// postToRestfulApi -
// Note: params in the addr field need to be URLEncoded
private String postToRestfulApi(
String addr, String data, HttpServletRequest request, HttpServletResponse response) {
if (localCookie) CookieHandler.setDefault(cm);
String result = "";
try {
URLConnection connection = new URL(API_ROOT + addr).openConnection();
String cookieVal = getBrowserInfiniteCookie(request);
if (cookieVal != null) {
connection.addRequestProperty("Cookie", "infinitecookie=" + cookieVal);
connection.setDoInput(true);
}
connection.setDoOutput(true);
connection.setRequestProperty("Accept-Charset", "UTF-8");
// Post JSON string to URL
OutputStream os = connection.getOutputStream();
byte[] b = data.getBytes("UTF-8");
os.write(b);
// Receive results back from API
InputStream is = connection.getInputStream();
result = IOUtils.toString(is, "UTF-8");
String newCookie = getConnectionInfiniteCookie(connection);
if (newCookie != null && response != null) {
setBrowserInfiniteCookie(response, newCookie, request.getServerPort());
}
} catch (Exception e) {
// System.out.println("Exception: " + e.getMessage());
}
return result;
} // TESTED
@Override
public void write(byte[] b) throws IOException {
synchronized (statusLock) {
// Make sure HTTP status and header is specified.
statusLock.notifyAll();
committed = true;
}
target.write(b);
}
@Override
public void flush() throws IOException {
synchronized (statusLock) {
// Make sure HTTP status and header is specified.
statusLock.notifyAll();
}
byte[] b = Arrays.copyOf(buffer, offset);
target.write(b);
offset = 0;
}
/**
* This method must be invoked at the end of processing. The streams are closed and their content
* is analyzed. Actual XSLT processing takes place here.
*/
@SuppressWarnings("unchecked")
void finishResponse() throws IOException {
if (writer != null) {
writer.close();
} else {
if (stream != null) stream.close();
}
/*
* If we're not in passthrough mode, then we need to finalize XSLT transformation.
*/
if (false == passthrough) {
if (stream != null) {
final byte[] bytes = ((DeferredOutputStream) stream).getBytes();
final boolean processingSuppressed =
(origRequest.getAttribute(XSLTFilterConstants.NO_XSLT_PROCESSING) != null)
| (origRequest.getParameter(XSLTFilterConstants.NO_XSLT_PROCESSING) != null);
if (processingSuppressed) {
// Just copy the buffered data to the output directly.
final OutputStream os = origResponse.getOutputStream();
os.write(bytes);
os.close();
} else {
// Otherwise apply XSLT transformation to it.
try {
processWithXslt(
bytes,
(Map<String, Object>) origRequest.getAttribute(XSLTFilterConstants.XSLT_PARAMS_MAP),
origResponse);
} catch (TransformerException e) {
final Throwable t = unwrapCause(e);
if (t instanceof IOException) {
throw (IOException) t;
}
filterError("Error applying stylesheet.", e);
}
}
}
}
}
public void doProcess(HttpServletRequest req, HttpServletResponse res, boolean isPost) {
StringBuffer bodyContent = null;
OutputStream out = null;
PrintWriter writer = null;
String serviceKey = null;
try {
BufferedReader in = req.getReader();
String line = null;
while ((line = in.readLine()) != null) {
if (bodyContent == null) bodyContent = new StringBuffer();
bodyContent.append(line);
}
} catch (Exception e) {
}
try {
if (requireSession) {
// check to see if there was a session created for this request
// if not assume it was from another domain and blow up
// Wrap this to prevent Portlet exeptions
HttpSession session = req.getSession(false);
if (session == null) {
res.setStatus(HttpServletResponse.SC_FORBIDDEN);
return;
}
}
serviceKey = req.getParameter("id");
// only to preven regressions - Remove before 1.0
if (serviceKey == null) serviceKey = req.getParameter("key");
// check if the services have been loaded or if they need to be reloaded
if (services == null || configUpdated()) {
getServices(res);
}
String urlString = null;
String xslURLString = null;
String userName = null;
String password = null;
String format = "json";
String callback = req.getParameter("callback");
String urlParams = req.getParameter("urlparams");
String countString = req.getParameter("count");
// encode the url to prevent spaces from being passed along
if (urlParams != null) {
urlParams = urlParams.replace(' ', '+');
}
try {
if (services.has(serviceKey)) {
JSONObject service = services.getJSONObject(serviceKey);
// default to the service default if no url parameters are specified
if (urlParams == null && service.has("defaultURLParams")) {
urlParams = service.getString("defaultURLParams");
}
String serviceURL = service.getString("url");
// build the URL
if (urlParams != null && serviceURL.indexOf("?") == -1) {
serviceURL += "?";
} else if (urlParams != null) {
serviceURL += "&";
}
String apikey = "";
if (service.has("username")) userName = service.getString("username");
if (service.has("password")) password = service.getString("password");
if (service.has("apikey")) apikey = service.getString("apikey");
urlString = serviceURL + apikey;
if (urlParams != null) urlString += "&" + urlParams;
if (service.has("xslStyleSheet")) {
xslURLString = service.getString("xslStyleSheet");
}
}
// code for passing the url directly through instead of using configuration file
else if (req.getParameter("url") != null) {
String serviceURL = req.getParameter("url");
// build the URL
if (urlParams != null && serviceURL.indexOf("?") == -1) {
serviceURL += "?";
} else if (urlParams != null) {
serviceURL += "&";
}
urlString = serviceURL;
if (urlParams != null) urlString += urlParams;
} else {
writer = res.getWriter();
if (serviceKey == null)
writer.write("XmlHttpProxyServlet Error: id parameter specifying serivce required.");
else
writer.write(
"XmlHttpProxyServlet Error : service for id '" + serviceKey + "' not found.");
writer.flush();
return;
}
} catch (Exception ex) {
getLogger().severe("XmlHttpProxyServlet Error loading service: " + ex);
}
Map paramsMap = new HashMap();
paramsMap.put("format", format);
// do not allow for xdomain unless the context level setting is enabled.
if (callback != null && allowXDomain) {
paramsMap.put("callback", callback);
}
if (countString != null) {
paramsMap.put("count", countString);
}
InputStream xslInputStream = null;
if (urlString == null) {
writer = res.getWriter();
writer.write(
"XmlHttpProxyServlet parameters: id[Required] urlparams[Optional] format[Optional] callback[Optional]");
writer.flush();
return;
}
// default to JSON
res.setContentType(responseContentType);
out = res.getOutputStream();
// get the stream for the xsl stylesheet
if (xslURLString != null) {
// check the web root for the resource
URL xslURL = null;
xslURL = ctx.getResource(resourcesDir + "xsl/" + xslURLString);
// if not in the web root check the classpath
if (xslURL == null) {
xslURL =
XmlHttpProxyServlet.class.getResource(classpathResourcesDir + "xsl/" + xslURLString);
}
if (xslURL != null) {
xslInputStream = xslURL.openStream();
} else {
String message =
"Could not locate the XSL stylesheet provided for service id "
+ serviceKey
+ ". Please check the XMLHttpProxy configuration.";
getLogger().severe(message);
try {
out.write(message.getBytes());
out.flush();
return;
} catch (java.io.IOException iox) {
}
}
}
if (!isPost) {
xhp.doGet(urlString, out, xslInputStream, paramsMap, userName, password);
} else {
if (bodyContent == null)
getLogger()
.info(
"XmlHttpProxyServlet attempting to post to url "
+ urlString
+ " with no body content");
xhp.doPost(
urlString,
out,
xslInputStream,
paramsMap,
bodyContent.toString(),
req.getContentType(),
userName,
password);
}
} catch (Exception iox) {
iox.printStackTrace();
getLogger().severe("XmlHttpProxyServlet: caught " + iox);
try {
writer = res.getWriter();
writer.write(iox.toString());
writer.flush();
} catch (java.io.IOException ix) {
ix.printStackTrace();
}
return;
} finally {
try {
if (out != null) out.close();
if (writer != null) writer.close();
} catch (java.io.IOException iox) {
}
}
}
public void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException {
String retval = "<html> <H4>";
try {
// Create a message factory.
MessageFactory mf = MessageFactory.newInstance();
// Create a message from the message factory.
SOAPMessage msg = mf.createMessage();
// Message creation takes care of creating the SOAPPart - a
// required part of the message as per the SOAP 1.1
// specification.
SOAPPart sp = msg.getSOAPPart();
// Retrieve the envelope from the soap part to start building
// the soap message.
SOAPEnvelope envelope = sp.getEnvelope();
// Create a soap header from the envelope.
SOAPHeader hdr = envelope.getHeader();
// Create a soap body from the envelope.
SOAPBody bdy = envelope.getBody();
// Add a soap body element to the soap body
SOAPBodyElement gltp =
bdy.addBodyElement(
envelope.createName("GetLastTradePrice", "ztrade", "http://wombat.ztrade.com"));
gltp.addChildElement(envelope.createName("symbol", "ztrade", "http://wombat.ztrade.com"))
.addTextNode("SUNW");
StringBuffer urlSB = new StringBuffer();
urlSB.append(req.getScheme()).append("://").append(req.getServerName());
urlSB.append(":").append(req.getServerPort()).append(req.getContextPath());
String reqBase = urlSB.toString();
if (data == null) {
data = reqBase + "/index.html";
}
// Want to set an attachment from the following url.
// Get context
URL url = new URL(data);
AttachmentPart ap = msg.createAttachmentPart(new DataHandler(url));
ap.setContentType("text/html");
// Add the attachment part to the message.
msg.addAttachmentPart(ap);
// Create an endpoint for the recipient of the message.
if (to == null) {
to = reqBase + "/receiver";
}
URL urlEndpoint = new URL(to);
System.err.println("Sending message to URL: " + urlEndpoint);
System.err.println("Sent message is logged in \"sent.msg\"");
retval += " Sent message (check \"sent.msg\") and ";
FileOutputStream sentFile = new FileOutputStream("sent.msg");
msg.writeTo(sentFile);
sentFile.close();
// Send the message to the provider using the connection.
SOAPMessage reply = con.call(msg, urlEndpoint);
if (reply != null) {
FileOutputStream replyFile = new FileOutputStream("reply.msg");
reply.writeTo(replyFile);
replyFile.close();
System.err.println("Reply logged in \"reply.msg\"");
retval += " received reply (check \"reply.msg\").</H4> </html>";
} else {
System.err.println("No reply");
retval += " no reply was received. </H4> </html>";
}
} catch (Throwable e) {
e.printStackTrace();
logger.severe("Error in constructing or sending message " + e.getMessage());
retval += " There was an error " + "in constructing or sending message. </H4> </html>";
}
try {
OutputStream os = resp.getOutputStream();
os.write(retval.getBytes());
os.flush();
os.close();
} catch (IOException e) {
e.printStackTrace();
logger.severe("Error in outputting servlet response " + e.getMessage());
}
}
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// set the response
Shepherd myShepherd = new Shepherd();
Vector rEncounters = new Vector();
// setup data dir
String rootWebappPath = getServletContext().getRealPath("/");
File webappsDir = new File(rootWebappPath).getParentFile();
File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName());
// if(!shepherdDataDir.exists()){shepherdDataDir.mkdir();}
File encountersDir = new File(shepherdDataDir.getAbsolutePath() + "/encounters");
// if(!encountersDir.exists()){encountersDir.mkdir();}
// set up the files
String gisFilename = "geneGIS_export_" + request.getRemoteUser() + ".csv";
File gisFile = new File(encountersDir.getAbsolutePath() + "/" + gisFilename);
myShepherd.beginDBTransaction();
try {
// set up the output stream
FileOutputStream fos = new FileOutputStream(gisFile);
OutputStreamWriter outp = new OutputStreamWriter(fos);
try {
EncounterQueryResult queryResult =
EncounterQueryProcessor.processQuery(
myShepherd, request, "year descending, month descending, day descending");
rEncounters = queryResult.getResult();
int numMatchingEncounters = rEncounters.size();
// build the CSV file header
StringBuffer locusString = new StringBuffer("");
int numLoci = 2; // most covered species will be loci
try {
numLoci = (new Integer(CommonConfiguration.getProperty("numLoci"))).intValue();
} catch (Exception e) {
System.out.println("numPloids configuration value did not resolve to an integer.");
e.printStackTrace();
}
for (int j = 0; j < numLoci; j++) {
locusString.append(",Locus" + (j + 1) + " A1,Locus" + (j + 1) + " A2");
}
// out.println("<html><body>");
// out.println("Individual ID,Other ID 1,Date,Time,Latitude,Longitude,Area,Sub
// Area,Sex,Haplotype"+locusString.toString());
outp.write(
"Individual ID,Other ID 1,Date,Time,Latitude,Longitude,Area,Sub Area,Sex,Haplotype"
+ locusString.toString()
+ "\n");
for (int i = 0; i < numMatchingEncounters; i++) {
Encounter enc = (Encounter) rEncounters.get(i);
String assembledString = "";
if (enc.getIndividualID() != null) {
assembledString += enc.getIndividualID();
}
if (enc.getAlternateID() != null) {
assembledString += "," + enc.getAlternateID();
} else {
assembledString += ",";
}
String dateString = ",";
if (enc.getYear() > 0) {
dateString += enc.getYear();
if (enc.getMonth() > 0) {
dateString += ("-" + enc.getMonth());
if (enc.getDay() > 0) {
dateString += ("-" + enc.getDay());
}
}
}
assembledString += dateString;
String timeString = ",";
if (enc.getHour() > -1) {
timeString += enc.getHour() + ":" + enc.getMinutes();
}
assembledString += timeString;
if ((enc.getDecimalLatitude() != null) && (enc.getDecimalLongitude() != null)) {
assembledString += "," + enc.getDecimalLatitude();
assembledString += "," + enc.getDecimalLongitude();
} else {
assembledString += ",,";
}
assembledString += "," + enc.getVerbatimLocality();
assembledString += "," + enc.getLocationID();
assembledString += "," + enc.getSex();
// find and print the haplotype
String haplotypeString = ",";
if (enc.getHaplotype() != null) {
haplotypeString += enc.getHaplotype();
}
// find and print the ms markers
String msMarkerString = "";
List<TissueSample> samples = enc.getTissueSamples();
int numSamples = samples.size();
boolean foundMsMarkers = false;
for (int k = 0; k < numSamples; k++) {
if (!foundMsMarkers) {
TissueSample t = samples.get(k);
List<GeneticAnalysis> analyses = t.getGeneticAnalyses();
int aSize = analyses.size();
for (int l = 0; l < aSize; l++) {
GeneticAnalysis ga = analyses.get(l);
if (ga.getAnalysisType().equals("MicrosatelliteMarkers")) {
foundMsMarkers = true;
MicrosatelliteMarkersAnalysis ga2 = (MicrosatelliteMarkersAnalysis) ga;
List<Locus> loci = ga2.getLoci();
int localLoci = loci.size();
for (int m = 0; m < localLoci; m++) {
Locus locus = loci.get(m);
if (locus.getAllele0() != null) {
msMarkerString += "," + locus.getAllele0();
} else {
msMarkerString += ",";
}
if (locus.getAllele1() != null) {
msMarkerString += "," + locus.getAllele1();
} else {
msMarkerString += ",";
}
}
}
}
}
}
// out.println("<p>"+assembledString+haplotypeString+msMarkerString+"</p>");
outp.write(assembledString + haplotypeString + msMarkerString + "\n");
}
outp.close();
outp = null;
// now write out the file
response.setContentType("text/csv");
response.setHeader("Content-Disposition", "attachment;filename=" + gisFilename);
ServletContext ctx = getServletContext();
// InputStream is = ctx.getResourceAsStream("/encounters/"+gisFilename);
InputStream is = new FileInputStream(gisFile);
int read = 0;
byte[] bytes = new byte[BYTES_DOWNLOAD];
OutputStream os = response.getOutputStream();
while ((read = is.read(bytes)) != -1) {
os.write(bytes, 0, read);
}
os.flush();
os.close();
} catch (Exception ioe) {
ioe.printStackTrace();
response.setContentType("text/html");
PrintWriter out = response.getWriter();
out.println(ServletUtilities.getHeader(request));
out.println(
"<html><body><p><strong>Error encountered</strong> with file writing. Check the relevant log.</p>");
out.println(
"<p>Please let the webmaster know you encountered an error at: EncounterSearchExportGeneGISFormat servlet</p></body></html>");
out.println(ServletUtilities.getFooter());
out.close();
outp.close();
outp = null;
}
} catch (Exception e) {
e.printStackTrace();
response.setContentType("text/html");
PrintWriter out = response.getWriter();
out.println(ServletUtilities.getHeader(request));
out.println("<html><body><p><strong>Error encountered</strong></p>");
out.println(
"<p>Please let the webmaster know you encountered an error at: EncounterSearchExportGeneGISFormat servlet</p></body></html>");
out.println(ServletUtilities.getFooter());
out.close();
}
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
}
private static void sendBinaryResponse(HttpServletResponse res, byte[] bytes) throws IOException {
res.setContentType("application/binary-encoded");
OutputStream out = res.getOutputStream(); // care to handle errors later?
out.write(bytes);
out.flush();
}