public static String showSecurity(HttpServletRequest req, String role) {
StringBuilder sbuff = new StringBuilder();
sbuff.append("Security Info\n");
sbuff.append(" req.getRemoteUser(): ").append(req.getRemoteUser()).append("\n");
sbuff.append(" req.getUserPrincipal(): ").append(req.getUserPrincipal()).append("\n");
sbuff
.append(" req.isUserInRole(")
.append(role)
.append("):")
.append(req.isUserInRole(role))
.append("\n");
sbuff.append(" ------------------\n");
return sbuff.toString();
}
/**
* Show details about the request
*
* @param servlet used to get teh servlet context, may be null
* @param req the request
* @return string showing the details of the request.
*/
public static String showRequestDetail(HttpServlet servlet, HttpServletRequest req) {
StringBuilder sbuff = new StringBuilder();
sbuff.append("Request Info\n");
sbuff.append(" req.getServerName(): ").append(req.getServerName()).append("\n");
sbuff.append(" req.getServerPort(): ").append(req.getServerPort()).append("\n");
sbuff.append(" req.getContextPath:").append(req.getContextPath()).append("\n");
sbuff.append(" req.getServletPath:").append(req.getServletPath()).append("\n");
sbuff.append(" req.getPathInfo:").append(req.getPathInfo()).append("\n");
sbuff.append(" req.getQueryString:").append(req.getQueryString()).append("\n");
sbuff
.append(" getQueryStringDecoded:")
.append(EscapeStrings.urlDecode(req.getQueryString()))
.append("\n");
/*try {
sbuff.append(" getQueryStringDecoded:").append(URLDecoder.decode(req.getQueryString(), "UTF-8")).append("\n");
} catch (UnsupportedEncodingException e1) {
e1.printStackTrace();
}*/
sbuff.append(" req.getRequestURI:").append(req.getRequestURI()).append("\n");
sbuff.append(" getRequestBase:").append(getRequestBase(req)).append("\n");
sbuff.append(" getRequestServer:").append(getRequestServer(req)).append("\n");
sbuff.append(" getRequest:").append(getRequest(req)).append("\n");
sbuff.append("\n");
sbuff.append(" req.getPathTranslated:").append(req.getPathTranslated()).append("\n");
String path = req.getPathTranslated();
if ((path != null) && (servlet != null)) {
ServletContext context = servlet.getServletContext();
sbuff.append(" getMimeType:").append(context.getMimeType(path)).append("\n");
}
sbuff.append("\n");
sbuff.append(" req.getScheme:").append(req.getScheme()).append("\n");
sbuff.append(" req.getProtocol:").append(req.getProtocol()).append("\n");
sbuff.append(" req.getMethod:").append(req.getMethod()).append("\n");
sbuff.append("\n");
sbuff.append(" req.getContentType:").append(req.getContentType()).append("\n");
sbuff.append(" req.getContentLength:").append(req.getContentLength()).append("\n");
sbuff.append(" req.getRemoteAddr():").append(req.getRemoteAddr());
try {
sbuff
.append(" getRemoteHost():")
.append(java.net.InetAddress.getByName(req.getRemoteHost()).getHostName())
.append("\n");
} catch (java.net.UnknownHostException e) {
sbuff.append(" getRemoteHost():").append(e.getMessage()).append("\n");
}
sbuff.append(" getRemoteUser():").append(req.getRemoteUser()).append("\n");
sbuff.append("\n");
sbuff.append("Request Parameters:\n");
Enumeration params = req.getParameterNames();
while (params.hasMoreElements()) {
String name = (String) params.nextElement();
String values[] = req.getParameterValues(name);
if (values != null) {
for (int i = 0; i < values.length; i++) {
sbuff
.append(" ")
.append(name)
.append(" (")
.append(i)
.append("): ")
.append(values[i])
.append("\n");
}
}
}
sbuff.append("\n");
sbuff.append("Request Headers:\n");
Enumeration names = req.getHeaderNames();
while (names.hasMoreElements()) {
String name = (String) names.nextElement();
Enumeration values = req.getHeaders(name); // support multiple values
if (values != null) {
while (values.hasMoreElements()) {
String value = (String) values.nextElement();
sbuff.append(" ").append(name).append(": ").append(value).append("\n");
}
}
}
sbuff.append(" ------------------\n");
return sbuff.toString();
}
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();
}