import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.Date;
- import java.util.List;
import java.util.Map;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
+ import compbio.engine.JobStatus;
-import compbio.cassandra.CassandraReader;
import compbio.cassandra.DateBean;
-import compbio.cassandra.DateFormatter;
import compbio.cassandra.TotalJobsStatisticBean;
import compbio.statistic.CassandraRequester;
-
++import compbio.statistic.StatisticsProt;
/**
* @author Alexander Sherstnev
* @author Natasha Sherstneva
*/
@Controller
- public class DailyStatisticsController {
+ public class DailyStatisticsController extends BasicController {
- Calendar cal = Calendar.getInstance();
- final SimpleDateFormat formaterDDMMYY = DateFormatter.getFormatDDMMYY();
- final SimpleDateFormat formaterYYMMDD = DateFormatter.getFormatYYMMDD();
- String theEaerlistDate = DateFormatter.DateLongToString(CassandraReader.earliestDate(), formaterYYMMDD);
- String theCurrentDate = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
-
+
- @RequestMapping(value = "/stat", method = RequestMethod.GET)
+ @RequestMapping(value = "/stat/jobs/query", method = RequestMethod.GET)
public String initFindForm(Map<String, Object> model) {
+ model.put("username", getPrincipalName());
+ Calendar cal = Calendar.getInstance();
String date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
cal.add(Calendar.DATE, -3);
String date1 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DATE);
+
model.put("date1", date1);
model.put("date2", date2);
+
- return "queryJobStatistics";
+ return "query/JobStatistics";
}
- @RequestMapping(value = "/stat/query", method = RequestMethod.GET)
+ @RequestMapping(value = "/stat/jobsdaily/results", method = RequestMethod.GET)
public String findJobsInPeriod(@RequestParam("date1") String date1, @RequestParam("date2") String date2,
@RequestParam("option") String option, Map<String, Object> model) {
+ model.put("username", getPrincipalName());
- final long startTime = System.currentTimeMillis();
+ final long startTime = System.currentTimeMillis();
+
CassandraRequester cr = new CassandraRequester();
if (option.equals("AllDates,off")) {
- date1 = theEaerlistDate;
- date2 = theCurrentDate;
- }
-
- // dates in string format
- String trimmeddate1 = date1.replaceAll("\\s", "");
- String trimmeddate2 = date2.replaceAll("\\s", "");
- // dates in long format
- long longDate1 = DateFormatter.DateParsing(date1,formaterYYMMDD);
- long longDate2 = DateFormatter.DateParsing(date2, formaterYYMMDD);
- String error = DateChecking(trimmeddate1, trimmeddate2, longDate1, longDate2);
- if (error != null) {
- model.put("error", error);
- model.put("date1", date1);
- model.put("date2", date2);
- return "query/JobStatistics";
+ Calendar cal = Calendar.getInstance();
- date1 = cr.earliestDateString();
++ date1 = StatisticsProt.DateFormatYYMMDD(cr.earliestDate());
+ date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
}
-
- if (longDate1 < CassandraReader.earliestDate())
- longDate1 = CassandraReader.earliestDate();
- if (longDate2 > cal.getTimeInMillis())
- longDate2 = cal.getTimeInMillis();
-
- date1 = DateFormatter.DateLongToString(longDate1, formaterYYMMDD);
- date2 = DateFormatter.DateLongToString(longDate2, formaterYYMMDD);
model.put("date1", date1);
model.put("date2", date2);
TotalJobsStatisticBean res = cr.countJobs(date1, date2);
return "/reportJobStatistics";
}
- @RequestMapping(value = "/stat/oneday", method = RequestMethod.GET)
- public String findJobsInOneDay(@RequestParam("date") String date, Map<String, Object> model) throws ParseException {
+ @RequestMapping(value = "/stat/jobsoneday/results", method = RequestMethod.GET)
+ public String findJobsInOneDay(@RequestParam("date") String date, @RequestParam("status") String status, Map<String, Object> model)
+ throws ParseException {
+ model.put("username", getPrincipalName());
final long startTime = System.currentTimeMillis();
String realdate;
+ final SimpleDateFormat formaterDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
+ final SimpleDateFormat formaterYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
try {
long thetime = formaterYYMMDD.parse(date).getTime();
if (thetime < 0) {
realdate = date;
}
+ if (null == JobStatus.getJobStatus(status)) {
+ return "support/Notimplemented";
+ }
+
CassandraRequester cr = new CassandraRequester();
// IMPORTANT: input should be suppied in the format: DD/MM/YYYY
- DateBean r = cr.readJobByDay(realdate);
+ DateBean r = cr.readJobByDay(realdate, JobStatus.getJobStatus(status));
model.put("results", r);
if (r != null)
model.put("njobs", r.getJobidAndSeq().size());
model.put("date", realdate);
+ model.put("status", status);
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
return "/reportJobStatisticsOneDay";
}
-
- private String DateChecking(String trimmeddate1, String trimmeddate2, long longDate1, long longDate2) {
-
- if (trimmeddate1.equalsIgnoreCase("") || trimmeddate2.equalsIgnoreCase(""))
- return "The date cann't be empty";
- else if (!DateFormatter.isThisDateValid(trimmeddate1, formaterYYMMDD) || !DateFormatter.isThisDateValid(trimmeddate2, formaterYYMMDD))
- return "The date format in invalid. Try format yyyy/mm/dd";
- else if (longDate2 < CassandraReader.earliestDate())
- return "The date2 is after the earlestDate " + theEaerlistDate;
- else if (longDate1 > cal.getTimeInMillis())
- return "The date1 is before the current date " + theCurrentDate;
- else if (longDate1 > longDate2)
- return "Wrong date's diaposon. The date1 is more than date2.";
- else
- return null;
- }
}
package compbio.listeners;
import java.io.IOException;
-import java.text.SimpleDateFormat;
import java.util.Calendar;
-import java.util.Date;
import java.util.List;
import javax.servlet.RequestDispatcher;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
+ import compbio.cassandra.DataBase;
import compbio.statistic.CassandraRequester;
++import compbio.statistic.StatisticsProt;
@WebServlet("/ServletJobsByDate")
public class ServletJobsByDate extends HttpServlet {
CassandraRequester cr = new CassandraRequester();
if (null != request.getParameter("option")) {
Calendar cal = Calendar.getInstance();
- // date1 = StatisticsProt.DateFormatYYMMDD(cr.earliestDate());
- date1 = DateFormatYYMMDD(cr.earliestDate());
++ date1 = StatisticsProt.DateFormatYYMMDD(cr.earliestDate());
date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
}
request.setAttribute("data1", date1);
doGet(request, response);
}
- private String DateFormatYYMMDD(long indate) {
- SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
- String dateString = datformat.format(new Date(indate));
- return dateString;
- }
-
}
package compbio.listeners;
import java.io.IOException;
-import java.text.SimpleDateFormat;
import java.util.Calendar;
-import java.util.Date;
import javax.servlet.RequestDispatcher;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
++import compbio.statistic.StatisticsProt;
import compbio.statistic.CassandraRequester;
/**
CassandraRequester sp = new CassandraRequester();
if (null != request.getParameter("option")) {
Calendar cal = Calendar.getInstance();
- // date1 = CassandraRequester.DateFormatYYMMDD(sp.earliestDate());
- date1 = DateFormatYYMMDD(sp.earliestDate());
++ date1 = StatisticsProt.DateFormatYYMMDD(sp.earliestDate());
date2 = cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH);
}
request.setAttribute("data1", date1);
request.setAttribute("data2", date2);
- // request.setAttribute("result", sp.extractExecutionTime(date1, date2));
+ request.setAttribute("result", sp.extractExecutionTime(date1, date2));
request.setAttribute("flag", request.getParameter("option"));
final long endTime = System.currentTimeMillis();
request.setAttribute("timeExecution", (endTime - startTime));
protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
doGet(request, response);
}
-
- private String DateFormatYYMMDD(long indate) {
- SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
- String dateString = datformat.format(new Date(indate));
- return dateString;
- }
}
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
- import java.util.Iterator;
+ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import compbio.cassandra.DateBean;
import compbio.cassandra.ProteinBean;
import compbio.cassandra.CassandraNativeConnector;
-import compbio.cassandra.CassandraReaderOld;
+import compbio.cassandra.CassandraReader;
+ import compbio.cassandra.DataBase;
import compbio.cassandra.Pair;
import compbio.cassandra.JobBean;
import compbio.cassandra.Total;
import compbio.cassandra.TotalByCounterBean;
import compbio.cassandra.TotalJobsStatisticBean;
import compbio.cassandra.UserBean;
+ import compbio.engine.JobStatus;
public class CassandraRequester {
- private CassandraReaderOld db = new CassandraReaderOld();
+ private CassandraReader db = new CassandraReader();
+ private ArrayList<DataBase> query;
private static long currentDate = 0;
private static long earlestDate = 0;
private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
/*
* query: execution time for the period from date1 till date2
-
+ */
public List<DataBase> extractExecutionTime(String date1, String date2) {
if (null == date1) {
date1 = "1970/1/1";
db.setTimeTotalExec(totalTime);
query.add(db);
return query;
- <<<<<<< HEAD
- }*/
-
+ }
+
/*
* query: total number of jobs for the period from date1 till date2
*/
public TotalJobsStatisticBean countJobs(String date1, String date2) {
- /* if (null == date1) {
+ if (null == date1) {
date1 = "1970/1/1";
}
if (null == date2) {
if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
return null;
- }*/
+ }
SetDateRange();
long dateStart = DateParsing(date1, formatYYMMDD);
long dateEnd = DateParsing(date2, formatYYMMDD);
-/* if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
+ if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
return null;
if (dateStart < earlestDate)
dateStart = earlestDate;
if (dateEnd > currentDate)
- dateStart = currentDate;*/
+ dateStart = currentDate;
+
Calendar start = Calendar.getInstance();
start.setTime(new Date(dateStart));
Calendar end = Calendar.getInstance();
/*
* query: jobs and sequence at date
*/
- public DateBean readJobByDay(String date) {
+ public DateBean readJobByDay(String date, JobStatus status) {
if (!isThisDateValid(date, formatDDMMYY)) {
System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
return null;
long day = DateParsing(date, formatDDMMYY);
if (day < earlestDate || day > currentDate)
return null;
- return db.ReadProteinData(day, date);
+
+ if (status == JobStatus.OK) {
+ return db.ReadProteinData(day, date);
+ }
+ return db.ReadFailedJobs(day, date, status);
}
/*
* query: protein sequence
*/
- public List<ProteinBean> readProteins(String protIn, String flag) {
+ public List<ProteinBean> readProteins(String protIn, String searchtype) {
List<ProteinBean> result;
- if (flag.equals("whole"))
+ if (searchtype.equals("whole"))
result = db.ReadWholeSequence(protIn);
else
result = db.ReadPartOfSequence(protIn);
if (result == null)
return null;
- if (flag.equals("part")) {
+ if (searchtype.equals("partial")) {
for (ProteinBean entry : result) {
entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
}
}
return result;
}
+
+ /*
+ * query: protein feature
+ */
+ public Map<String, String> readProteinsPrediction(String feature, int percent) {
+ Map<String, String> result = db.ReadProtein();;
+ if (result == null)
+ return null;
+ Map<String, String> query = new HashMap<String, String>();
+ for (Map.Entry<String, String> entry : result.entrySet()) {
+ String pred = entry.getValue();
+ if (pred.replaceAll("[^"+feature+"]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
+ // if (!entry.getKey().equals(""))
+ query.put(entry.getKey(), pred);
+ }
+ }
+ return query;
+ }
/*
* query protein sequences with number of jobs
SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
return datformat.format(new Date(inDate));
}
-
- // convert long to date in string format
- private static String DateFormatYYMMDD(long inDate) {
- SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
- return datformat.format(new Date(inDate));
- }
/*
* set earlest date and current dates. earlestDate is static and should be
earlestDate = CassandraNativeConnector.getEarliestDateInDB();
return earlestDate;
}
-
- /*
- * find the earliest date in the database in String format
- */
- public String earliestDateString() {
- earlestDate = CassandraNativeConnector.getEarliestDateInDB();
- return DateFormatYYMMDD(earlestDate);
- }
-
+
}
git://source.jalview.org / proteocache.git / commitdiff