/**
* @param req The request.
* @return The query string of the request in its raw (not URI-encoded) form. This is suitable for
* passing as the 'query' parameter to one of the multi-argument {@link URI} constructors.
*/
private static String getQueryString(HttpServletRequest req) throws UnsupportedEncodingException {
StringBuilder buf = new StringBuilder();
Map<String, String[]> params = req.getParameterMap();
if (params.size() == 0) return null;
for (Entry<String, String[]> entry : params.entrySet()) {
String name = entry.getKey();
String[] values = entry.getValue();
if (values.length == 0) {
buf.append("&").append(name);
} else {
for (String value : values) {
buf.append("&").append(name).append("=").append(value);
}
}
}
return buf.substring(1);
}
static {
CONTENT_TYPES.put(ContentType.HTTP, Response.HTTP);
CONTENT_TYPES.put(ContentType.MULTIPART, Response.MULTIPART);
CONTENT_TYPES.put(ContentType.XML, Response.XML);
for (final Entry<ContentType, String> entry : CONTENT_TYPES.entrySet())
TYPE_CONTENTS.put(entry.getValue(), entry.getKey());
}
/**
* 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());
}
}
/**
* 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;
}
/**
* Returns all query parameters.
*
* @return parameters
*/
public Map<String, String[]> params() {
final Map<String, String[]> params = new HashMap<String, String[]>();
final Map<?, ?> map = req.getParameterMap();
for (final Entry<?, ?> s : map.entrySet()) {
final String key = s.getKey().toString();
final String[] vals =
s.getValue() instanceof String[]
? (String[]) s.getValue()
: new String[] {s.getValue().toString()};
params.put(key, vals);
}
return params;
}
@Override
public void handle(
String target, Request baseRequest, HttpServletRequest request, HttpServletResponse response)
throws IOException, ServletException {
if (!path.equals(request.getRequestURI())) {
return;
}
response.setStatus(HttpServletResponse.SC_OK);
response.setContentType("text/plain");
PrintWriter out = null;
try {
DateFormat df = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss Z");
out = response.getWriter();
Map<String, Endpoint> endpointMap = tracker.getEndpointMap();
Map<String, Long> expirationMap = tracker.getExpirationMap();
out.println("Active sessions:");
out.println();
for (Map.Entry<String, Endpoint> ep : endpointMap.entrySet()) {
String key = ep.getKey();
out.print(ep.getKey());
out.print(" => ");
out.print(ep.getValue());
Long expiration = expirationMap.get(key);
if (expiration == null) {
out.println(" (expiration unknown)");
} else {
out.print(" (expires ");
out.print(df.format(new Date(expiration)));
out.println(")");
}
}
out.println();
out.println("Events:");
out.println();
for (EndpointEvent event : tracker.getEvents()) {
out.print(df.format(new Date(event.getTimestamp())));
out.print(" ");
out.print(event.getStatus().name());
out.print(" ");
out.print(event.getConnectionId());
out.print(" ");
out.print(event.getDetails());
out.println();
}
} finally {
try {
if (out != null) {
out.close();
}
} catch (Throwable ignored) {
}
}
baseRequest.setHandled(true);
}
@Override
public Enumeration<String> getAttributeNames() {
return new Enumerator(attributes.entrySet());
}
/**
* Constructs a new MultipartRequest to handle the specified request, saving any uploaded files to
* the given directory, and limiting the upload size to the specified length. If the content is
* too large, an IOException is thrown. This constructor actually parses the
* <tt>multipart/form-data</tt> and throws an IOException if there's any problem reading or
* parsing the request.
*
* <p>To avoid file collisions, this constructor takes an implementation of the FileRenamePolicy
* interface to allow a pluggable rename policy.
*
* @param request the servlet request.
* @param saveDirectory the directory in which to save any uploaded files.
* @param maxPostSize the maximum size of the POST content.
* @param encoding the encoding of the response, such as ISO-8859-1
* @param policy a pluggable file rename policy
* @exception IOException if the uploaded content is larger than <tt>maxPostSize</tt> or there's a
* problem reading or parsing the request.
*/
public CosMultipartRequest(
HttpServletRequest request,
String saveDirectory,
int maxPostSize,
String encoding,
FileRenamePolicy policy)
throws IOException {
// Sanity check values
if (request == null) throw new IllegalArgumentException("request cannot be null");
if (saveDirectory == null) throw new IllegalArgumentException("saveDirectory cannot be null");
if (maxPostSize <= 0) {
throw new IllegalArgumentException("maxPostSize must be positive");
}
// Save the dir
File dir = new File(saveDirectory);
// Check saveDirectory is truly a directory
if (!dir.isDirectory()) throw new IllegalArgumentException("Not a directory: " + saveDirectory);
// Check saveDirectory is writable
if (!dir.canWrite()) throw new IllegalArgumentException("Not writable: " + saveDirectory);
// Parse the incoming multipart, storing files in the dir provided,
// and populate the meta objects which describe what we found
MultipartParser parser = new MultipartParser(request, maxPostSize, true, true, encoding);
// Some people like to fetch query string parameters from
// MultipartRequest, so here we make that possible. Thanks to
// Ben Johnson, [email protected], for the idea.
if (request.getQueryString() != null) {
// Let HttpUtils create a name->String[] structure
Map<String, String[]> queryParameters =
RequestUtils.parseQueryString(request.getQueryString());
// For our own use, name it a name->Vector structure
for (Entry<String, String[]> entry : queryParameters.entrySet()) {
parameters.put(entry.getKey(), Arrays.asList(entry.getValue()));
}
}
Part part;
while ((part = parser.readNextPart()) != null) {
String name = part.getName();
if (name == null) {
throw new IOException("Malformed input: parameter name missing (known Opera 7 bug)");
}
if (part.isParam()) {
// It's a parameter part, add it to the vector of values
ParamPart paramPart = (ParamPart) part;
String value = paramPart.getStringValue();
List<String> existingValues = parameters.get(name);
if (existingValues == null) {
existingValues = new ArrayList<String>();
parameters.put(name, existingValues);
}
existingValues.add(value);
} else if (part.isFile()) {
// It's a file part
FilePart filePart = (FilePart) part;
String fileName = filePart.getFileName();
if (fileName != null) {
filePart.setRenamePolicy(policy); // null policy is OK
// The part actually contained a file
filePart.writeTo(dir);
files.put(
name,
new UploadedFile(
dir.toString(), filePart.getFileName(), fileName, filePart.getContentType()));
} else {
// The field did not contain a file
files.put(name, new UploadedFile(null, null, null, null));
}
}
}
}
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");
}
}
