public int doEndTag() throws JspException {
if ((jspFile.indexOf("..") >= 0)
|| (jspFile.toUpperCase().indexOf("/WEB-INF/") != 0)
|| (jspFile.toUpperCase().indexOf("/META-INF/") != 0))
throw new JspTagException("Invalid JSP file " + jspFile);
InputStream in = pageContext.getServletContext().getResourceAsStream(jspFile);
if (in == null) throw new JspTagException("Unable to find JSP file: " + jspFile);
InputStreamReader reader = new InputStreamReader(in);
JspWriter out = pageContext.getOut();
try {
out.println("<body>");
out.println("<pre>");
for (int ch = in.read(); ch != -1; ch = in.read())
if (ch == '<') out.print("<");
else out.print((char) ch);
out.println("</pre>");
out.println("</body>");
} catch (IOException ex) {
throw new JspTagException("IOException: " + ex.toString());
}
return super.doEndTag();
}
public static String getResTxtContent(ClassLoader cl, String p) throws IOException {
String s = res2txt_cont.get(p);
if (s != null) return s;
InputStream is = null;
try {
is = cl.getResourceAsStream(p);
// is = this.getClass().getResourceAsStream(p);
if (is == null) return null;
byte[] buf = new byte[1024];
ByteArrayOutputStream baos = new ByteArrayOutputStream();
int len;
while ((len = is.read(buf)) >= 0) {
baos.write(buf, 0, len);
}
byte[] cont = baos.toByteArray();
s = new String(cont, "UTF-8");
res2txt_cont.put(p, s);
return s;
} finally {
if (is != null) is.close();
}
}
public static void renderFile(
HttpServletResponse resp,
String filename,
InputStream cont_stream,
boolean showpic,
boolean ignorespace)
throws IOException {
if (cont_stream == null) return;
if (ignorespace) filename = filename.replace(" ", "");
if (!showpic)
resp.addHeader(
"Content-Disposition",
"attachment; filename=" + new String(filename.getBytes(), "iso8859-1"));
resp.setContentType(Mime.getContentType(filename));
ServletOutputStream os = resp.getOutputStream();
byte[] buf = new byte[1024];
int len = 0;
while ((len = cont_stream.read(buf)) != -1) {
os.write(buf, 0, len);
}
os.flush();
}
private void processEncrypt(final ServletRequest servletRequest ,final HttpServletRequest httpRequest,final ServletResponse servletResponse,
final FilterChain filterChain)throws IOException, ServletException{
InputStream inputStream = servletRequest.getInputStream();
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
byte buf[] = new byte[1024];
int letti=-1;
while ((letti = inputStream.read(buf)) > 0){
byteArrayOutputStream.write(buf, 0, letti);
}
final BufferedRequestWrapper bufferedRequest = new BufferedRequestWrapper(httpRequest,doEncrypt(byteArrayOutputStream));
final HttpServletResponse response = (HttpServletResponse) servletResponse;
final ByteArrayPrintWriter pw = new ByteArrayPrintWriter();
HttpServletResponse wrappedResp = new HttpServletResponseWrapper(response) {
public PrintWriter getWriter() {
return pw.getWriter();
}
public ServletOutputStream getOutputStream() {
return pw.getStream();
}
};
filterChain.doFilter(bufferedRequest, wrappedResp);
}
protected Object exec(Object[] args, Context context) {
int nargs = args.length;
if (nargs != 1 && nargs != 2) {
undefined(args, context);
return null;
}
HttpServletRequest request = (HttpServletRequest) args[0];
String enc;
if (nargs == 1) {
enc = ServletEncoding.getDefaultInputEncoding(context);
} else {
enc = (String) args[1];
}
String contentType = request.getContentType();
if (contentType != null && contentType.startsWith("multipart/form-data")) {
throw new RuntimeException("not yet implemented");
} else {
try {
ByteArrayOutputStream bout = new ByteArrayOutputStream();
byte[] buf = new byte[512];
int n;
InputStream in = request.getInputStream();
while ((n = in.read(buf, 0, buf.length)) != -1) {
bout.write(buf, 0, n);
}
in.close();
String qs = new String(bout.toByteArray());
Map map = URLEncoding.parseQueryString(qs, enc);
return new ServletParameter(map);
} catch (IOException e) {
throw new PnutsException(e, context);
}
}
}
public BufferedRequestWrapper(HttpServletRequest req) throws IOException {
super(req);
InputStream is = req.getInputStream();
baos = new ByteArrayOutputStream();
byte buf[] = new byte[1024];
int letti;
while ((letti = is.read(buf)) > 0) {
baos.write(buf, 0, letti);
}
buffer = baos.toByteArray();
}
protected void service(HttpServletRequest req, HttpServletResponse resp)
throws ServletException, java.io.IOException {
String p = req.getParameter("r");
if (p == null || (p = p.trim()).equals("")) {
String pi = req.getPathInfo();
return;
}
byte[] cont = res2cont.get(p);
if (cont != null) {
resp.setContentType(Mime.getContentType(p));
ServletOutputStream os = resp.getOutputStream();
os.write(cont);
os.flush();
return;
}
InputStream is = null;
try {
is = appCL.getResourceAsStream(p); // getInputStreamByPath(p) ;
if (is == null) {
is = new Object().getClass().getResourceAsStream(p);
if (is == null) return;
}
byte[] buf = new byte[1024];
ByteArrayOutputStream baos = new ByteArrayOutputStream();
int len;
while ((len = is.read(buf)) >= 0) {
baos.write(buf, 0, len);
}
cont = baos.toByteArray();
res2cont.put(p, cont);
resp.setContentType(Mime.getContentType(p));
ServletOutputStream os = resp.getOutputStream();
os.write(cont);
os.flush();
return;
} finally {
if (is != null) is.close();
}
}
/**
* return OutputStream of JasperReport object, this page could only be viewed from localhost for
* security concern. parameter can be (id), or (table and type)
*
* @param id - report id, or
* @param table - table name
* @param type - reporttype "s","l","o", case insensitive
* @param client(*) - client domain
* @param version - version number, default to -1
*/
public void process(HttpServletRequest request, HttpServletResponse response) throws Exception {
String clientName = request.getParameter("client");
int objectId = ParamUtils.getIntAttributeOrParameter(request, "id", -1);
if (objectId == -1) {
// try using table and type
objectId =
getReportId(clientName, request.getParameter("table"), request.getParameter("type"));
}
if (objectId == -1) {
logger.error("report not found, request is:" + Tools.toString(request));
throw new NDSException("report not found");
}
int version = ParamUtils.getIntAttributeOrParameter(request, "version", -1);
File reportXMLFile = new File(ReportTools.getReportFile(objectId, clientName));
if (reportXMLFile.exists()) {
// generate jasperreport if file not exists or not newer
String reportName =
reportXMLFile.getName().substring(0, reportXMLFile.getName().lastIndexOf("."));
File reportJasperFile = new File(reportXMLFile.getParent(), reportName + ".jasper");
if (!reportJasperFile.exists()
|| reportJasperFile.lastModified() < reportXMLFile.lastModified()) {
JasperCompileManager.compileReportToFile(
reportXMLFile.getAbsolutePath(), reportJasperFile.getAbsolutePath());
}
InputStream is = new FileInputStream(reportJasperFile);
response.setContentType("application/octetstream;");
response.setContentLength((int) reportJasperFile.length());
// response.setHeader("Content-Disposition","inline;filename=\""+reportJasperFile.getName()+"\"");
ServletOutputStream os = response.getOutputStream();
byte[] b = new byte[8192];
int bInt;
while ((bInt = is.read(b, 0, b.length)) != -1) {
os.write(b, 0, bInt);
}
is.close();
os.flush();
os.close();
} else {
throw new NDSException("Not found report template");
}
}
package com.jspsmart.upload;
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();
}
