}
if (doc.getEntities() != null) {
System.out.println("\tentities:");
for (DocEntity entity : doc.getEntities()) {
System.out.println(
"\t\ttitle: "
+ entity.getTitle()
+ "\n\t\tsentiment: "
+ Float.toString(entity.getSentimentScore())
+ "\n\t\tsentiment polarity: "
+ entity.getSentimentPolarity());
System.out.println();
sbr.append(
checkNull(entity.getTitle())
+ ","
+ checkNull(Float.toString(entity.getSentimentScore()))
+ ","
+ checkNull(entity.getSentimentPolarity()));
}
} else {
sbr.append("null," + "null," + "null");
}
}
System.out.println("processed results : \n" + sbr.toString());
} catch (Exception e) {
System.out.println(e.getMessage());
}
}