Merge branch 'DAO'

Conflicts:
	server/compbio/controllers/JobController.java

diff --combined datadb/compbio/cassandra/CassandraNativeConnector.java
index 909e041,bb807c1..f02000c
--- 1/datadb/compbio/cassandra/CassandraNativeConnector.java
--- 2/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@@ -88,11 -88,8 +88,11 @@@ public class CassandraNativeConnector 
                session.execute("CREATE TABLE IF NOT EXISTS JobDateInfo "
                                + "(jobday bigint, Total bigint,  TotalOK bigint, TotalStopped bigint, TotalError bigint, TotalTimeOut bigint, Program varchar, Version varchar, PRIMARY KEY(jobday));");
  
 -              String com = "CREATE TABLE IF NOT EXISTS Users "
 -                              + "(name varchar, id bigint, email varchar, password varchar, organisation varchar, position varchar, signedtolist boolean, registrationdate bigint, PRIMARY KEY(id));";
 +              session.execute("CREATE TABLE IF NOT EXISTS Programs "
 +                              + "(Program varchar, Version varchar, Description varchar, weblink varchar, PRIMARY KEY(Program,Version));");
 +
 +              session.execute("CREATE TABLE IF NOT EXISTS Users "
 +                              + "(name varchar, id bigint, email varchar, password varchar, organisation varchar, position varchar, signedtolist boolean, registrationdate bigint, PRIMARY KEY(id));");
  
                // session.execute("ALTER TABLE ProteinLog ADD ProgramName ascii;");
                // session.execute("ALTER TABLE ProteinLog ADD ProgramVersion ascii;");
@@@ -118,7 -115,6 +118,6 @@@
         */
        public static long getEarliestDateInDB() {
                String com = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
-               System.out.println("Command: " + com);
                ResultSet results = session.execute(com);
  
                if (!results.isExhausted()) {

diff --combined server/compbio/controllers/JobController.java
index 8033620,ff834bd..0dd39f8
--- 1/server/compbio/controllers/JobController.java
--- 2/server/compbio/controllers/JobController.java
+++ b/server/compbio/controllers/JobController.java
@@@ -3,7 -3,11 +3,9 @@@ package compbio.controllers
  import java.io.IOException;
  import java.net.HttpURLConnection;
  import java.net.URL;
+ import java.text.ParseException;
 -import java.text.SimpleDateFormat;
  import java.util.Calendar;
+ import java.util.Date;
 -import java.util.List;
  import java.util.Map;
  
  import org.apache.log4j.Logger;
@@@ -13,22 -17,25 +15,24 @@@ import org.springframework.web.bind.ann
  import org.springframework.web.bind.annotation.RequestParam;
  
  import compbio.statistic.CassandraRequester;
+ import compbio.beans.DateBean;
  import compbio.beans.ExecutionTimeBean;
 -import compbio.beans.Total;
  import compbio.beans.TotalExecutionTime;
 -import compbio.beans.TotalJobsStatisticBean;
 -import compbio.cassandra.DataBase;
  import compbio.cassandra.DateFormatter;
  import compbio.cassandra.readers.CassandraReader;
 -import compbio.cassandra.readers.DailyStatisticsReader;
  import compbio.cassandra.readers.ExecutionTimeReader;
  import compbio.cassandra.readers.JobReader;
+ import compbio.engine.ExecutionInterval;
  import compbio.engine.archive.ArchivedJob;
  
  /**
 + * Spring controller for supporting job queries. This version works in the
 + * servlet style.
 + * 
   * @author Alexander Sherstnev
   * @author Natasha Sherstneva
 - * @version 1.0 Dec 2013
 + * @version 1.0
 + * @since Dec 2013
   */
  @Controller
  public class JobController extends BasicController {
@@@ -77,28 -84,22 +81,28 @@@
        /**
         * form a report page for a job execution time statistics.
         * 
 +       * @param date1
 +       *            initial date for requested statistics
 +       * @param date2
 +       *            final date for requested statistics
 +       * @param alldates
 +       *            All available jobs are analyzed if alldates="AllDates,off"
         * @param model
         *            MVC model
         * @return link to the JSP query page
         */
        @RequestMapping(value = "/stat/exectime/results", method = RequestMethod.GET)
        public String findExecTimeData(@RequestParam("date1") String date1, @RequestParam("date2") String date2,
 -                      @RequestParam(value = "option", required = false) String option, Map<String, Object> model) {
 +                      @RequestParam(value = "option", required = false) String alldates, Map<String, Object> model) {
                model.put("username", getPrincipalName());
                final long startTime = System.currentTimeMillis();
                Calendar loccal = Calendar.getInstance();
                ExecutionTimeReader reader = new ExecutionTimeReader();
 -              if (option.equals("AllDates,off")) {
 +              if (alldates.equals("AllDates,off")) {
                        date1 = theEaerlistDate;
                        date2 = theCurrentDate;
                }
 -              
 +
                // dates in string format
                String trimmeddate1 = date1.replaceAll("\\s", "");
                String trimmeddate2 = date2.replaceAll("\\s", "");
@@@ -112,7 -113,7 +116,7 @@@
                        model.put("date2", date2);
                        return "query/JobTimeExecution";
                }
 -              
 +
                if (longDate1 < CassandraReader.earliestDate())
                        longDate1 = CassandraReader.earliestDate();
                if (longDate2 > loccal.getTimeInMillis())
@@@ -122,35 -123,80 +126,82 @@@
                date2 = DateFormatter.DateLongToString(longDate2, formaterYYMMDD);
                model.put("date1", date1);
                model.put("date2", date2);
 -              model.put("option", option);
 -              ExecutionTimeBean res = reader.query(longDate1, longDate2);;
 +              model.put("option", alldates);
 +              ExecutionTimeBean res = reader.query(longDate1, longDate2);
 +              ;
                model.put("result", res);
                Map<String, TotalExecutionTime> results = res.getDateTotal();
 -              String csvline = "";
 +              StringBuilder csvline = new StringBuilder("");
                if (0 < res.getDateTotal().size()) {
 -                      csvline = "\'Date\',\'Total\',\'0-30 sec\',\'30-60 sec\',\'1-2 min\',\'2-10 min\',\'more 10 min\'%0A";
 +                      csvline.append("\'Date\',\'Total\',\'0-30 sec\',\'30-60 sec\',\'1-2 min\',\'2-10 min\',\'more 10 min\'%0A");
                        for (Map.Entry<String, TotalExecutionTime> entry : results.entrySet()) {
 -                              csvline += "\'" + entry.getKey() + "\',\'" + entry.getValue().getTotal() + "\',\'" + entry.getValue().getTotal0_30s() + "\',\'"
 -                                              + entry.getValue().getTotal30_60s() + "\',\'" + entry.getValue().getTotal1_2m() + "\',\'"
 -                                              + entry.getValue().getTotal2_10m() + "\',\'" + entry.getValue().getTotal10m() + "\'%0A";
 +                              csvline.append("\'" + entry.getKey() + "\',\'" + entry.getValue().getTotal() + "\',\'" + entry.getValue().getTotal0_30s()
 +                                              + "\',\'" + entry.getValue().getTotal30_60s() + "\',\'" + entry.getValue().getTotal1_2m() + "\',\'"
 +                                              + entry.getValue().getTotal2_10m() + "\',\'" + entry.getValue().getTotal10m() + "\'%0A");
                        }
                }
 -              model.put("csvfile", csvline);
 +              model.put("csvfile", csvline.toString());
                model.put("ndays", res.getDateTotal().size() - 1);
                final long endTime = System.currentTimeMillis();
                model.put("timeExecution", (endTime - startTime));
                return "/reports/TimeExecution";
        }
+       
+       /**
+        * form a report page for job statistics for one day only.
+        * 
+        * @param model
+        *            MVC model object
+        * @param date
+        *            date for the report
+        * @param status
+        * 
+        * @return link to the report JSP page
+        */
+       @RequestMapping(value = "/stat/jobsoneday/executionTime", method = RequestMethod.GET)
+       public String findJobsInOneDay(@RequestParam("date") String date, @RequestParam("interval") String interval, Map<String, Object> model)
+                       throws ParseException {
+               model.put("username", getPrincipalName());
+               final long startTime = System.currentTimeMillis();
+ 
+               String realdate;
+               long thetime = 0;
+               try {
+                       thetime = formaterYYMMDD.parse(date).getTime();
+                       if (thetime < 0) {
+                               realdate = date;
+                       } else {
+                               realdate = formaterDDMMYY.format(new Date(thetime));
+                       }
+               } catch (ParseException e) {
+                       realdate = date;
+                       thetime = formaterDDMMYY.parse(realdate).getTime();
+               }
+ 
+               if (null == ExecutionInterval.getExecutionInterval(interval)) 
+                       return "support/Notimplemented";
+ 
 -
+               ExecutionTimeReader reader = new ExecutionTimeReader();
+               // IMPORTANT: input should be suppied in the format: DD/MM/YYYY
+               DateBean r = reader.readJobByDay(thetime, realdate, ExecutionInterval.getBoundsInterval(interval));
+               model.put("results", r);
+               if (r != null)
+                       model.put("njobs", r.getJobidAndSeq().size());
+               model.put("date", realdate);
+               model.put("status", interval);
+               final long endTime = System.currentTimeMillis();
+               model.put("timeExecution", (endTime - startTime));
+               return "reports/JobStatisticsOneDay";
+       }
  
        /**
 -       * form a query page for a job. The servlet should no be visible to users at
 -       * all.
 +       * form result page for one job with a given job ID.
         * 
 +       * @param jobid
 +       *            job ID
         * @param model
         *            MVC model
 +       * 
         * @return link to the JSP query page
         * @throws IOException
         */
@@@ -164,7 -210,6 +215,7 @@@
                model.put("timeExecution", (endTime - startTime));
                model.put("IdJob", jobid);
  
 +              // prepare archive file for the job for downloading
                ArchivedJob aj = new ArchivedJob(jobid);
                try {
                        model.put("jobarchive", aj.prepareJobArchiveToWeb());
@@@ -182,4 -227,18 +233,4 @@@
                return "reports/Job";
        }
  
 -      /**
 -       * convert date from the standard long representation (milliseconds from 1
 -       * Jan 1970) to yyyy/mm/dd
 -       * 
 -       * @param indate
 -       *            date in milliseconds from 1 Jan 1970
 -       * @return date in the form of yyyy/mm/dd
 -       */
 -      private String DateFormatYYMMDD(long indate) {
 -              SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
 -              String dateString = datformat.format(new Date(indate));
 -              return dateString;
 -      }
 -
  }