public ReaderHandler(LowLevelDbAccess lowLevelDbAccess, String webDir) {
loginInfoDb = new LoginInfo.DB(lowLevelDbAccess);
userDb = new User.DB(lowLevelDbAccess);
feedDb = new Feed.DB(lowLevelDbAccess);
articleDb = new Article.DB(lowLevelDbAccess);
readArticlesCollDb = new ReadArticlesColl.DB(lowLevelDbAccess);
userHelpers = new UserHelpers(loginInfoDb, userDb);
setContextPath("/");
File warPath = new File(webDir);
setWar(warPath.getAbsolutePath());
if (isInJar) {
for (Map.Entry<String, String> entry : PATH_MAPPING.entrySet()) {
addPrebuiltJsp(entry.getKey(), "jsp." + entry.getValue().replaceAll("_", "_005f") + "_jsp");
}
} else {
for (Map.Entry<String, String> entry : PATH_MAPPING.entrySet()) {
addServlet(
new ServletHolder(new RedirectServlet("/" + entry.getValue() + ".jsp")),
entry.getKey());
}
}
setErrorHandler(new ReaderErrorHandler());
}
/** Destructor. */
public void remove() {
for (Iterator<Map.Entry<Long, WImage>> it_it = this.grid_.entrySet().iterator();
it_it.hasNext(); ) {
Map.Entry<Long, WImage> it = it_it.next();
;
if (it.getValue() != null) it.getValue().remove();
}
super.remove();
}
/**
* Regenerates and redraws the image pieces.
*
* <p>This method invalidates all current grid images, and recreates them.
*/
public void redrawAll() {
for (Iterator<Map.Entry<Long, WImage>> it_it = this.grid_.entrySet().iterator();
it_it.hasNext(); ) {
Map.Entry<Long, WImage> it = it_it.next();
;
if (it.getValue() != null) it.getValue().remove();
}
this.grid_.clear();
this.generateGridItems(this.currentX_, this.currentY_);
}
/**
* OPTION requests are treated as CORS preflight requests
*
* @param req the original request
* @param resp the response the answer are written to
*/
@Override
protected void doOptions(HttpServletRequest req, HttpServletResponse resp)
throws ServletException, IOException {
Map<String, String> responseHeaders =
requestHandler.handleCorsPreflightRequest(
req.getHeader("Origin"), req.getHeader("Access-Control-Request-Headers"));
for (Map.Entry<String, String> entry : responseHeaders.entrySet()) {
resp.setHeader(entry.getKey(), entry.getValue());
}
}
private void cleanGrid() {
WVirtualImage.Rect cleanNb =
this.neighbourhood(
this.currentX_, this.currentY_, this.viewPortWidth_ * 3, this.viewPortHeight_ * 3);
long i1 = cleanNb.x1 / this.gridImageSize_;
long j1 = cleanNb.y1 / this.gridImageSize_;
long i2 = cleanNb.x2 / this.gridImageSize_ + 1;
long j2 = cleanNb.y2 / this.gridImageSize_ + 1;
for (Iterator<Map.Entry<Long, WImage>> it_it = this.grid_.entrySet().iterator();
it_it.hasNext(); ) {
Map.Entry<Long, WImage> it = it_it.next();
WVirtualImage.Coordinate coordinate = new WVirtualImage.Coordinate();
this.decodeKey(it.getKey(), coordinate);
if (coordinate.i < i1 || coordinate.i > i2 || coordinate.j < j1 || coordinate.j > j2) {;
if (it.getValue() != null) it.getValue().remove();
it_it.remove();
} else {
}
}
}
/**
* Parses HTTP parameters in an appropriate format and return back map of values to predefined
* list of names.
*
* @param req Request.
* @return Map of parsed parameters.
*/
@SuppressWarnings({"unchecked"})
private Map<String, Object> parameters(ServletRequest req) {
Map<String, String[]> params = req.getParameterMap();
if (F.isEmpty(params)) return Collections.emptyMap();
Map<String, Object> map = U.newHashMap(params.size());
for (Map.Entry<String, String[]> entry : params.entrySet())
map.put(entry.getKey(), parameter(entry.getValue()));
return map;
}
@Nullable
public String getMapping() {
final StringBuilder sb = new StringBuilder();
for (Map.Entry<Pattern, ScopeMapping> patternAndMapping : _patternToMapping.entrySet()) {
if (patternAndMapping.getKey() != null) {
if (sb.length() > 0) {
sb.append(",\n");
}
sb.append(patternAndMapping.getKey())
.append('>')
.append(patternAndMapping.getValue().getDefaultName());
}
}
return sb.length() > 0 ? sb.toString() : null;
}
@Nullable
protected ScopeMapping getMappingFor(@Nonnull String path) {
ScopeMapping mapping;
synchronized (_pathToMappingCache) {
mapping = _pathToMappingCache.get(path);
}
if (mapping == null) {
for (Map.Entry<Pattern, ScopeMapping> patternAndScope : _patternToMapping.entrySet()) {
final Pattern pattern = patternAndScope.getKey();
if (pattern != null && pattern.matcher(path).matches()) {
mapping = patternAndScope.getValue();
break;
}
}
synchronized (_pathToMappingCache) {
_pathToMappingCache.put(path, mapping);
}
}
return mapping;
}
/**
* Builds the vendor events tree.
*
* @param notice the selected notification so that events that match this notification can be
* preselected
* @param vendorExcludeList a list of vendors to exclude from the result
* @return an xml tree of vendors and their events
*/
public String buildTree(Notification notice, List vendorExcludeList)
throws IOException, FileNotFoundException {
StringBuffer buffer = new StringBuffer();
String itemPrefix = "i_";
String sectionPrefix = "s_";
int sid = 1, iid = 1;
List ueiExcludeList = NotificationWizardServlet.getExcludeList();
buffer
.append("<xTree>")
.append("<item id=\"")
.append(sectionPrefix)
.append(sid)
.append("\">")
.append("<itemPrimaryData><![CDATA[System Monitoring Events]]></itemPrimaryData>")
.append("<subitems>");
List vendors = EventConfigurationManager.getVendorNames();
for (Iterator iter = vendors.iterator(); iter.hasNext(); ) {
String vendor = (String) iter.next();
// Don't show any excluded vendors
if (vendorExcludeList != null && vendorExcludeList.contains(vendor)) {
continue;
}
sid++;
buffer
.append("<item id=\"")
.append(sectionPrefix)
.append(sid)
.append("\">")
.append("<itemPrimaryData><![CDATA[<input type=\"checkbox\" id=\"c_")
.append(sectionPrefix)
.append(sid)
.append("\" onClick=\"tcs('")
.append(sectionPrefix)
.append(sid)
.append("');us()\">");
// Write the vendor name
buffer.append(vendor);
buffer.append("]]></itemPrimaryData>").append("<subitems>");
// Now write all the events for the vendor.
List eventVendors = EventConfigurationManager.getEventsByVendor(vendor);
SortedMap sortedEvents = (SortedMap) new TreeMap();
for (Iterator iter2 = eventVendors.iterator(); iter2.hasNext(); ) {
com.jjlabs.model.EventVendor e = (com.jjlabs.model.EventVendor) iter2.next();
sortedEvents.put(e.getLabel(), e);
}
for (Iterator iter2 = sortedEvents.entrySet().iterator(); iter2.hasNext(); ) {
Map.Entry entry = (Map.Entry) iter2.next();
com.jjlabs.model.EventVendor e = (com.jjlabs.model.EventVendor) entry.getValue();
String uei = e.getUei();
if (!ueiExcludeList.contains(NotificationWizardServlet.stripUei(uei))) {
iid++;
boolean inNotification = NotificationWizardServlet.isEventInNotification(notice, e);
buffer
.append("<item id=\"")
.append(itemPrefix)
.append(iid)
.append("\">")
.append(
"<itemPrimaryData><![CDATA[<input type=\"checkbox\" name=\"tree_check\" id=\"c_")
.append(itemPrefix)
.append(iid)
.append("\" value=\"")
.append(e.getId())
.append("\" onClick=\"us()\"")
.append((inNotification ? " checked" : ""))
.append(">");
// Write the event info
buffer.append(e.getLabel());
buffer.append("]]></itemPrimaryData>").append("</item>");
}
}
buffer.append("</subitems></item>");
}
buffer.append("</subitems></item></xTree>");
return buffer.toString();
}
private void dnaCommand(HttpServletRequest req, DazzleResponse resp, DazzleDataSource dds)
throws IOException, DataSourceException, ServletException, DazzleException {
DazzleReferenceSource drs = (DazzleReferenceSource) dds;
List segments = DazzleTools.getSegments(dds, req, resp);
if (segments.size() == 0) {
throw new DazzleException(
DASStatus.STATUS_BAD_COMMAND_ARGUMENTS, "No segments specified for dna command");
}
// Fetch and validate the requests.
Map segmentResults = new HashMap();
for (Iterator i = segments.iterator(); i.hasNext(); ) {
Segment seg = (Segment) i.next();
try {
Sequence seq = drs.getSequence(seg.getReference());
if (seq.getAlphabet() != DNATools.getDNA()) {
throw new DazzleException(
DASStatus.STATUS_SERVER_ERROR,
"Sequence " + seg.toString() + " is not in the DNA alphabet");
}
if (seg.isBounded()) {
if (seg.getMin() < 1 || seg.getMax() > seq.length()) {
throw new DazzleException(
DASStatus.STATUS_BAD_COORDS,
"Segment " + seg.toString() + " doesn't fit sequence of length " + seq.length());
}
}
segmentResults.put(seg, seq);
} catch (NoSuchElementException ex) {
throw new DazzleException(DASStatus.STATUS_BAD_REFERENCE, ex);
} catch (DataSourceException ex) {
throw new DazzleException(DASStatus.STATUS_SERVER_ERROR, ex);
}
}
//
// Looks okay -- generate the response document
//
XMLWriter xw = resp.startDasXML("DASDNA", "dasdna.dtd");
try {
xw.openTag("DASDNA");
for (Iterator i = segmentResults.entrySet().iterator(); i.hasNext(); ) {
Map.Entry me = (Map.Entry) i.next();
Segment seg = (Segment) me.getKey();
Sequence seq = (Sequence) me.getValue();
xw.openTag("SEQUENCE");
xw.attribute("id", seg.getReference());
xw.attribute("version", drs.getLandmarkVersion(seg.getReference()));
if (seg.isBounded()) {
xw.attribute("start", "" + seg.getStart());
xw.attribute("stop", "" + seg.getStop());
} else {
xw.attribute("start", "" + 1);
xw.attribute("stop", "" + seq.length());
}
SymbolList syms = seq;
if (seg.isBounded()) {
syms = syms.subList(seg.getMin(), seg.getMax());
}
if (seg.isInverted()) {
syms = DNATools.reverseComplement(syms);
}
xw.openTag("DNA");
xw.attribute("length", "" + syms.length());
for (int pos = 1; pos <= syms.length(); pos += 60) {
int maxPos = Math.min(syms.length(), pos + 59);
xw.println(syms.subStr(pos, maxPos));
}
xw.closeTag("DNA");
xw.closeTag("SEQUENCE");
}
xw.closeTag("DASDNA");
xw.close();
} catch (Exception ex) {
throw new DazzleException(ex, "Error writing DNA document");
}
}