public static void informInterestedParties(
HttpServletRequest request, String number, String message, String context) {
// String context="context0";
// context=ServletUtilities.getContext(request);
Shepherd myShepherd = new Shepherd(context);
myShepherd.beginDBTransaction();
if (myShepherd.isEncounter(number)) {
Encounter enc = myShepherd.getEncounter(number);
if (enc.getInterestedResearchers() != null) {
Vector notifyMe = enc.getInterestedResearchers();
int size = notifyMe.size();
String[] interested = new String[size];
for (int i = 0; i < size; i++) {
interested[i] = (String) notifyMe.get(i);
}
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
if (size > 0) {
Vector e_images = new Vector();
String mailMe = interested[0];
String email =
getText("dataUpdate.txt")
.replaceAll(
"INSERTTEXT",
("Encounter "
+ number
+ ": "
+ message
+ "\n\nLink to encounter: http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ number));
email +=
("\n\nWant to stop tracking this set of encounter data? Use this link.\nhttp://"
+ CommonConfiguration.getURLLocation(request)
+ "/dontTrack?number="
+ number
+ "&email=");
ThreadPoolExecutor es = MailThreadExecutorService.getExecutorService();
es.execute(
new NotificationMailer(
CommonConfiguration.getMailHost(context),
CommonConfiguration.getAutoEmailAddress(context),
mailMe,
("Encounter data update: " + number),
(email + mailMe),
e_images,
context));
// NotificationMailer mailer=new NotificationMailer(CommonConfiguration.getMailHost(),
// CommonConfiguration.getAutoEmailAddress(), mailMe, ("Encounter data update: "+number),
// (email+mailMe), e_images);
for (int j = 1; j < size; j++) {
mailMe = interested[j];
es.execute(
new NotificationMailer(
CommonConfiguration.getMailHost(context),
CommonConfiguration.getAutoEmailAddress(context),
mailMe,
("Encounter data update: " + number),
(email + mailMe),
e_images,
context));
}
}
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
}
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
}
}
// inform researchers that have logged an interest with the encounter or marked individual
public static void informInterestedIndividualParties(
HttpServletRequest request, String shark, String message, String context) {
Shepherd myShepherd = new Shepherd(context);
myShepherd.beginDBTransaction();
if (myShepherd.isMarkedIndividual(shark)) {
MarkedIndividual sharkie = myShepherd.getMarkedIndividual(shark);
if (sharkie.getInterestedResearchers() != null) {
Vector notifyMe = sharkie.getInterestedResearchers();
int size = notifyMe.size();
String[] interested = new String[size];
for (int i = 0; i < size; i++) {
interested[i] = (String) notifyMe.get(i);
}
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
if (size > 0) {
ThreadPoolExecutor es = MailThreadExecutorService.getExecutorService();
Vector e_images = new Vector();
String mailMe = interested[0];
String email =
getText("dataUpdate.txt")
.replaceAll(
"INSERTTEXT",
("Tag "
+ shark
+ ": "
+ message
+ "\n\nLink to individual: http://"
+ CommonConfiguration.getURLLocation(request)
+ "/individuals.jsp?number="
+ shark));
email +=
("\n\nWant to stop tracking this set of this individual's data? Use this link.\n\nhttp://"
+ CommonConfiguration.getURLLocation(request)
+ "/dontTrack?shark="
+ shark
+ "&email=");
es.execute(
new NotificationMailer(
CommonConfiguration.getMailHost(context),
CommonConfiguration.getAutoEmailAddress(context),
mailMe,
("Marked individual data update: " + shark),
(email + mailMe),
e_images,
context));
for (int j = 1; j < size; j++) {
mailMe = interested[j];
es.execute(
new NotificationMailer(
CommonConfiguration.getMailHost(context),
CommonConfiguration.getAutoEmailAddress(context),
mailMe,
("Individual data update: " + shark),
(email + mailMe),
e_images,
context));
}
}
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
}
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
}
}
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();
}
