Merge branch 'master' into servlets

Conflicts:
	server/compbio/controllers/DailyStatisticsController.java
	server/compbio/controllers/JobExecutionTimeController.java
	server/compbio/controllers/SequenceController.java
	server/compbio/listeners/ServletJobsByDate.java
	server/compbio/listeners/ServletTimeExecution.java
	server/compbio/statistic/CassandraRequester.java

diff --cc server/compbio/controllers/DailyStatisticsController.java
index b6d5bde,ef399f5..d6a0c1e
--- 1/server/compbio/controllers/DailyStatisticsController.java
--- 2/server/compbio/controllers/DailyStatisticsController.java
+++ b/server/compbio/controllers/DailyStatisticsController.java
@@@ -12,41 -11,69 +11,45 @@@ import org.springframework.web.bind.ann
  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);

diff --cc server/compbio/listeners/ServletJobsByDate.java
index 83b2e4d,fe24750..8ae389f
--- 1/server/compbio/listeners/ServletJobsByDate.java
--- 2/server/compbio/listeners/ServletJobsByDate.java
+++ b/server/compbio/listeners/ServletJobsByDate.java
@@@ -11,7 -13,8 +11,9 @@@ import javax.servlet.http.HttpServlet
  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 {
@@@ -28,7 -31,7 +30,7 @@@
                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);

diff --cc server/compbio/listeners/ServletTimeExecution.java
index 563cf42,93b3faf..c380604
--- 1/server/compbio/listeners/ServletTimeExecution.java
--- 2/server/compbio/listeners/ServletTimeExecution.java
+++ b/server/compbio/listeners/ServletTimeExecution.java
@@@ -10,6 -12,6 +10,7 @@@ import javax.servlet.http.HttpServlet
  import javax.servlet.http.HttpServletRequest;
  import javax.servlet.http.HttpServletResponse;
  
++import compbio.statistic.StatisticsProt;
  import compbio.statistic.CassandraRequester;
  
  /**
@@@ -30,7 -32,7 +31,7 @@@ public class ServletTimeExecution exten
                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);

diff --cc server/compbio/statistic/CassandraRequester.java
index 6a54800,3e5db8a..f2336e7
--- 1/server/compbio/statistic/CassandraRequester.java
--- 2/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@@ -12,16 -12,19 +12,19 @@@ 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");