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.Pair;
  17 import compbio.cassandra.JobBean;
  18 import compbio.cassandra.Total;
  19 import compbio.cassandra.TotalByCounterBean;
  20 import compbio.cassandra.TotalJobsStatisticBean;
  21 import compbio.cassandra.UserBean;
  22
  23 public class CassandraRequester {
  24         private CassandraReader db = new CassandraReader();
  25         private static long currentDate = 0;
  26         private static long earlestDate = 0;
  27         private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
  28         private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
  29
  30         /*
  31          * query: execution time for the period from date1 till date2
  32
  33         public List<DataBase> extractExecutionTime(String date1, String date2) {
  34                 if (null == date1) {
  35                         date1 = "1970/1/1";
  36                 }
  37                 if (null == date2) {
  38                         date1 = "2100/1/1";
  39                 }
  40                 if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
  41                         System.out.println("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2);
  42                         return null;
  43                 }
  44                 SetDateRange();
  45                 int nbins = 5;
  46                 long dateStart = DateParsing(date1, formatYYMMDD);
  47                 long dateEnd = DateParsing(date2, formatYYMMDD);
  48                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
  49                         return null;
  50                 if (dateStart < earlestDate)
  51                         dateStart = earlestDate;
  52                 if (dateEnd > currentDate)
  53                         dateStart = currentDate;
  54
  55                 Calendar start = Calendar.getInstance();
  56                 start.setTime(new Date(dateStart));
  57                 Calendar end = Calendar.getInstance();
  58                 end.setTime(new Date(dateEnd));
  59                 query = new ArrayList<DataBase>();
  60                 List<Integer> totalTime = new ArrayList<Integer>();
  61                 for (int i = 0; i < nbins; i++)
  62                         totalTime.add(i, 0);
  63                 List<Pair<String, String>> res = db.ReadProteinDataTable();
  64                 List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
  65
  66                 for (Pair<String, String> entry : res) {
  67                         SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
  68                         try {
  69                                 Date jobstartdate = dateformatter.parse(entry.getElement0());
  70                                 long date = jobstartdate.getTime();
  71                                 if (dateStart <= date && date <= dateEnd) {
  72                                         SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
  73                                         Date jobstarttime = datetimeformatter.parse(entry.getElement0());
  74                                         Date jobendtime = datetimeformatter.parse(entry.getElement1());
  75                                         long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
  76                                         Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
  77                                         numres.add(pair);
  78                                 }
  79                         } catch (ParseException e) {
  80                                 e.printStackTrace();
  81                         }
  82                 }
  83
  84                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
  85                         List<Integer> timeResult = new ArrayList<Integer>();
  86                         for (int i = 0; i < nbins; i++)
  87                                 timeResult.add(i, 0);
  88                         for (Pair<Date, Long> p : numres) {
  89                                 if (date.equals(p.getElement0())) {
  90                                         long lenResult = p.getElement1().longValue();
  91                                         if (lenResult <= 30)
  92                                                 timeResult.set(0, timeResult.get(0) + 1);
  93                                         else if (lenResult > 30 && lenResult <= 60)
  94                                                 timeResult.set(1, timeResult.get(1) + 1);
  95                                         else if (lenResult > 60 && lenResult <= 120)
  96                                                 timeResult.set(2, timeResult.get(2) + 1);
  97                                         else if (lenResult > 120 && lenResult <= 600)
  98                                                 timeResult.set(3, timeResult.get(3) + 1);
  99                                         else {
 100                                                 timeResult.set(4, timeResult.get(4) + 1);
 101                                         }
 102                                 }
 103                         }
 104                         for (int i = 0; i < nbins; i++)
 105                                 totalTime.set(i, totalTime.get(i) + timeResult.get(i));
 106                         DataBase db = new DataBase();
 107                         db.setTimeRez(timeResult);
 108                         db.setDate(DateFormat(date.getTime()));
 109                         query.add(db);
 110                 }
 111
 112                 DataBase db = new DataBase();
 113                 db.setTimeTotalExec(totalTime);
 114                 query.add(db);
 115                 return query;
 116 <<<<<<< HEAD
 117         }*/
 118
 119         /*
 120          * query: total number of jobs for the period from date1 till date2
 121          */
 122         public TotalJobsStatisticBean countJobs(String date1, String date2) {
 123                 if (null == date1) {
 124                         date1 = "1970/1/1";
 125                 }
 126                 if (null == date2) {
 127                         date1 = "2100/1/1";
 128                 }
 129                 if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
 130                         System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
 131                         return null;
 132                 }
 133                 SetDateRange();
 134                 long dateStart = DateParsing(date1, formatYYMMDD);
 135                 long dateEnd = DateParsing(date2, formatYYMMDD);
 136                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 137                         return null;
 138                 if (dateStart < earlestDate)
 139                         dateStart = earlestDate;
 140                 if (dateEnd > currentDate)
 141                         dateStart = currentDate;
 142
 143                 Calendar start = Calendar.getInstance();
 144                 start.setTime(new Date(dateStart));
 145                 Calendar end = Calendar.getInstance();
 146                 end.setTime(new Date(dateEnd));
 147                 TotalJobsStatisticBean query = new TotalJobsStatisticBean();
 148                 Total wholeTotal = new Total(0, 0, 0, 0, 0);
 149                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
 150                         Total res = db.ReadDateTable(date.getTime());
 151                         if (res == null)
 152                                 continue;
 153                         query.setDateTotal(DateFormat(date.getTime()), res);
 154                         wholeTotal.setTotal(res.getTotal() + wholeTotal.getTotal());
 155                         wholeTotal.setTotalOK(res.getTotalOK() + wholeTotal.getTotalOK());
 156                         wholeTotal.setTotalStopped(res.getTotalStopped() + wholeTotal.getTotalStopped());
 157                         wholeTotal.setTotalError(res.getTotalError() + wholeTotal.getTotalError());
 158                         wholeTotal.setTotalTimeOut(res.getTotalTimeOut() + wholeTotal.getTotalTimeOut());
 159                 }
 160                 query.setWholeTotal(wholeTotal);
 161                 return query;
 162         }
 163
 164         /*
 165          * query: jobs and sequence at date
 166          */
 167         public DateBean readJobByDay(String date) {
 168                 if (!isThisDateValid(date, formatDDMMYY)) {
 169                         System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
 170                         return null;
 171                 }
 172                 SetDateRange();
 173                 long day = DateParsing(date, formatDDMMYY);
 174                 if (day < earlestDate || day > currentDate)
 175                         return null;
 176                 return db.ReadProteinData(day, date);
 177         }
 178
 179         /*
 180          * query: protein sequence
 181          */
 182         public List<ProteinBean> readProteins(String protIn, String flag) {
 183                 List<ProteinBean> result;
 184                 if (flag.equals("whole"))
 185                         result = db.ReadWholeSequence(protIn);
 186                 else
 187                         result = db.ReadPartOfSequence(protIn);
 188                 if (result == null)
 189                         return null;
 190
 191                 if (flag.equals("part")) {
 192                         for (ProteinBean entry : result) {
 193                                 entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
 194                         }
 195                 }
 196                 return result;
 197         }
 198
 199         /*
 200          * query protein sequences with number of jobs
 201          */
 202         public List<TotalByCounterBean> readProteinByCounter(int minimalcounter) {
 203                 List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
 204                 Map<String, Integer> map = db.ReadProteinSequenceByCounter();
 205                 if (map == null)
 206                         return null;
 207                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 208                         if (entry.getValue() > minimalcounter) {
 209                                 TotalByCounterBean bean = new TotalByCounterBean();
 210                                 bean.setTotaljobs(entry.getValue());
 211                                 bean.setName(entry.getKey());
 212                                 query.add(bean);
 213                         }
 214                 }
 215                 return query;
 216         }
 217
 218         /*
 219          * query ip with number of jobs
 220          */
 221         public List<TotalByCounterBean> readIpByCounter(Integer minimalcounter) {
 222                 List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
 223                 Map<String, Integer> map = db.ReadIpByCounter();
 224                 if (minimalcounter == null)
 225                         minimalcounter = 0;
 226                 if (map == null)
 227                         return null;
 228                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 229                         if (entry.getValue() > minimalcounter) {
 230                                 TotalByCounterBean bean = new TotalByCounterBean();
 231                                 bean.setTotaljobs(entry.getValue());
 232                                 bean.setName(entry.getKey());
 233                                 query.add(bean);
 234                         }
 235                 }
 236                 return query;
 237         }
 238
 239         /*
 240          * query jobs log info
 241          */
 242         public JobBean readJobLog(String jobid) {
 243                 if (jobid == null)
 244                         return null;
 245                 return db.ReadJobLog(jobid);
 246         }
 247
 248         /*
 249          * query jobs by ipStructureJobLog
 250          */
 251         public UserBean readIp(String ip) {
 252                 if (ip == null)
 253                         return null;
 254                 Map<String, String[]> res = db.ReadIpWithJobs(ip);
 255                 if (res == null)
 256                         return null;
 257                 UserBean query = new UserBean(ip);
 258                 query.setMainInfo(res);
 259                 return query;
 260         }
 261
 262         /*
 263          * create list of parts of protein sequence;
 264          */
 265         private static List<String> CreateSubprot(String protein, String subprot) {
 266                 List<String> sub = new ArrayList<String>();
 267                 String subStr = protein;
 268                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 269                         String first = subStr.substring(0, subStr.indexOf(subprot));
 270                         if (first.length() > 0)
 271                                 sub.add(first);
 272                         sub.add(subprot);
 273                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 274                 }
 275                 if (subStr.length() > 0)
 276                         sub.add(subStr);
 277                 return sub;
 278         }
 279
 280         /*
 281          * convert String date into long date (miliseconds since the epoch start)
 282          */
 283         private static long DateParsing(String datInput, SimpleDateFormat formatter) {
 284                 if (datInput == null) {
 285                         return 0;
 286                 }
 287                 long dateWorkSt = 0;
 288
 289                 try {
 290                         dateWorkSt = formatter.parse(datInput).getTime();
 291                 } catch (ParseException e) {
 292                         e.printStackTrace();
 293                 }
 294                 return dateWorkSt;
 295         }
 296
 297         // convert long to date in string format
 298         private static String DateFormat(long inDate) {
 299                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 300                 return datformat.format(new Date(inDate));
 301         }
 302
 303         // convert long to date in string format
 304                 private static String DateFormatYYMMDD(long inDate) {
 305                         SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
 306                         return datformat.format(new Date(inDate));
 307                 }
 308
 309         /*
 310          * set earlest date and current dates. earlestDate is static and should be
 311          * set at the 1st call currentDate should be re-calculated every time
 312          */
 313         private static void SetDateRange() {
 314                 Calendar cal = Calendar.getInstance();
 315                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH),
 316                                 formatYYMMDD);
 317                 if (0 == earlestDate) {
 318                         CassandraRequester cr = new CassandraRequester();
 319                         earlestDate = cr.earliestDate();
 320                 }
 321         }
 322
 323         public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
 324                 if (dateToValidate == null || dateToValidate.equals("")) {
 325                         return false;
 326                 }
 327                 try {
 328                         // if not valid, this will throw ParseException
 329                         sdf.setLenient(false);
 330                         Date date = sdf.parse(dateToValidate);
 331                 } catch (ParseException e) {
 332                         e.printStackTrace();
 333                         return false;
 334                 }
 335                 return true;
 336         }
 337
 338         /*
 339          * find the earliest date in the database
 340          */
 341         public long earliestDate() {
 342                 earlestDate = CassandraNativeConnector.getEarliestDateInDB();
 343                 return earlestDate;
 344         }
 345
 346         /*
 347          * find the earliest date in the database in String format
 348          */
 349         public String earliestDateString() {
 350                 earlestDate = CassandraNativeConnector.getEarliestDateInDB();
 351                 return DateFormatYYMMDD(earlestDate);
 352         }
 353
 354 }