/**
  * @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);
  }
Exemple #7
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 @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));
        }
      }
    }
  }
Exemple #9
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  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");
    }
  }