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.HashMap;
   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 import compbio.engine.JobStatus;
  24
  25 public class CassandraRequester {
  26         private CassandraReader db = new CassandraReader();
  27         private ArrayList<DataBase> query;
  28         private static long currentDate = 0;
  29         private static long earlestDate = 0;
  30         private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
  31         private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
  32
  33         /*
  34          * query: execution time for the period from date1 till date2
  35          */
  36         public List<DataBase> extractExecutionTime(String date1, String date2) {
  37                 if (null == date1) {
  38                         date1 = "1970/1/1";
  39                 }
  40                 if (null == date2) {
  41                         date1 = "2100/1/1";
  42                 }
  43                 if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
  44                         System.out.println("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2);
  45                         return null;
  46                 }
  47                 SetDateRange();
  48                 int nbins = 5;
  49                 long dateStart = DateParsing(date1, formatYYMMDD);
  50                 long dateEnd = DateParsing(date2, formatYYMMDD);
  51                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
  52                         return null;
  53                 if (dateStart < earlestDate)
  54                         dateStart = earlestDate;
  55                 if (dateEnd > currentDate)
  56                         dateStart = currentDate;
  57
  58                 Calendar start = Calendar.getInstance();
  59                 start.setTime(new Date(dateStart));
  60                 Calendar end = Calendar.getInstance();
  61                 end.setTime(new Date(dateEnd));
  62                 query = new ArrayList<DataBase>();
  63                 List<Integer> totalTime = new ArrayList<Integer>();
  64                 for (int i = 0; i < nbins; i++)
  65                         totalTime.add(i, 0);
  66                 List<Pair<String, String>> res = db.ReadProteinDataTable();
  67                 List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
  68
  69                 for (Pair<String, String> entry : res) {
  70                         SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
  71                         try {
  72                                 Date jobstartdate = dateformatter.parse(entry.getElement0());
  73                                 long date = jobstartdate.getTime();
  74                                 if (dateStart <= date && date <= dateEnd) {
  75                                         SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
  76                                         Date jobstarttime = datetimeformatter.parse(entry.getElement0());
  77                                         Date jobendtime = datetimeformatter.parse(entry.getElement1());
  78                                         long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
  79                                         Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
  80                                         numres.add(pair);
  81                                 }
  82                         } catch (ParseException e) {
  83                                 e.printStackTrace();
  84                         }
  85                 }
  86
  87                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
  88                         List<Integer> timeResult = new ArrayList<Integer>();
  89                         for (int i = 0; i < nbins; i++)
  90                                 timeResult.add(i, 0);
  91                         for (Pair<Date, Long> p : numres) {
  92                                 if (date.equals(p.getElement0())) {
  93                                         long lenResult = p.getElement1().longValue();
  94                                         if (lenResult <= 30)
  95                                                 timeResult.set(0, timeResult.get(0) + 1);
  96                                         else if (lenResult > 30 && lenResult <= 60)
  97                                                 timeResult.set(1, timeResult.get(1) + 1);
  98                                         else if (lenResult > 60 && lenResult <= 120)
  99                                                 timeResult.set(2, timeResult.get(2) + 1);
 100                                         else if (lenResult > 120 && lenResult <= 600)
 101                                                 timeResult.set(3, timeResult.get(3) + 1);
 102                                         else {
 103                                                 timeResult.set(4, timeResult.get(4) + 1);
 104                                         }
 105                                 }
 106                         }
 107                         for (int i = 0; i < nbins; i++)
 108                                 totalTime.set(i, totalTime.get(i) + timeResult.get(i));
 109                         DataBase db = new DataBase();
 110                         db.setTimeRez(timeResult);
 111                         db.setDate(DateFormat(date.getTime()));
 112                         query.add(db);
 113                 }
 114
 115                 DataBase db = new DataBase();
 116                 db.setTimeTotalExec(totalTime);
 117                 query.add(db);
 118                 return query;
 119         }
 120
 121         /*
 122          * query: total number of jobs for the period from date1 till date2
 123          */
 124         public TotalJobsStatisticBean countJobs(String date1, String date2) {
 125                 if (null == date1) {
 126                         date1 = "1970/1/1";
 127                 }
 128                 if (null == date2) {
 129                         date1 = "2100/1/1";
 130                 }
 131                 if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
 132                         System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
 133                         return null;
 134                 }
 135                 SetDateRange();
 136                 long dateStart = DateParsing(date1, formatYYMMDD);
 137                 long dateEnd = DateParsing(date2, formatYYMMDD);
 138                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 139                         return null;
 140                 if (dateStart < earlestDate)
 141                         dateStart = earlestDate;
 142                 if (dateEnd > currentDate)
 143                         dateStart = currentDate;
 144
 145                 Calendar start = Calendar.getInstance();
 146                 start.setTime(new Date(dateStart));
 147                 Calendar end = Calendar.getInstance();
 148                 end.setTime(new Date(dateEnd));
 149                 TotalJobsStatisticBean query = new TotalJobsStatisticBean();
 150                 Total wholeTotal = new Total(0, 0, 0, 0, 0);
 151                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
 152                         Total res = db.ReadDateTable(date.getTime());
 153                         if (res == null)
 154                                 continue;
 155                         query.setDateTotal(DateFormat(date.getTime()), res);
 156                         wholeTotal.setTotal(res.getTotal() + wholeTotal.getTotal());
 157                         wholeTotal.setTotalOK(res.getTotalOK() + wholeTotal.getTotalOK());
 158                         wholeTotal.setTotalStopped(res.getTotalStopped() + wholeTotal.getTotalStopped());
 159                         wholeTotal.setTotalError(res.getTotalError() + wholeTotal.getTotalError());
 160                         wholeTotal.setTotalTimeOut(res.getTotalTimeOut() + wholeTotal.getTotalTimeOut());
 161                 }
 162                 query.setWholeTotal(wholeTotal);
 163                 return query;
 164         }
 165
 166         /*
 167          * query: jobs and sequence at date
 168          */
 169         public DateBean readJobByDay(String date, JobStatus status) {
 170                 if (!isThisDateValid(date, formatDDMMYY)) {
 171                         System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
 172                         return null;
 173                 }
 174                 SetDateRange();
 175                 long day = DateParsing(date, formatDDMMYY);
 176                 if (day < earlestDate || day > currentDate)
 177                         return null;
 178
 179                 if (status == JobStatus.OK) {
 180                         return db.ReadProteinData(day, date);
 181                 }
 182                 return db.ReadFailedJobs(day, date, status);
 183         }
 184
 185         /*
 186          * query: protein sequence
 187          */
 188         public List<ProteinBean> readProteins(String protIn, String searchtype) {
 189                 List<ProteinBean> result;
 190                 if (searchtype.equals("whole"))
 191                         result = db.ReadWholeSequence(protIn);
 192                 else
 193                         result = db.ReadPartOfSequence(protIn);
 194                 if (result == null)
 195                         return null;
 196
 197                 if (searchtype.equals("partial")) {
 198                         for (ProteinBean entry : result) {
 199                                 entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
 200                         }
 201                 }
 202                 return result;
 203         }
 204
 205         /*
 206          * query: protein feature
 207          */
 208         public Map<String, String> readProteinsPrediction(String feature, int percent) {
 209                 Map<String, String> result = db.ReadProtein();;
 210                 if (result == null)
 211                         return null;
 212                 Map<String, String> query = new HashMap<String, String>();
 213                 for (Map.Entry<String, String> entry : result.entrySet()) {
 214                         String pred = entry.getValue();
 215                         if (pred.replaceAll("[^"+feature+"]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
 216                         //      if (!entry.getKey().equals(""))
 217                                         query.put(entry.getKey(), pred);
 218                         }
 219                 }
 220                 return query;
 221         }
 222
 223         /*
 224          * query protein sequences with number of jobs
 225          */
 226         public List<TotalByCounterBean> readProteinByCounter(int minimalcounter) {
 227                 List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
 228                 Map<String, Integer> map = db.ReadProteinSequenceByCounter();
 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         /*
 243          * query ip with number of jobs
 244          */
 245         public List<TotalByCounterBean> readIpByCounter(Integer minimalcounter) {
 246                 List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
 247                 Map<String, Integer> map = db.ReadIpByCounter();
 248                 if (minimalcounter == null)
 249                         minimalcounter = 0;
 250                 if (map == null)
 251                         return null;
 252                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 253                         if (entry.getValue() > minimalcounter) {
 254                                 TotalByCounterBean bean = new TotalByCounterBean();
 255                                 bean.setTotaljobs(entry.getValue());
 256                                 bean.setName(entry.getKey());
 257                                 query.add(bean);
 258                         }
 259                 }
 260                 return query;
 261         }
 262
 263         /*
 264          * query jobs log info
 265          */
 266         public JobBean readJobLog(String jobid) {
 267                 if (jobid == null)
 268                         return null;
 269                 return db.ReadJobLog(jobid);
 270         }
 271
 272         /*
 273          * query jobs by ipStructureJobLog
 274          */
 275         public UserBean readIp(String ip) {
 276                 if (ip == null)
 277                         return null;
 278                 Map<String, String[]> res = db.ReadIpWithJobs(ip);
 279                 if (res == null)
 280                         return null;
 281                 UserBean query = new UserBean(ip);
 282                 query.setMainInfo(res);
 283                 return query;
 284         }
 285
 286         /*
 287          * create list of parts of protein sequence;
 288          */
 289         private static List<String> CreateSubprot(String protein, String subprot) {
 290                 List<String> sub = new ArrayList<String>();
 291                 String subStr = protein;
 292                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 293                         String first = subStr.substring(0, subStr.indexOf(subprot));
 294                         if (first.length() > 0)
 295                                 sub.add(first);
 296                         sub.add(subprot);
 297                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 298                 }
 299                 if (subStr.length() > 0)
 300                         sub.add(subStr);
 301                 return sub;
 302         }
 303
 304         /*
 305          * convert String date into long date (miliseconds since the epoch start)
 306          */
 307         private static long DateParsing(String datInput, SimpleDateFormat formatter) {
 308                 if (datInput == null) {
 309                         return 0;
 310                 }
 311                 long dateWorkSt = 0;
 312
 313                 try {
 314                         dateWorkSt = formatter.parse(datInput).getTime();
 315                 } catch (ParseException e) {
 316                         e.printStackTrace();
 317                 }
 318                 return dateWorkSt;
 319         }
 320
 321         // convert long to date in string format
 322         private static String DateFormat(long inDate) {
 323                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 324                 return datformat.format(new Date(inDate));
 325         }
 326
 327         /*
 328          * set earlest date and current dates. earlestDate is static and should be
 329          * set at the 1st call currentDate should be re-calculated every time
 330          */
 331         private static void SetDateRange() {
 332                 Calendar cal = Calendar.getInstance();
 333                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH),
 334                                 formatYYMMDD);
 335                 if (0 == earlestDate) {
 336                         CassandraRequester cr = new CassandraRequester();
 337                         earlestDate = cr.earliestDate();
 338                 }
 339         }
 340
 341         public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
 342                 if (dateToValidate == null || dateToValidate.equals("")) {
 343                         return false;
 344                 }
 345                 try {
 346                         // if not valid, this will throw ParseException
 347                         sdf.setLenient(false);
 348                         Date date = sdf.parse(dateToValidate);
 349                 } catch (ParseException e) {
 350                         e.printStackTrace();
 351                         return false;
 352                 }
 353                 return true;
 354         }
 355
 356         /*
 357          * find the earliest date in the database
 358          */
 359         public long earliestDate() {
 360                 earlestDate = CassandraNativeConnector.getEarliestDateInDB();
 361                 return earlestDate;
 362         }
 363
 364 }