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 void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
super.doPost(request, response);
try {
if (!ServletFileUpload.isMultipartContent(request)) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST);
return;
}
ServletFileUpload sfU = new ServletFileUpload();
FileItemIterator items = sfU.getItemIterator(request);
while (items.hasNext()) {
FileItemStream item = items.next();
if (!item.isFormField()) {
InputStream stream = item.openStream();
Document doc = editor.toDocument(stream);
stream.close();
handleDocument(request, response, doc);
return;
}
}
response.sendError(HttpServletResponse.SC_BAD_REQUEST, "No XML uploaded");
} catch (FileUploadException fuE) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST, fuE.getMessage());
} catch (JDOMException jE) {
response.sendError(HttpServletResponse.SC_BAD_REQUEST, jE.getMessage());
}
}
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();
}
}
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();
}
/**
* 根据XORM定义和对应的文件属性列,输出文件内容.
*
* @param resp
* @param filename
* @param xorm_c
* @param xorm_prop
* @param xorm_pk
*/
public static void renderFile(
HttpServletResponse resp, String filename, Class xorm_c, String xorm_prop, long xorm_pk)
throws Exception {
InputStream is = null;
try {
is = GDB.getInstance().getXORMFileStreamByPkId(xorm_c, xorm_prop, xorm_pk);
if (is == null) return;
renderFile(resp, filename, is);
} 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 static synchronized String getJavascript() {
if (jstext == null) {
InputStream istr = null;
try {
ClassLoader loader = Thread.currentThread().getContextClassLoader();
istr = loader.getResourceAsStream(JAVASCRIPT_RESOURCE);
jstext = StringUtil.fromInputStream(istr);
istr.close();
} catch (Exception e) {
log.error("Can't load javascript", e);
} finally {
IOUtil.safeClose(istr);
}
}
return jstext;
}
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();
}
}
public static void main(String args[]) throws IOException {
// Function References
String path =
"http://motherlode.ucar.edu:8081/thredds/radarServer/nexrad/level3/IDD/dataset.xml";
try {
catURI = new URI(StringUtil2.escape(path, "/:-_."));
} catch (URISyntaxException e) {
System.out.println("radarServer main: URISyntaxException=" + e.getMessage());
return;
}
// read the catalog
System.out.println("radarServer main: full path=" + path);
InputStream ios = null;
try {
URL url = new URL(path);
ios = url.openStream();
// ios = new FileInputStream(path);
// acat = factory.readXML(ios, catURI );
BufferedReader dataIS = new BufferedReader(new InputStreamReader(ios));
while (true) {
String line = dataIS.readLine();
if (line == null) break;
System.out.println(line);
}
} catch (Throwable t) {
System.out.println("radarServer main: Exception on catalog=" + path + " " + t.getMessage());
return;
} finally {
if (ios != null) {
try {
ios.close();
} catch (IOException e) {
System.out.println("radarServer main: error closing" + path);
}
}
}
return;
}
/**
* 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");
}
}
protected void processConfiguration(FilterConfig filterConfig) {
InputStream is;
if (isNullOrEmpty(this.configFile)) {
is = servletContext.getResourceAsStream(CONFIG_FILE_LOCATION);
} else {
try {
is = new FileInputStream(this.configFile);
} catch (FileNotFoundException e) {
throw logger.samlIDPConfigurationError(e);
}
}
PicketLinkType picketLinkType;
String configurationProviderName = filterConfig.getInitParameter(CONFIGURATION_PROVIDER);
if (configurationProviderName != null) {
try {
Class<?> clazz = SecurityActions.loadClass(getClass(), configurationProviderName);
if (clazz == null) {
throw new ClassNotFoundException(ErrorCodes.CLASS_NOT_LOADED + configurationProviderName);
}
this.configProvider = (SAMLConfigurationProvider) clazz.newInstance();
} catch (Exception e) {
throw new RuntimeException(
"Could not create configuration provider [" + configurationProviderName + "].", e);
}
}
try {
// Work on the IDP Configuration
if (configProvider != null) {
try {
if (is == null) {
// Try the older version
is =
servletContext.getResourceAsStream(
GeneralConstants.DEPRECATED_CONFIG_FILE_LOCATION);
// Additionally parse the deprecated config file
if (is != null && configProvider instanceof AbstractSAMLConfigurationProvider) {
((AbstractSAMLConfigurationProvider) configProvider).setConfigFile(is);
}
} else {
// Additionally parse the consolidated config file
if (is != null && configProvider instanceof AbstractSAMLConfigurationProvider) {
((AbstractSAMLConfigurationProvider) configProvider).setConsolidatedConfigFile(is);
}
}
picketLinkType = configProvider.getPicketLinkConfiguration();
picketLinkType.setIdpOrSP(configProvider.getSPConfiguration());
} catch (ProcessingException e) {
throw logger.samlSPConfigurationError(e);
} catch (ParsingException e) {
throw logger.samlSPConfigurationError(e);
}
} else {
if (is != null) {
try {
picketLinkType = ConfigurationUtil.getConfiguration(is);
} catch (ParsingException e) {
logger.trace(e);
throw logger.samlSPConfigurationError(e);
}
} else {
is = servletContext.getResourceAsStream(GeneralConstants.DEPRECATED_CONFIG_FILE_LOCATION);
if (is == null) {
throw logger.configurationFileMissing(configFile);
}
picketLinkType = new PicketLinkType();
picketLinkType.setIdpOrSP(ConfigurationUtil.getSPConfiguration(is));
}
}
// Close the InputStream as we no longer need it
if (is != null) {
try {
is.close();
} catch (IOException e) {
// ignore
}
}
Boolean enableAudit = picketLinkType.isEnableAudit();
// See if we have the system property enabled
if (!enableAudit) {
String sysProp = SecurityActions.getSystemProperty(GeneralConstants.AUDIT_ENABLE, "NULL");
if (!"NULL".equals(sysProp)) {
enableAudit = Boolean.parseBoolean(sysProp);
}
}
if (enableAudit) {
if (auditHelper == null) {
String securityDomainName = PicketLinkAuditHelper.getSecurityDomainName(servletContext);
auditHelper = new PicketLinkAuditHelper(securityDomainName);
}
}
SPType spConfiguration = (SPType) picketLinkType.getIdpOrSP();
processIdPMetadata(spConfiguration);
this.serviceURL = spConfiguration.getServiceURL();
this.canonicalizationMethod = spConfiguration.getCanonicalizationMethod();
this.picketLinkConfiguration = picketLinkType;
this.issuerID = filterConfig.getInitParameter(ISSUER_ID);
this.characterEncoding = filterConfig.getInitParameter(CHARACTER_ENCODING);
this.samlHandlerChainClass = filterConfig.getInitParameter(SAML_HANDLER_CHAIN_CLASS);
logger.samlSPSettingCanonicalizationMethod(canonicalizationMethod);
XMLSignatureUtil.setCanonicalizationMethodType(canonicalizationMethod);
try {
this.initKeyProvider();
this.initializeHandlerChain(picketLinkType);
} catch (Exception e) {
throw new RuntimeException(e);
}
logger.trace("Identity Provider URL=" + getConfiguration().getIdentityURL());
} catch (Exception e) {
throw new RuntimeException(e);
}
}
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// Variable initializations.
HttpSession session = request.getSession();
FileItem image_file = null;
int record_id = 0;
int image_id;
// Check if a record ID has been entered.
if (request.getParameter("recordID") == null || request.getParameter("recordID").equals("")) {
// If no ID has been entered, send message to jsp.
response_message =
"<p><font color=FF0000>No Record ID Detected, Please Enter One.</font></p>";
session.setAttribute("msg", response_message);
response.sendRedirect("UploadImage.jsp");
}
try {
// Parse the HTTP request to get the image stream.
DiskFileUpload fu = new DiskFileUpload();
// Will get multiple image files if that happens and can be accessed through FileItems.
List<FileItem> FileItems = fu.parseRequest(request);
// Connect to the database and create a statement.
conn = getConnected(drivername, dbstring, username, password);
stmt = conn.createStatement();
// Process the uploaded items, assuming only 1 image file uploaded.
Iterator<FileItem> i = FileItems.iterator();
while (i.hasNext()) {
FileItem item = (FileItem) i.next();
// Test if item is a form field and matches recordID.
if (item.isFormField()) {
if (item.getFieldName().equals("recordID")) {
// Covert record id from string to integer.
record_id = Integer.parseInt(item.getString());
String sql = "select count(*) from radiology_record where record_id = " + record_id;
int count = 0;
try {
rset = stmt.executeQuery(sql);
while (rset != null && rset.next()) {
count = (rset.getInt(1));
}
} catch (SQLException e) {
response_message = e.getMessage();
}
// Check if recordID is in the database.
if (count == 0) {
// Invalid recordID, send message to jsp.
response_message =
"<p><font color=FF0000>Record ID Does Not Exist In Database.</font></p>";
session.setAttribute("msg", response_message);
// Close connection.
conn.close();
response.sendRedirect("UploadImage.jsp");
}
}
} else {
image_file = item;
if (image_file.getName().equals("")) {
// No file, send message to jsp.
response_message = "<p><font color=FF0000>No File Selected For Record ID.</font></p>";
session.setAttribute("msg", response_message);
// Close connection.
conn.close();
response.sendRedirect("UploadImage.jsp");
}
}
}
// Get the image stream.
InputStream instream = image_file.getInputStream();
BufferedImage full_image = ImageIO.read(instream);
BufferedImage thumbnail = shrink(full_image, 10);
BufferedImage regular_image = shrink(full_image, 5);
// First, to generate a unique img_id using an SQL sequence.
rset1 = stmt.executeQuery("SELECT image_id_sequence.nextval from dual");
rset1.next();
image_id = rset1.getInt(1);
// Insert an empty blob into the table first. Note that you have to
// use the Oracle specific function empty_blob() to create an empty blob.
stmt.execute(
"INSERT INTO pacs_images VALUES("
+ record_id
+ ","
+ image_id
+ ", empty_blob(), empty_blob(), empty_blob())");
// to retrieve the lob_locator
// Note that you must use "FOR UPDATE" in the select statement
String cmd = "SELECT * FROM pacs_images WHERE image_id = " + image_id + " FOR UPDATE";
rset = stmt.executeQuery(cmd);
rset.next();
BLOB myblobFull = ((OracleResultSet) rset).getBLOB(5);
BLOB myblobThumb = ((OracleResultSet) rset).getBLOB(3);
BLOB myblobRegular = ((OracleResultSet) rset).getBLOB(4);
// Write the full size image to the blob object.
OutputStream fullOutstream = myblobFull.getBinaryOutputStream();
ImageIO.write(full_image, "jpg", fullOutstream);
// Write the thumbnail size image to the blob object.
OutputStream thumbOutstream = myblobThumb.getBinaryOutputStream();
ImageIO.write(thumbnail, "jpg", thumbOutstream);
// Write the regular size image to the blob object.
OutputStream regularOutstream = myblobRegular.getBinaryOutputStream();
ImageIO.write(regular_image, "jpg", regularOutstream);
// Commit the changes to database.
stmt.executeUpdate("commit");
response_message = "<p><font color=00CC00>Upload Successful.</font></p>";
session.setAttribute("msg", response_message);
instream.close();
fullOutstream.close();
thumbOutstream.close();
regularOutstream.close();
// Close connection.
conn.close();
response.sendRedirect("UploadImage.jsp");
instream.close();
fullOutstream.close();
thumbOutstream.close();
regularOutstream.close();
// Close connection.
conn.close();
} catch (Exception ex) {
response_message = ex.getMessage();
}
}
private void datasetInfoHtml(
RadarType radarType, String pathInfo, PrintWriter pw, HttpServletResponse res)
throws IOException {
pathInfo = pathInfo.replace("/dataset.html", "");
pathInfo = pathInfo.replace("/catalog.html", "");
Element root = new Element("RadarNexrad");
Document doc = new Document(root);
if (pathInfo.startsWith("/")) pathInfo = pathInfo.substring(1);
for (int i = 0; i < datasets.size(); i++) {
InvDatasetScan ds = (InvDatasetScan) datasets.get(i);
if (!(pathInfo.equals(ds.getPath()))) {
continue;
}
// at this point a valid dataset
// fix the location
root.setAttribute("location", "/thredds/radarServer/" + ds.getPath());
// spatial range
ThreddsMetadata.GeospatialCoverage gc = ds.getGeospatialCoverage();
LatLonRect bb = new LatLonRect();
gc.setBoundingBox(bb);
String north = Double.toString(gc.getLatNorth());
String south = Double.toString(gc.getLatSouth());
String east = Double.toString(gc.getLonEast());
String west = Double.toString(gc.getLonWest());
Element LatLonBox = new Element("LatLonBox");
LatLonBox.addContent(new Element("north").addContent(north));
LatLonBox.addContent(new Element("south").addContent(south));
LatLonBox.addContent(new Element("east").addContent(east));
LatLonBox.addContent(new Element("west").addContent(west));
root.addContent(LatLonBox);
// get the time range
Element timeSpan = new Element("TimeSpan");
CalendarDateRange dr = ds.getCalendarDateCoverage();
timeSpan.addContent(new Element("begin").addContent(dr.getStart().toString()));
timeSpan.addContent(new Element("end").addContent(dr.getEnd().toString()));
root.addContent(timeSpan);
ThreddsMetadata.Variables cvs = (ThreddsMetadata.Variables) ds.getVariables().get(0);
List vl = cvs.getVariableList();
for (int j = 0; j < vl.size(); j++) {
ThreddsMetadata.Variable v = (ThreddsMetadata.Variable) vl.get(j);
Element variable = new Element("variable");
variable.setAttribute("name", v.getName());
root.addContent(variable);
}
// add pointer to the station list XML
/*
Element stnList = new Element("stationList");
stnList.setAttribute("title", "Available Stations", XMLEntityResolver.xlinkNS);
stnList.setAttribute("href", "/thredds/radarServer/"+ pathInfo +"/stations.xml",
XMLEntityResolver.xlinkNS);
root.addContent(stnList);
*/
// String[] stations = rns.stationsDS( dataLocation.get( ds.getPath() ));
// rns.printStations( stations );
// add accept list
Element a = new Element("AcceptList");
a.addContent(new Element("accept").addContent("xml"));
a.addContent(new Element("accept").addContent("html"));
root.addContent(a);
}
ServerMethods sm = new ServerMethods(log);
InputStream xslt = sm.getInputStream(contentPath + getPath() + "radar.xsl", RadarServer.class);
try {
// what's wrong here xslt = getXSLT( "radar.xsl" );
XSLTransformer transformer = new XSLTransformer(xslt);
Document html = transformer.transform(doc);
XMLOutputter fmt = new XMLOutputter(Format.getPrettyFormat());
String infoString = fmt.outputString(html);
res.setContentType("text/html; charset=iso-8859-1");
pw = res.getWriter();
pw.println(infoString);
pw.flush();
} catch (Exception e) {
log.error("radarServer reading " + contentPath + getPath() + "radar.xsl");
log.error("radarServer XSLTransformer problem for web form ", e);
} finally {
if (xslt != null) {
try {
xslt.close();
} catch (IOException e) {
log.error("radarServer radar.xsl: error closing" + contentPath + getPath() + "radar.xsl");
}
}
}
return;
}
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();
}