server/compbio/statistic/CassandraRequester.java

   1 package compbio.statistic;
   2
   3 import java.text.ParseException;
   4 import java.text.SimpleDateFormat;
   5 import java.util.ArrayList;
   6 import java.util.Calendar;
   7 import java.util.Date;
   8 import java.util.Iterator;
   9 import java.util.List;
  10 import java.util.Map;
  11
  12 import compbio.cassandra.DateBean;
  13 import compbio.cassandra.ProteinBean;
  14 import compbio.cassandra.CassandraNativeConnector;
  15 import compbio.cassandra.CassandraReader;
  16 import compbio.cassandra.DataBase;
  17 import compbio.cassandra.Pair;
  18 import compbio.cassandra.JobBean;
  19 import compbio.cassandra.Total;
  20 import compbio.cassandra.TotalByCounterBean;
  21 import compbio.cassandra.TotalJobsStatisticBean;
  22 import compbio.cassandra.UserBean;
  23
  24 public class CassandraRequester {
  25         private CassandraReader db = new CassandraReader();
  26         private ArrayList<DataBase> query;
  27         private static long currentDate = 0;
  28         private static long earlestDate = 0;
  29         private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
  30         private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
  31
  32         /*
  33          * query: execution time for the period from date1 till date2
  34          */
  35         public List<DataBase> extractExecutionTime(String date1, String date2) {
  36                 if (null == date1) {
  37                         date1 = "1970/1/1";
  38                 }
  39                 if (null == date2) {
  40                         date1 = "2100/1/1";
  41                 }
  42                 if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
  43                         System.out.println("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2);
  44                         return null;
  45                 }
  46                 SetDateRange();
  47                 int nbins = 5;
  48                 long dateStart = DateParsing(date1, formatYYMMDD);
  49                 long dateEnd = DateParsing(date2, formatYYMMDD);
  50                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
  51                         return null;
  52                 if (dateStart < earlestDate)
  53                         dateStart = earlestDate;
  54                 if (dateEnd > currentDate)
  55                         dateStart = currentDate;
  56
  57                 Calendar start = Calendar.getInstance();
  58                 start.setTime(new Date(dateStart));
  59                 Calendar end = Calendar.getInstance();
  60                 end.setTime(new Date(dateEnd));
  61                 query = new ArrayList<DataBase>();
  62                 List<Integer> totalTime = new ArrayList<Integer>();
  63                 for (int i = 0; i < nbins; i++)
  64                         totalTime.add(i, 0);
  65                 List<Pair<String, String>> res = db.ReadProteinDataTable();
  66                 List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
  67
  68                 for (Pair<String, String> entry : res) {
  69                         SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
  70                         try {
  71                                 Date jobstartdate = dateformatter.parse(entry.getElement0());
  72                                 long date = jobstartdate.getTime();
  73                                 if (dateStart <= date && date <= dateEnd) {
  74                                         SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
  75                                         Date jobstarttime = datetimeformatter.parse(entry.getElement0());
  76                                         Date jobendtime = datetimeformatter.parse(entry.getElement1());
  77                                         long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
  78                                         Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
  79                                         numres.add(pair);
  80                                 }
  81                         } catch (ParseException e) {
  82                                 e.printStackTrace();
  83                         }
  84                 }
  85
  86                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
  87                         List<Integer> timeResult = new ArrayList<Integer>();
  88                         for (int i = 0; i < nbins; i++)
  89                                 timeResult.add(i, 0);
  90                         for (Pair<Date, Long> p : numres) {
  91                                 if (date.equals(p.getElement0())) {
  92                                         long lenResult = p.getElement1().longValue();
  93                                         if (lenResult <= 30)
  94                                                 timeResult.set(0, timeResult.get(0) + 1);
  95                                         else if (lenResult > 30 && lenResult <= 60)
  96                                                 timeResult.set(1, timeResult.get(1) + 1);
  97                                         else if (lenResult > 60 && lenResult <= 120)
  98                                                 timeResult.set(2, timeResult.get(2) + 1);
  99                                         else if (lenResult > 120 && lenResult <= 600)
 100                                                 timeResult.set(3, timeResult.get(3) + 1);
 101                                         else {
 102                                                 timeResult.set(4, timeResult.get(4) + 1);
 103                                         }
 104                                 }
 105                         }
 106                         for (int i = 0; i < nbins; i++)
 107                                 totalTime.set(i, totalTime.get(i) + timeResult.get(i));
 108                         DataBase db = new DataBase();
 109                         db.setTimeRez(timeResult);
 110                         db.setDate(DateFormat(date.getTime()));
 111                         query.add(db);
 112                 }
 113
 114                 DataBase db = new DataBase();
 115                 db.setTimeTotalExec(totalTime);
 116                 query.add(db);
 117                 return query;
 118         }
 119
 120         /*
 121          * query: total number of jobs  for the period from date1 till date2
 122          */
 123         public TotalJobsStatisticBean countJobs(String date1, String date2) {
 124                 if (null == date1) {
 125                         date1 = "1970/1/1";
 126                 }
 127                 if (null == date2) {
 128                         date1 = "2100/1/1";
 129                 }
 130                 if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
 131                         System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
 132                         return null;
 133                 }
 134                 SetDateRange();
 135                 long dateStart = DateParsing(date1, formatYYMMDD);
 136                 long dateEnd = DateParsing(date2, formatYYMMDD);
 137                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 138                         return null;
 139                 if (dateStart < earlestDate)
 140                         dateStart = earlestDate;
 141                 if (dateEnd > currentDate)
 142                         dateStart = currentDate;
 143
 144                 Calendar start = Calendar.getInstance();
 145                 start.setTime(new Date(dateStart));
 146                 Calendar end = Calendar.getInstance();
 147                 end.setTime(new Date(dateEnd));
 148                 TotalJobsStatisticBean query = new TotalJobsStatisticBean();
 149                 Total wholeTotal = new Total(0,0,0,0,0);
 150                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
 151                         Total res = db.ReadDateTable(date.getTime());
 152                         if (res == null)
 153                                 continue;
 154                         query.setDateTotal(DateFormat(date.getTime()), res);
 155                         wholeTotal.setTotal(res.getTotal() + wholeTotal.getTotal());
 156                         wholeTotal.setTotalOK(res.getTotalOK() + wholeTotal.getTotalOK());
 157                         wholeTotal.setTotalStopped(res.getTotalStopped() + wholeTotal.getTotalStopped());
 158                         wholeTotal.setTotalError(res.getTotalError() + wholeTotal.getTotalError());
 159                         wholeTotal.setTotalTimeOut(res.getTotalTimeOut() + wholeTotal.getTotalTimeOut());
 160                 }
 161                 query.setWholeTotal(wholeTotal);
 162                 return query;
 163         }
 164
 165         /*
 166          * query: jobs and sequence at date
 167          */
 168         public DateBean readJobByDay (String date) {
 169                 if (!isThisDateValid(date, formatDDMMYY)) {
 170                         System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
 171                         return null;
 172                 }
 173                 SetDateRange();
 174                 long day = DateParsing(date, formatDDMMYY);
 175                 if (day < earlestDate || day > currentDate)
 176                         return null;
 177                 return db.ReadProteinData(day, date);
 178         }
 179
 180
 181         /*
 182          * query: protein sequence
 183          **/
 184         public List<ProteinBean> readProteins(String protIn, String flag) {
 185                 List<ProteinBean> result;
 186                 if (flag.equals("whole"))
 187                         result = db.ReadWholeSequence(protIn);
 188                  else
 189                          result = db.ReadPartOfSequence(protIn);
 190                 if (result == null)
 191                         return null;
 192
 193                 if (flag.equals("part")) {
 194                         for (ProteinBean entry : result) {
 195                                 entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
 196                         }
 197                 }
 198                 return result;
 199         }
 200
 201
 202         /*
 203          * query protein sequences with number of jobs
 204          */
 205         public List<TotalByCounterBean> readProteinByCounter(int minimalcounter) {
 206                 List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
 207                 Map<String, Integer> map = db.ReadProteinSequenceByCounter();
 208                 if (map == null)
 209                         return null;
 210                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 211                         if (entry.getValue() > minimalcounter) {
 212                                 TotalByCounterBean bean = new TotalByCounterBean();
 213                                 bean.setTotaljobs(entry.getValue());
 214                                 bean.setName(entry.getKey());
 215                                 query.add(bean);
 216                         }
 217                 }
 218                 return query;
 219         }
 220
 221         /*
 222          * query ip with number of jobs
 223          */
 224         public List<TotalByCounterBean> readIpByCounter(Integer minimalcounter) {
 225                 List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
 226                 Map<String, Integer> map = db.ReadIpByCounter();
 227                 if (minimalcounter == null)
 228                         minimalcounter = 0;
 229                 if (map == null)
 230                         return null;
 231                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 232                         if (entry.getValue() > minimalcounter) {
 233                                 TotalByCounterBean bean = new TotalByCounterBean();
 234                                 bean.setTotaljobs(entry.getValue());
 235                                 bean.setName(entry.getKey());
 236                                 query.add(bean);
 237                         }
 238                 }
 239                 return query;
 240         }
 241         /*
 242          * query jobs log info
 243          */
 244         public JobBean readJobLog(String jobid) {
 245                 if (jobid == null)
 246                         return null;
 247                 return db.ReadJobLog(jobid);
 248         }
 249
 250
 251         /*
 252          * query jobs by ipStructureJobLog
 253          */
 254         public UserBean readIp(String ip) {
 255                 if (ip == null)
 256                         return null;
 257                 Map<String, String[]> res = db.ReadIpWithJobs(ip);
 258                 if (res == null)
 259                         return null;
 260                 UserBean query = new UserBean(ip);
 261                 query.setMainInfo(res);
 262                 return query;
 263         }
 264
 265         /*
 266          * create list of parts of protein sequence;
 267          */
 268         private static List<String> CreateSubprot (String protein, String subprot) {
 269                 List<String> sub = new ArrayList<String>();
 270                 String subStr = protein;
 271                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 272                         String first = subStr.substring(0, subStr.indexOf(subprot));
 273                         if (first.length() > 0)
 274                                 sub.add(first);
 275                         sub.add(subprot);
 276                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 277                 }
 278                 if (subStr.length() > 0)
 279                         sub.add(subStr);
 280                 return sub;
 281         }
 282         /*
 283          * convert String date into long date (miliseconds since the epoch start)
 284          */
 285         private static long DateParsing(String datInput, SimpleDateFormat formatter) {
 286                 if (datInput == null) {
 287                         return 0;
 288                 }
 289                 long dateWorkSt = 0;
 290
 291                 try {
 292                         dateWorkSt = formatter.parse(datInput).getTime();
 293                 } catch (ParseException e) {
 294                         e.printStackTrace();
 295                 }
 296                 return dateWorkSt;
 297         }
 298
 299         // convert long to date in string format
 300         private static String DateFormat(long inDate) {
 301                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 302                 return datformat.format(new Date(inDate));
 303         }
 304
 305         /*
 306          * set earlest date and current dates. earlestDate is static and should be
 307          * set at the 1st call currentDate should be re-calculated every time
 308          */
 309         private static void SetDateRange() {
 310                 Calendar cal = Calendar.getInstance();
 311                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH), formatYYMMDD);
 312                 if (0 == earlestDate) {
 313                         CassandraRequester cr = new CassandraRequester();
 314                         earlestDate = cr.earliestDate();
 315                 }
 316         }
 317
 318         public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
 319                 if (dateToValidate == null || dateToValidate.equals("")) {
 320                         return false;
 321                 }
 322                 try {
 323                         // if not valid, this will throw ParseException
 324                         sdf.setLenient(false);
 325                         Date date = sdf.parse(dateToValidate);
 326                 } catch (ParseException e) {
 327                         e.printStackTrace();
 328                         return false;
 329                 }
 330                 return true;
 331         }
 332
 333         /*
 334          * find the earliest date in the database
 335          */
 336         public long earliestDate() {
 337                 earlestDate = CassandraNativeConnector.getEarliestDateInDB();
 338                 return earlestDate;
 339         }
 340
 341 }