static {
_reachableStoppers.add(HttpServer.class);
_reachableStoppers.add(AppServer.class);
_reachableStoppers.add(DBTCP.class);
_reachableStoppers.add(Mongo.class);
_reachableStoppers.add(WeakBag.class);
_reachableStoppers.add(WeakValueMap.class);
}
public boolean isProtectedMethod(String method) {
boolean retval = false;
if (protectedMethods.isEmpty() || protectedMethods.contains(method)) {
retval = true;
}
return retval;
}
/** Gets all Genomic Data. */
private ProfileDataSummary getGenomicData(
String cancerStudyId,
HashMap<String, GeneticProfile> defaultGeneticProfileSet,
SampleList defaultSampleSet,
String geneListStr,
ArrayList<SampleList> sampleList,
HttpServletRequest request,
HttpServletResponse response)
throws IOException, ServletException, DaoException {
// parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
double zScore =
ZScoreUtil.getZScore(
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
request);
double rppaScore = ZScoreUtil.getRPPAScore(request);
ParserOutput theOncoPrintSpecParserOutput =
OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(
geneListStr,
new HashSet<String>(defaultGeneticProfileSet.keySet()),
new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
zScore,
rppaScore);
ArrayList<String> geneList = new ArrayList<String>();
geneList.addAll(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes());
ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
Set<String> warningUnion = new HashSet<String>();
for (GeneticProfile profile : defaultGeneticProfileSet.values()) {
try {
GetProfileData remoteCall =
new GetProfileData(
profile, geneList, StringUtils.join(defaultSampleSet.getSampleList(), " "));
ProfileData pData = remoteCall.getProfileData();
warningUnion.addAll(remoteCall.getWarnings());
profileDataList.add(pData);
} catch (IllegalArgumentException e) {
e.getStackTrace();
}
}
ProfileMerger merger = new ProfileMerger(profileDataList);
ProfileData mergedProfile = merger.getMergedProfile();
ProfileDataSummary dataSummary =
new ProfileDataSummary(
mergedProfile,
theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(),
zScore,
rppaScore);
return dataSummary;
}
/** Process an HTML get or post. */
public boolean filterURL(
String strURL, String[] strPlus, String[] strMinus, Set setstrExtensions) {
boolean bOkay = true;
String strExtension = BLANK;
if (strURL != null) {
int iEndDot = strURL.indexOf('?');
if (iEndDot == -1) iEndDot = strURL.length();
int iStartDot = strURL.lastIndexOf('.', iEndDot - 1);
if (iStartDot > 0) strExtension = strURL.substring(iStartDot + 1, iEndDot);
}
setstrExtensions.add(strExtension);
if (strPlus != null)
if (strPlus.length > 0) {
bOkay = false;
for (int i = 0; i < strPlus.length; i++) {
if (strPlus[i].equalsIgnoreCase(strExtension)) bOkay = true;
}
}
if (strMinus != null)
if (strMinus.length > 0) {
for (int i = 0; i < strMinus.length; i++) {
if (strMinus[i].equalsIgnoreCase(strExtension)) bOkay = false;
}
}
return bOkay;
}
static {
_knownInitScopeThings.add("mapUrlToJxpFileCore");
_knownInitScopeThings.add("mapUrlToJxpFile");
_knownInitScopeThings.add("allowed");
_knownInitScopeThings.add("staticCacheTime");
_knownInitScopeThings.add("handle404");
_knownInitScopeThings.add(INIT_ADAPTER_TYPE);
_knownInitScopeThings.add(INIT_ADAPTER_SELECTOR);
}
/**
* Process an HTML get or post.
*
* @exception ServletException From inherited class.
* @exception IOException From inherited class.
*/
public void scanOutXML(
PrintWriter out,
String strDirectory,
String strFilename,
String[] strPlus,
String[] strMinus,
boolean bExcludeParams,
boolean bAnalyzeParams)
throws IOException {
File dir = new File(strDirectory + '/' + strFilename);
if (dir.isDirectory()) return;
try {
FileReader is = new FileReader(strDirectory + '/' + strFilename);
BufferedReader r = new BufferedReader(is);
String string = null;
Hashtable ht = new Hashtable();
Set setstrExtensions = new HashSet();
int iCount = 0;
int iBytes = 0;
while ((string = r.readLine()) != null) {
StringTokenizer st = new StringTokenizer(string, " \"", false);
Data data = new Data();
int iTokenCount = 0;
while (st.hasMoreTokens()) {
iTokenCount++;
string = st.nextToken();
if (iTokenCount == IP) data.m_IP = string;
if (iTokenCount == URL) {
if (bExcludeParams)
if (string.indexOf('?') != -1) string = string.substring(0, string.indexOf('?'));
if (bAnalyzeParams)
if (string.indexOf('?') != -1) string = string.substring(string.indexOf('?') + 1);
data.m_URL = string;
}
if (iTokenCount == PROTOCOL)
if (!string.startsWith("HTTP")) {
data.m_URL += " " + string;
iTokenCount--;
}
if (iTokenCount == BYTES) data.m_iBytes = Integer.parseInt(string);
}
if (!this.filterURL(data.m_URL, strPlus, strMinus, setstrExtensions)) continue;
iCount++;
iBytes += data.m_iBytes;
if (ht.get(data.m_URL) == null) ht.put(data.m_URL, data);
else {
int iThisBytes = data.m_iBytes;
data = (Data) ht.get(data.m_URL);
data.m_iCount++;
data.m_iBytes += iThisBytes;
}
}
Comparator comparator = new Test();
TreeMap tm = new TreeMap(comparator);
Iterator iterator = ht.values().iterator();
while (iterator.hasNext()) {
Data data = (Data) iterator.next();
tm.put(new Integer(data.m_iCount), data);
}
out.println("<file>");
this.printXML(out, "directory", strDirectory);
this.printXML(out, "name", strFilename);
iterator = tm.values().iterator();
while (iterator.hasNext()) {
out.println("<data>");
Data data = (Data) iterator.next();
this.printXML(out, "url", data.m_URL);
this.printXML(out, "count", Integer.toString(data.m_iCount));
out.println("</data>");
}
this.printXML(out, "hits", Integer.toString(iCount));
this.printXML(out, "bytes", Integer.toString(iBytes));
this.printXML(out, "unique", Integer.toString(tm.size()));
iterator = setstrExtensions.iterator();
out.println("<extensions>");
while (iterator.hasNext()) {
this.printXML(out, "extension", (String) iterator.next());
}
out.println("</extensions>");
out.println("</file>");
} catch (FileNotFoundException ex) {
ex.printStackTrace();
} catch (IOException ex) {
ex.printStackTrace();
}
}