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();
}
}
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
Shepherd myShepherd = new Shepherd();
// set up for response
response.setContentType("text/html");
PrintWriter out = response.getWriter();
boolean locked = false;
String email = "None", encounterNumber = "None", shark = "None";
email = request.getParameter("email");
encounterNumber = request.getParameter("number");
myShepherd.beginDBTransaction();
if ((request.getParameter("number") != null)
&& (myShepherd.isEncounter(request.getParameter("number")))
&& (email != null)
&& (!email.equals(""))
&& (email.indexOf("@") != -1)) {
Encounter enc = myShepherd.getEncounter(encounterNumber);
// int positionInList=0;
try {
Vector interested = enc.getInterestedResearchers();
interested.add(email);
} catch (Exception le) {
locked = true;
myShepherd.rollbackDBTransaction();
}
if (!locked) {
myShepherd.commitDBTransaction();
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success!</strong> I have successfully added the tracking of encounter#"
+ encounterNumber
+ " for e-mail address "
+ email
+ ".");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ encounterNumber
+ "\">Return to encounter "
+ encounterNumber
+ "</a></p>\n");
out.println(ServletUtilities.getFooter());
Vector e_images = new Vector();
String message =
"This is a confirmation that e-mail tracking of data changes to encounter "
+ encounterNumber
+ " has now started. You should receive e-mail updates any time changes to this encounter are made.";
NotificationMailer mailer =
new NotificationMailer(
CommonConfiguration.getMailHost(),
CommonConfiguration.getAutoEmailAddress(),
email,
("Encounter data tracking started for encounter: " + encounterNumber),
message,
e_images);
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure!</strong> This encounter is currently being modified by another user, or the database is locked. Please wait a few seconds before trying to add this e-mail address for tracking again.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ encounterNumber
+ "\">Return to encounter "
+ encounterNumber
+ "</a></p>\n");
out.println(ServletUtilities.getFooter());
}
} else if ((request.getParameter("individual") != null)
&& (myShepherd.isMarkedIndividual(request.getParameter("individual")))
&& (email != null)
&& (!email.equals(""))
&& (email.indexOf("@") != -1)) {
shark = request.getParameter("individual");
MarkedIndividual sharkie = myShepherd.getMarkedIndividual(shark);
// myShepherd.beginDBTransaction();
// int positionInList=0;
try {
Vector interested = sharkie.getInterestedResearchers();
interested.add(email);
} catch (Exception le) {
locked = true;
myShepherd.rollbackDBTransaction();
}
if (!locked) {
myShepherd.commitDBTransaction();
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success!</strong> I have successfully added the tracking of "
+ shark
+ " for e-mail address "
+ email
+ ".");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/individuals.jsp?number="
+ shark
+ "\">Return to "
+ shark
+ "</a></p>\n");
out.println(ServletUtilities.getFooter());
Vector e_images = new Vector();
String message =
"This is a confirmation that e-mail tracking of data changes to "
+ shark
+ " has now started. You should receive e-mail updates any time changes to this record are made.";
NotificationMailer mailer =
new NotificationMailer(
CommonConfiguration.getMailHost(),
CommonConfiguration.getAutoEmailAddress(),
email,
("Data tracking started for encounter: " + shark),
message,
e_images);
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure!</strong> This record is currently being modified by another user, or the database is locked. Please wait a few seconds before trying to add this e-mail address for tracking again.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/individuals.jsp?number="
+ shark
+ "\">Return to "
+ shark
+ "</a></p>\n");
out.println(ServletUtilities.getFooter());
}
} else {
myShepherd.rollbackDBTransaction();
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Error:</strong> I was unable to add your e-mail address to the tracking list. I cannot find the record that you indicated in the database, or your e-mail address is invalid.");
out.println(ServletUtilities.getFooter());
}
out.close();
myShepherd.closeDBTransaction();
}
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
String context = "context0";
context = ServletUtilities.getContext(request);
String langCode = ServletUtilities.getLanguageCode(request);
Shepherd myShepherd = new Shepherd(context);
// set up for response
response.setContentType("text/html");
PrintWriter out = response.getWriter();
boolean locked = false;
boolean isOwner = true;
if (request.getParameter("number") != null) {
myShepherd.beginDBTransaction();
Encounter enc2reject = myShepherd.getEncounter(request.getParameter("number"));
setDateLastModified(enc2reject);
boolean isOK = enc2reject.isAssignedToMarkedIndividual().equals("Unassigned");
myShepherd.rollbackDBTransaction();
if (isOK) {
myShepherd.beginDBTransaction();
try {
// enc2reject.reject();
enc2reject.setState("unidentifiable");
enc2reject.addComments(
"<p><em>"
+ request.getRemoteUser()
+ " on "
+ (new java.util.Date()).toString()
+ "</em><br>Set this encounter as unidentifiable in the database.</p>");
// enc2reject.approved = false;
enc2reject.setState("unidentifiable");
} catch (Exception le) {
locked = true;
le.printStackTrace();
myShepherd.rollbackDBTransaction();
}
if (!locked) {
String submitterEmail = enc2reject.getSubmitterEmail();
myShepherd.commitDBTransaction();
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success:</strong> I have set encounter "
+ request.getParameter("number")
+ " as unidentifiable in the database.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ request.getParameter("number")
+ "\">View unidentifiable encounter #"
+ request.getParameter("number")
+ "</a></p>\n");
ArrayList<String> allStates =
CommonConfiguration.getSequentialPropertyValues("encounterState", context);
int allStatesSize = allStates.size();
if (allStatesSize > 0) {
for (int i = 0; i < allStatesSize; i++) {
String stateName = allStates.get(i);
out.println(
"<p><a href=\"encounters/searchResults.jsp?state="
+ stateName
+ "\">View all "
+ stateName
+ " encounters</a></font></p>");
}
}
out.println(ServletUtilities.getFooter(context));
String message =
"Encounter "
+ request.getParameter("number")
+ " was set as unidentifiable in the database.";
ServletUtilities.informInterestedParties(
request, request.getParameter("number"), message, context);
// Email submitter about change
Map<String, String> tagMap = NotificationMailer.createBasicTagMap(request, enc2reject);
tagMap.put("@TEXT_CONTENT@", message);
ThreadPoolExecutor es = MailThreadExecutorService.getExecutorService();
NotificationMailer mailer =
new NotificationMailer(context, null, submitterEmail, "encounterDataUpdate", tagMap);
es.execute(mailer);
es.shutdown();
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure:</strong> I have NOT modified encounter "
+ request.getParameter("number")
+ " in the database because another user is currently modifying its entry. Please try this operation again in a few seconds.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ request.getParameter("number")
+ "\">View unidentifiable encounter #"
+ request.getParameter("number")
+ "</a></p>\n");
ArrayList<String> allStates =
CommonConfiguration.getSequentialPropertyValues("encounterState", context);
int allStatesSize = allStates.size();
if (allStatesSize > 0) {
for (int i = 0; i < allStatesSize; i++) {
String stateName = allStates.get(i);
out.println(
"<p><a href=\"encounters/searchResults.jsp?state="
+ stateName
+ "\">View all "
+ stateName
+ " encounters</a></font></p>");
}
}
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"Encounter# "
+ request.getParameter("number")
+ " is assigned to an individual and cannot be set as unidentifiable until it has been removed from that individual.");
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Error:</strong> I do not know which encounter you are trying to remove.");
out.println(ServletUtilities.getFooter(context));
}
out.close();
myShepherd.closeDBTransaction();
}
private void setDateLastModified(Encounter enc) {
String strOutputDateTime = ServletUtilities.getDate();
enc.setDWCDateLastModified(strOutputDateTime);
}
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();
}
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
String context = "context0";
context = ServletUtilities.getContext(request);
Shepherd myShepherd = new Shepherd(context);
GridManager gm = GridManagerFactory.getGridManager();
// set up for response
response.setContentType("text/html");
PrintWriter out = response.getWriter();
String action = request.getParameter("action");
System.out.println("scanTaskHandler action is: " + action);
if (action != null) {
if ((action.equals("removeTask")) && (request.getParameter("taskID") != null)) {
myShepherd.beginDBTransaction();
boolean locked = false;
// gotta check if it's a valid scanTask to begin with!
// check for permissions to delete this scanTask
boolean deletePermission = false;
deletePermission = true;
if ((myShepherd.isScanTask(request.getParameter("taskID"))) && (deletePermission)) {
try {
// change
ThreadPoolExecutor es = SharkGridThreadExecutorService.getExecutorService();
ScanTask st = myShepherd.getScanTask(request.getParameter("taskID"));
myShepherd.getPM().deletePersistent(st);
myShepherd.commitDBTransaction();
// scanTaskCleanupThread swiThread=new
// scanTaskCleanupThread(request.getParameter("taskID"));
es.execute(new ScanTaskCleanupThread(request.getParameter("taskID")));
} catch (Exception e) {
locked = true;
System.out.println("I encounter the following error while deleting a scanTask:");
e.printStackTrace();
myShepherd.rollbackDBTransaction();
}
if (!locked) {
// confirm success
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success:</strong> The scanTask <i>"
+ request.getParameter("taskID")
+ "</i> has been removed.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Return to scanTask administration page.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Error:</strong> The scanTask <i>"
+ request.getParameter("taskID")
+ "</i> was not removed. The task may be locked by another user or in process. Check the logs for more information.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Return to scanTask administration page.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else {
myShepherd.rollbackDBTransaction();
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Error:</strong> The scanTask <i>"
+ request.getParameter("taskID")
+ "</i> was not identified in the database.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Return to scanTask administration page.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else if ((action.equals("addTask")) && (request.getParameter("encounterNumber") != null)) {
myShepherd.getPM().setIgnoreCache(true);
boolean locked = false;
// String readableName="";
boolean successfulStore = false;
// set up our properties
java.util.Properties props2 = new java.util.Properties();
String secondRun = "true";
String rightScan = "false";
boolean isRightScan = false;
boolean writeThis = true;
// String uniqueNum="";
if (request.getParameter("writeThis") == null) {
writeThis = false;
}
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightScan = "true";
isRightScan = true;
}
props2.setProperty("epsilon", "0.01");
props2.setProperty("R", "8");
props2.setProperty("Sizelim", "0.85");
props2.setProperty("maxTriangleRotation", "10");
props2.setProperty("C", "0.99");
props2.setProperty("secondRun", secondRun);
props2.setProperty("rightScan", rightScan);
// let's check if a scanTask for this exists
System.out.println("scanTaskHandler: Checking whether this is a new scanTask...");
myShepherd.beginDBTransaction();
String sideIdentifier = "L";
if (rightScan.equals("true")) {
sideIdentifier = "R";
// numComparisons=myShepherd.getNumEncountersWithSpotData(true);
} else {
// numComparisons=myShepherd.getNumEncountersWithSpotData(false);
}
String taskIdentifier = "scan" + sideIdentifier + request.getParameter("encounterNumber");
ScanTask st = new ScanTask();
// let's do a check to see if too many scanTasks are in the queue
int taskLimit = gm.getScanTaskLimit();
int currentNumScanTasks = myShepherd.getNumUnfinishedScanTasks();
myShepherd.getPM().getFetchPlan().setGroup(FetchPlan.DEFAULT);
System.out.println("currentNumScanTasks is: " + currentNumScanTasks);
// int currentNumScanTasks=0;
if (currentNumScanTasks < taskLimit) {
int numComparisons = 0;
if (rightScan.equals("true")) {
// sideIdentifier="R";
numComparisons = myShepherd.getNumEncountersWithSpotData(true);
} else {
numComparisons = myShepherd.getNumEncountersWithSpotData(false);
}
myShepherd.getPM().getFetchPlan().setGroup(FetchPlan.DEFAULT);
System.out.println(
"scanTaskHandler: Under the limit, so proceeding to check for condiions for creating a new scanTask...");
if ((!myShepherd.isScanTask(taskIdentifier))) {
System.out.println("scanTaskHandler: This scanTask does not exist, so go create it...");
// check if this encounter has the needed spots to create the task
boolean hasNeededSpots = false;
Encounter enc = myShepherd.getEncounter(request.getParameter("encounterNumber"));
if ((rightScan.equals("true")) && (enc.getRightSpots() != null)) {
hasNeededSpots = true;
} else if (enc.getSpots() != null) {
hasNeededSpots = true;
}
if (hasNeededSpots) {
System.out.println("scanTaskHandler: I have needed spots...proceeding...");
st =
new ScanTask(
myShepherd,
taskIdentifier,
props2,
request.getParameter("encounterNumber"),
writeThis);
st.setNumComparisons(numComparisons - 1);
if (request.getRemoteUser() != null) {
st.setSubmitter(request.getRemoteUser());
}
System.out.println("scanTaskHandler: About to create a scanTask...");
successfulStore = myShepherd.storeNewTask(st);
if (!successfulStore) {
System.out.println("scanTaskHandler: Unsuccessful store...");
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
} else {
System.out.println("scanTaskHandler: Successful store...");
myShepherd.commitDBTransaction();
myShepherd.closeDBTransaction();
myShepherd = new Shepherd(context);
}
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
}
} else if (myShepherd.isScanTask(taskIdentifier)) {
System.out.println("scanTaskHandler: This is an existing scanTask...");
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
String rightFilter = "";
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightFilter = "&rightSide=true";
}
// if it exists already, advance to the scanTask administration page to await its
// completion
response.sendRedirect(
"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp");
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
}
}
if (!locked && successfulStore) {
try {
ThreadPoolExecutor es = SharkGridThreadExecutorService.getExecutorService();
es.execute(
new ScanWorkItemCreationThread(
taskIdentifier,
isRightScan,
request.getParameter("encounterNumber"),
writeThis,
context));
} catch (Exception e) {
System.out.println("I failed while constructing the workItems for a new scanTask.");
e.printStackTrace();
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
}
if (!locked) {
System.out.println("Trying to commit the add of the scanWorkItems");
// myShepherd.commitDBTransaction();
// myShepherd.closeDBTransaction();
System.out.println("I committed the workItems!");
String rightFilter = "L";
String rightURL = "";
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightFilter = "R";
rightURL = "&rightSide=true";
}
// confirm success
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success:</strong> Your scan was successfully added to the sharkGrid!");
// out.println("<p><a
// href=\"http://"+CommonConfiguration.getURLLocation()+"/encounters/workAppletScan.jsp?number=scan"+rightFilter+request.getParameter("encounterNumber")+rightURL+"\">Start scanning for a match.</a></p>\n");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ request.getParameter("encounterNumber")
+ "\">Return to encounter "
+ request.getParameter("encounterNumber")
+ ".</a></p>\n");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp"
+ "\">Go to sharkGrid administration to monitor for completion.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure:</strong> The scan could not be created or was not fully created!");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println("<strong>Failure:</strong> I have NOT added this scanTask to the queue.");
if (currentNumScanTasks < taskLimit) {
out.println(
"The unfinished task limit of "
+ taskLimit
+ " has been filled. Please try adding the task to the queue again after existing tasks have finished.");
}
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else if (action.equals("addTuningTask")) {
// myShepherd.getPM().setIgnoreCache(true);
boolean locked = false;
// String readableName="";
boolean successfulStore = false;
int maxNumWorkItems = 99999999;
if ((request.getParameter("maxNumWorkItems") != null)
&& (!request.getParameter("maxNumWorkItems").equals(""))) {
maxNumWorkItems = Integer.parseInt(request.getParameter("maxNumWorkItems"));
}
// set up our properties
java.util.Properties props2 = new java.util.Properties();
String secondRun = "true";
String rightScan = "false";
boolean isRightScan = false;
boolean writeThis = true;
// String uniqueNum="";
if (request.getParameter("writeThis") == null) {
writeThis = false;
}
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightScan = "true";
isRightScan = true;
}
props2.setProperty("epsilon", "0.01");
props2.setProperty("R", "8");
props2.setProperty("Sizelim", "0.85");
props2.setProperty("maxTriangleRotation", "10");
props2.setProperty("C", "0.99");
props2.setProperty("secondRun", secondRun);
props2.setProperty("rightScan", rightScan);
// let's check if a scanTask for this exists
System.out.println("scanTaskHandler: Checking whether this is a new scanTask...");
myShepherd.beginDBTransaction();
String sideIdentifier = "L";
if (rightScan.equals("true")) {
sideIdentifier = "R";
// numComparisons=myShepherd.getNumEncountersWithSpotData(true);
} else {
// numComparisons=myShepherd.getNumEncountersWithSpotData(false);
}
String taskIdentifier = "TuningTask";
ScanTask st = new ScanTask();
// let's do a check to see if too many scanTasks are in the queue
int taskLimit = gm.getScanTaskLimit();
int currentNumScanTasks = myShepherd.getNumUnfinishedScanTasks();
myShepherd.getPM().getFetchPlan().setGroup(FetchPlan.DEFAULT);
System.out.println("currentNumScanTasks is: " + currentNumScanTasks);
// int currentNumScanTasks=0;
if (currentNumScanTasks < taskLimit) {
Vector leftSharks = myShepherd.getPossibleTrainingIndividuals();
Vector rightSharks = myShepherd.getRightPossibleTrainingIndividuals();
int numComparisons = 0;
// calculate the number of comparisons that can be made
int numLeftSharks = leftSharks.size();
for (int i = 0; i < numLeftSharks; i++) {
MarkedIndividual s = (MarkedIndividual) leftSharks.get(i);
int numTrainable = s.getNumberTrainableEncounters();
// int numCompareEncounters=s.getNumberTrainableEncounters();
// for(int j=(numCompareEncounters-1);j>1;j--){
// numCompareEncounters=numCompareEncounters*j;
// }
// numCompareEncounters=numCompareEncounters/(2*(numTrainable-2));
// numComparisons=numComparisons+numCompareEncounters;
numComparisons = numComparisons + combinations(numTrainable, 2);
}
int numRightSharks = rightSharks.size();
for (int i = 0; i < numRightSharks; i++) {
MarkedIndividual s = (MarkedIndividual) rightSharks.get(i);
int numCompareEncounters = s.getNumberRightTrainableEncounters();
// for(int j=(numCompareEncounters-1);j>1;j--){
// numCompareEncounters=numCompareEncounters*j;
// }
// numComparisons=numComparisons+numCompareEncounters;
numComparisons = numComparisons + combinations(numCompareEncounters, 2);
}
System.out.println(
"scanTaskHandler: Under the limit, so proceeding to check for condiions for creating a new scanTask...");
if ((!myShepherd.isScanTask(taskIdentifier))) {
// System.out.println("scanTaskHandler: This scanTask does not exist, so go create
// it...");
st = new ScanTask(myShepherd, taskIdentifier, props2, "TuningTask", writeThis);
if (numComparisons < (2 * maxNumWorkItems)) {
st.setNumComparisons(numComparisons);
} else {
st.setNumComparisons((2 * maxNumWorkItems));
}
if (request.getRemoteUser() != null) {
st.setSubmitter(request.getRemoteUser());
}
System.out.println("scanTaskHandler: About to create a TuningTask...");
successfulStore = myShepherd.storeNewTask(st);
if (!successfulStore) {
System.out.println("scanTaskHandler: Unsuccessful TuningTask store...");
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
} else {
System.out.println("scanTaskHandler: Successful TuningTask store...");
myShepherd.commitDBTransaction();
myShepherd.closeDBTransaction();
myShepherd = new Shepherd(context);
}
} else if (myShepherd.isScanTask(taskIdentifier)) {
System.out.println("scanTaskHandler: This is an existing scanTask...");
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
String rightFilter = "";
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightFilter = "&rightSide=true";
}
// if it exists already, advance to the scan page to assist it
response.sendRedirect(
"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/workAppletScan.jsp?writeThis=true&number="
+ taskIdentifier
+ rightFilter);
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
}
}
if (!locked && successfulStore) {
try {
ThreadPoolExecutor es = SharkGridThreadExecutorService.getExecutorService();
es.execute(
new TuningTaskCreationThread(taskIdentifier, writeThis, maxNumWorkItems, context));
} catch (Exception e) {
System.out.println("I failed while constructing the workItems for a new scanTask.");
e.printStackTrace();
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
}
if (!locked) {
System.out.println("Trying to commit the add of the scanWorkItems");
// myShepherd.commitDBTransaction();
// myShepherd.closeDBTransaction();
System.out.println("I committed the workItems!");
String rightFilter = "L";
String rightURL = "";
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightFilter = "R";
rightURL = "&rightSide=true";
}
// confirm success
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success:</strong> Your scan was successfully added to the sharkGrid!");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp"
+ "\">Return to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure:</strong> The scan could not be created or was not fully created!");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println("<strong>Failure:</strong> I have NOT added this scanTask to the queue.");
if (currentNumScanTasks < taskLimit) {
out.println(
"The unfinished task limit of "
+ taskLimit
+ " has been filled. Please try adding the task to the queue again after existing tasks have finished.");
}
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else if (action.equals("addFalseMatchTask")) {
boolean locked = false;
boolean successfulStore = false;
int maxNumWorkItems = 99999999;
if ((request.getParameter("maxNumWorkItems") != null)
&& (!request.getParameter("maxNumWorkItems").equals(""))) {
maxNumWorkItems = Integer.parseInt(request.getParameter("maxNumWorkItems"));
}
// set up our properties
java.util.Properties props2 = new java.util.Properties();
String secondRun = "true";
String rightScan = "false";
boolean isRightScan = false;
boolean writeThis = true;
if (request.getParameter("writeThis") == null) {
writeThis = false;
}
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightScan = "true";
isRightScan = true;
}
props2.setProperty("epsilon", "0.01");
props2.setProperty("R", "8");
props2.setProperty("Sizelim", "0.85");
props2.setProperty("maxTriangleRotation", "10");
props2.setProperty("C", "0.99");
props2.setProperty("secondRun", secondRun);
props2.setProperty("rightScan", rightScan);
// let's check if a scanTask for this exists
System.out.println(
"scanTaskHandler: Checking whether this is a new False Match scanTask...");
myShepherd.beginDBTransaction();
String sideIdentifier = "L";
if (rightScan.equals("true")) {
sideIdentifier = "R";
}
String taskIdentifier = "FalseMatchTask";
ScanTask st = new ScanTask();
// let's do a check to see if too many scanTasks are in the queue
int taskLimit = gm.getScanTaskLimit();
int currentNumScanTasks = myShepherd.getNumUnfinishedScanTasks();
myShepherd.getPM().getFetchPlan().setGroup(FetchPlan.DEFAULT);
System.out.println("currentNumScanTasks is: " + currentNumScanTasks);
// int currentNumScanTasks=0;
if (currentNumScanTasks < taskLimit) {
// Vector leftSharks=myShepherd.getPossibleTrainingSharks();
// Vector rightSharks=myShepherd.getRightPossibleTrainingSharks();
int numComparisons = maxNumWorkItems * 2;
System.out.println(
"scanTaskHandler: Under the limit, so proceeding to check for condiions for creating a new scanTask...");
if ((!myShepherd.isScanTask(taskIdentifier))) {
// System.out.println("scanTaskHandler: This scanTask does not exist, so go create
// it...");
st = new ScanTask(myShepherd, taskIdentifier, props2, "FalseMatchTask", writeThis);
st.setNumComparisons(numComparisons);
if (request.getRemoteUser() != null) {
st.setSubmitter(request.getRemoteUser());
}
System.out.println("scanTaskHandler: About to create a TuningTask...");
successfulStore = myShepherd.storeNewTask(st);
if (!successfulStore) {
System.out.println("scanTaskHandler: Unsuccessful FalseMatchTask store...");
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
} else {
System.out.println("scanTaskHandler: Successful FalseMatchTask store...");
myShepherd.commitDBTransaction();
myShepherd.closeDBTransaction();
myShepherd = new Shepherd(context);
}
} else if (myShepherd.isScanTask(taskIdentifier)) {
System.out.println("scanTaskHandler: This is an existing scanTask...");
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
String rightFilter = "";
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightFilter = "&rightSide=true";
}
// if it exists already, advance to the scan page to assist it
response.sendRedirect(
"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/workAppletScan.jsp?writeThis=true&number="
+ taskIdentifier
+ rightFilter);
} else {
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
}
}
if (!locked && successfulStore) {
try {
ThreadPoolExecutor es = SharkGridThreadExecutorService.getExecutorService();
es.execute(new FalseMatchCreationThread(maxNumWorkItems, taskIdentifier, context));
} catch (Exception e) {
System.out.println("I failed while constructing the workItems for a new scanTask.");
e.printStackTrace();
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
locked = true;
}
if (!locked) {
System.out.println("Trying to commit the add of the scanWorkItems");
// myShepherd.commitDBTransaction();
// myShepherd.closeDBTransaction();
System.out.println("I committed the workItems!");
String rightFilter = "L";
String rightURL = "";
if ((request.getParameter("rightSide") != null)
&& (request.getParameter("rightSide").equals("true"))) {
rightFilter = "R";
rightURL = "&rightSide=true";
}
// confirm success
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success:</strong> Your scan was successfully added to the sharkGrid!");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp"
+ "\">Return to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure:</strong> The scan could not be created or was not fully created!");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println("<strong>Failure:</strong> I have NOT added this scanTask to the queue.");
if (currentNumScanTasks < taskLimit) {
out.println(
"The unfinished task limit of "
+ taskLimit
+ " has been filled. Please try adding the task to the queue again after existing tasks have finished.");
}
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
}
// delete all scan-related items
else if (action.equals("removeAllWorkItems")) {
try {
GridCleanupThread swiThread = new GridCleanupThread(context);
gm.removeAllWorkItems();
// confirm success
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success:</strong> I removed all outstanding scanWorkItems from the database.<br>/<strong>Warning!</strong> <em>This may cause any outstanding scanTasks to fail!</em>");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
} catch (Exception e) {
e.printStackTrace();
myShepherd.rollbackDBTransaction();
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure:</strong> I failed to remove all outstanding scanWorkItems from the database. Check the log for more information.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<p>I did not receive enough data to process your command, or you do not have the necessary permissions to perform this operation.</p>");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/appadmin/scanTaskAdmin.jsp\">Go to sharkGrid administration.</a></p>\n");
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<p>I did not receive enough data to process your command, or you do not have the necessary permissions to perform this operation. </p>");
out.println("<p>Please try again or <a href=\"welcome.jsp\">login here</a>.");
out.println(ServletUtilities.getFooter(context));
}
myShepherd.closeDBTransaction();
myShepherd = null;
out.flush();
out.close();
}
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
String context = "context0";
context = ServletUtilities.getContext(request);
Shepherd myShepherd = new Shepherd(context);
// set up for response
response.setContentType("text/html");
PrintWriter out = response.getWriter();
boolean locked = false;
boolean isOwner = true;
if ((request.getParameter("number") != null) && (request.getParameter("state") != null)) {
myShepherd.beginDBTransaction();
Encounter changeMe = myShepherd.getEncounter(request.getParameter("number"));
setDateLastModified(changeMe);
String state = request.getParameter("state");
String oldScar = "None";
try {
if (changeMe.getState() != null) {
oldScar = changeMe.getState();
}
changeMe.setState(state);
changeMe.addComments(
"<p><em>"
+ request.getRemoteUser()
+ " on "
+ (new java.util.Date()).toString()
+ "</em><br>Changed state from "
+ oldScar
+ " to "
+ state
+ ".</p>");
} catch (Exception le) {
locked = true;
le.printStackTrace();
myShepherd.rollbackDBTransaction();
}
if (!locked) {
myShepherd.commitDBTransaction();
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Success:</strong> Encounter state has been updated from "
+ oldScar
+ " to "
+ state
+ ".");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ request.getParameter("number")
+ "\">Return to encounter #"
+ request.getParameter("number")
+ "</a></p>\n");
List<String> allStates =
CommonConfiguration.getIndexedPropertyValues("encounterState", context);
int allStatesSize = allStates.size();
if (allStatesSize > 0) {
for (int i = 0; i < allStatesSize; i++) {
String stateName = allStates.get(i);
out.println(
"<p><a href=\"encounters/searchResults.jsp?state="
+ stateName
+ "\">View all "
+ stateName
+ " encounters</a></font></p>");
}
}
out.println(
"<p><a href=\"individualSearchResults.jsp\">View all individuals</a></font></p>");
out.println(ServletUtilities.getFooter(context));
String message =
"Encounter "
+ request.getParameter("number")
+ " state has been updated from "
+ oldScar
+ " to "
+ state
+ ".";
ServletUtilities.informInterestedParties(
request, request.getParameter("number"), message, context);
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Failure:</strong> Encounter state was NOT updated because another user is currently modifying this reconrd. Please try to reset the scarring again in a few seconds.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ request.getParameter("number")
+ "\">Return to encounter #"
+ request.getParameter("number")
+ "</a></p>\n");
List<String> allStates =
CommonConfiguration.getIndexedPropertyValues("encounterState", context);
int allStatesSize = allStates.size();
if (allStatesSize > 0) {
for (int i = 0; i < allStatesSize; i++) {
String stateName = allStates.get(i);
out.println(
"<p><a href=\"encounters/searchResults.jsp?state="
+ stateName
+ "\">View all "
+ stateName
+ " encounters</a></font></p>");
}
}
out.println(
"<p><a href=\"individualSearchResults.jsp\">View all individuals</a></font></p>");
out.println(ServletUtilities.getFooter(context));
}
} else {
out.println(ServletUtilities.getHeader(request));
out.println(
"<strong>Error:</strong> I don't have enough information to complete your request.");
out.println(
"<p><a href=\"http://"
+ CommonConfiguration.getURLLocation(request)
+ "/encounters/encounter.jsp?number="
+ request.getParameter("number")
+ "\">Return to encounter #"
+ request.getParameter("number")
+ "</a></p>\n");
List<String> allStates =
CommonConfiguration.getIndexedPropertyValues("encounterState", context);
int allStatesSize = allStates.size();
if (allStatesSize > 0) {
for (int i = 0; i < allStatesSize; i++) {
String stateName = allStates.get(i);
out.println(
"<p><a href=\"encounters/searchResults.jsp?state="
+ stateName
+ "\">View all "
+ stateName
+ " encounters</a></font></p>");
}
}
out.println("<p><a href=\"individualSearchResults.jsp\">View all individuals</a></font></p>");
out.println(ServletUtilities.getFooter(context));
}
out.close();
myShepherd.closeDBTransaction();
}