public static Connection getConnection() throws SQLException {
Connection conn = null;
Properties connectionProps = new Properties();
connectionProps.put(
"user", CommonConfiguration.getProperty("datanucleus.ConnectionUserName", "context0"));
connectionProps.put(
"password", CommonConfiguration.getProperty("datanucleus.ConnectionPassword", "context0"));
conn =
DriverManager.getConnection(
CommonConfiguration.getProperty("datanucleus.ConnectionURL", "context0"),
connectionProps);
System.out.println("Connected to database for authentication.");
return conn;
}
public static String getLanguageCode(HttpServletRequest request) {
String context = ServletUtilities.getContext(request);
// worst case scenario default to English
String langCode = "en";
// try to detect a default if defined
if (CommonConfiguration.getProperty("defaultLanguage", context) != null) {
langCode = CommonConfiguration.getProperty("defaultLanguage", context);
}
ArrayList<String> supportedLanguages = new ArrayList<String>();
if (CommonConfiguration.getSequentialPropertyValues("language", context) != null) {
supportedLanguages = CommonConfiguration.getSequentialPropertyValues("language", context);
}
// if specified directly, always accept the override
if (request.getParameter("langCode") != null) {
if (supportedLanguages.contains(request.getParameter("langCode"))) {
return request.getParameter("langCode");
}
}
// the request cookie is the next thing we check. this should be the primary means of figuring
// langCode out
Cookie[] cookies = request.getCookies();
if (cookies != null) {
for (Cookie cookie : cookies) {
if ("wildbookLangCode".equals(cookie.getName())) {
if (supportedLanguages.contains(cookie.getValue())) {
return cookie.getValue();
}
}
}
}
// finally, we will check the URL vs values defined in context.properties to see if we can set
// the right context
// TBD - future - detect browser supported language codes and locale from the HTTPServletRequest
// object
return langCode;
}
// Logs a new ATOM entry
public static synchronized void addATOMEntry(
String title, String link, String description, File atomFile, String context) {
try {
if (atomFile.exists()) {
// System.out.println("ATOM file found!");
/** Namespace URI for content:encoded elements */
String CONTENT_NS = "http://www.w3.org/2005/Atom";
/** Parses RSS or Atom to instantiate a SyndFeed. */
SyndFeedInput input = new SyndFeedInput();
/** Transforms SyndFeed to RSS or Atom XML. */
SyndFeedOutput output = new SyndFeedOutput();
// Load the feed, regardless of RSS or Atom type
SyndFeed feed = input.build(new XmlReader(atomFile));
// Set the output format of the feed
feed.setFeedType("atom_1.0");
List<SyndEntry> items = feed.getEntries();
int numItems = items.size();
if (numItems > 9) {
items.remove(0);
feed.setEntries(items);
}
SyndEntry newItem = new SyndEntryImpl();
newItem.setTitle(title);
newItem.setLink(link);
newItem.setUri(link);
SyndContent desc = new SyndContentImpl();
desc.setType("text/html");
desc.setValue(description);
newItem.setDescription(desc);
desc.setType("text/html");
newItem.setPublishedDate(new java.util.Date());
List<SyndCategory> categories = new ArrayList<SyndCategory>();
if (CommonConfiguration.getProperty("htmlTitle", context) != null) {
SyndCategory category2 = new SyndCategoryImpl();
category2.setName(CommonConfiguration.getProperty("htmlTitle", context));
categories.add(category2);
}
newItem.setCategories(categories);
if (CommonConfiguration.getProperty("htmlAuthor", context) != null) {
newItem.setAuthor(CommonConfiguration.getProperty("htmlAuthor", context));
}
items.add(newItem);
feed.setEntries(items);
feed.setPublishedDate(new java.util.Date());
FileWriter writer = new FileWriter(atomFile);
output.output(feed, writer);
writer.toString();
}
} catch (IOException ioe) {
System.out.println("ERROR: Could not find the ATOM file.");
ioe.printStackTrace();
} catch (Exception e) {
System.out.println("Unknown exception trying to add an entry to the ATOM file.");
e.printStackTrace();
}
}
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();
}