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.AnnotatedProteinSequenceBean;
  13 import compbio.cassandra.CassandraNativeConnector;
  14 import compbio.cassandra.CassandraReader;
  15 import compbio.cassandra.DataBase;
  16 import compbio.cassandra.Pair;
  17 import compbio.cassandra.StructureJobLog;
  18
  19 public class CassandraRequester {
  20         private CassandraReader db = new CassandraReader();
  21         private ArrayList<DataBase> query;
  22         private static long currentDate = 0;
  23         private static long earlestDate = 0;
  24         private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
  25         private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
  26
  27         /*
  28          * query: execution time for the period from date1 till date2
  29          */
  30         public List<DataBase> extractExecutionTime(String date1, String date2) {
  31                 if (null == date1) {
  32                         date1 = "1970/1/1";
  33                 }
  34                 if (null == date2) {
  35                         date1 = "2100/1/1";
  36                 }
  37                 if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
  38                         System.out.println("Wrong date: point 3");
  39                         return null;
  40                 }
  41                 SetDateRange();
  42                 int nbins = 5;
  43                 long dateStart = DateParsing(date1, formatYYMMDD);
  44                 long dateEnd = DateParsing(date2, formatYYMMDD);
  45                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
  46                         return null;
  47                 if (dateStart < earlestDate)
  48                         dateStart = earlestDate;
  49                 if (dateEnd > currentDate)
  50                         dateStart = currentDate;
  51
  52                 Calendar start = Calendar.getInstance();
  53                 start.setTime(new Date(dateStart));
  54                 Calendar end = Calendar.getInstance();
  55                 end.setTime(new Date(dateEnd));
  56                 query = new ArrayList<DataBase>();
  57                 List<Integer> totalTime = new ArrayList<Integer>();
  58                 for (int i = 0; i < nbins; i++)
  59                         totalTime.add(i, 0);
  60                 List<Pair<String, String>> res = db.ReadProteinDataTable();
  61                 List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
  62
  63                 for (Pair<String, String> entry : res) {
  64                         SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
  65                         try {
  66                                 Date jobstartdate = dateformatter.parse(entry.getElement0());
  67                                 long date = jobstartdate.getTime();
  68                                 if (dateStart <= date && date <= dateEnd) {
  69                                         SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
  70                                         Date jobstarttime = datetimeformatter.parse(entry.getElement0());
  71                                         Date jobendtime = datetimeformatter.parse(entry.getElement1());
  72                                         long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
  73                                         Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
  74                                         numres.add(pair);
  75                                 }
  76                         } catch (ParseException e) {
  77                                 e.printStackTrace();
  78                         }
  79                 }
  80
  81                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
  82                         List<Integer> timeResult = new ArrayList<Integer>();
  83                         for (int i = 0; i < nbins; i++)
  84                                 timeResult.add(i, 0);
  85                         for (Pair<Date, Long> p : numres) {
  86                                 if (date.equals(p.getElement0())) {
  87                                         long lenResult = p.getElement1().longValue();
  88                                         if (lenResult <= 30)
  89                                                 timeResult.set(0, timeResult.get(0) + 1);
  90                                         else if (lenResult > 30 && lenResult <= 60)
  91                                                 timeResult.set(1, timeResult.get(1) + 1);
  92                                         else if (lenResult > 60 && lenResult <= 120)
  93                                                 timeResult.set(2, timeResult.get(2) + 1);
  94                                         else if (lenResult > 120 && lenResult <= 600)
  95                                                 timeResult.set(3, timeResult.get(3) + 1);
  96                                         else {
  97                                                 timeResult.set(4, timeResult.get(4) + 1);
  98                                         }
  99                                 }
 100                         }
 101                         for (int i = 0; i < nbins; i++)
 102                                 totalTime.set(i, totalTime.get(i) + timeResult.get(i));
 103                         DataBase db = new DataBase();
 104                         db.setTimeRez(timeResult);
 105                         db.setDate(DateFormat(date.getTime()));
 106                         query.add(db);
 107                 }
 108
 109                 DataBase db = new DataBase();
 110                 db.setTimeTotalExec(totalTime);
 111                 query.add(db);
 112                 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 113                 return query;
 114         }
 115
 116         /*
 117          * query: total number of jobs  for the period from date1 till date2
 118          */
 119         public List<DataBase> countJobs(String date1, String date2) {
 120                 if (null == date1) {
 121                         date1 = "1970/1/1";
 122                 }
 123                 if (null == date2) {
 124                         date1 = "2100/1/1";
 125                 }
 126                 if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
 127                         System.out.println("Wrong date: point 3");
 128                         return null;
 129                 }
 130                 SetDateRange();
 131                 long dateStart = DateParsing(date1, formatYYMMDD);
 132                 long dateEnd = DateParsing(date2, formatYYMMDD);
 133                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 134                         return null;
 135                 if (dateStart < earlestDate)
 136                         dateStart = earlestDate;
 137                 if (dateEnd > currentDate)
 138                         dateStart = currentDate;
 139
 140                 Calendar start = Calendar.getInstance();
 141                 start.setTime(new Date(dateStart));
 142                 Calendar end = Calendar.getInstance();
 143                 end.setTime(new Date(dateEnd));
 144                 query = new ArrayList<DataBase>();
 145                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
 146                         List<Long> res = db.ReadDateTable(date.getTime());
 147                         if (res == null)
 148                                 continue;
 149                         DataBase bean = new DataBase();
 150                         bean.setTotal((int)(long)res.get(0));
 151                         bean.setTotalOK((int)(long)res.get(1));
 152                         bean.setTotalStopped((int)(long)res.get(2));
 153                         bean.setTotalError((int)(long)res.get(3));
 154                         bean.setTotalTimeOut((int)(long)res.get(4));
 155                         bean.setDate(DateFormat(date.getTime()));
 156                         query.add(bean);
 157                 }
 158                 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 159                 return query;
 160         }
 161
 162         /*
 163          * query: jobs and sequence at date
 164          */
 165         public List<DataBase> readJobByDay (String date) {
 166                 System.out.println(date);
 167                 if (null == date) {
 168                         return null;
 169                 }
 170                 if (!isThisDateValid(date, formatDDMMYY)) {
 171                         System.out.println("Wrong date: point 3");
 172                         return null;
 173                 }
 174                 SetDateRange();
 175                 long day = DateParsing(date, formatDDMMYY);
 176                 System.out.println(day);
 177                 if (day < earlestDate || day > currentDate)
 178                         return null;
 179                 List<Pair<String, String>>      res = db.ReadProteinData(day);
 180                 if (res == null)
 181                         return null;
 182                 query = new ArrayList<DataBase>();
 183                 for (Pair<String, String> entry : res) {
 184                         DataBase bean = new DataBase();
 185                         bean.setDate(date);
 186                         bean.setId(entry.getElement0());
 187                         bean.setProt(entry.getElement1());
 188                         query.add(bean);
 189                 }
 190                 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 191                 return query;
 192         }
 193
 194
 195         /*
 196          * query: protein sequence
 197          * */
 198         public List<DataBase> readProteins(String protIn, String flag) {
 199                 query = new ArrayList<DataBase>();
 200                 List<AnnotatedProteinSequenceBean> res;
 201                 if (flag.equals("whole"))
 202                         res = db.ReadWholeSequence(protIn);
 203                  else
 204                         res = db.ReadPartOfSequence(protIn);
 205                 if (res == null)
 206                         return null;
 207                 for (AnnotatedProteinSequenceBean entry : res) {
 208                         DataBase db = new DataBase();
 209                         db.setProt(entry.getSequence());
 210                         db.setPredictions(entry);
 211                         db.setId(entry.getJobid());
 212                         if (flag.equals("part")) {
 213                                 db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
 214                         }
 215                         query.add(db);
 216                 }
 217                 return query;
 218         }
 219
 220
 221         /*
 222          * query protein sequences with number of jobs
 223          */
 224         public List<DataBase> readProteinByCounter(int minimalcounter) {
 225                 query = new ArrayList<DataBase>();
 226                 Map<String, Integer> map = db.ReadProteinSequenceByCounter();
 227                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 228                         if (entry.getValue() > minimalcounter && entry.getKey().length() > 0) {
 229                                 DataBase bean = new DataBase();
 230                                 bean.setTotalId(entry.getValue());
 231                                 bean.setProt(entry.getKey());
 232                                 query.add(bean);
 233                         }
 234                 }
 235                 return query;
 236         }
 237
 238         /*
 239          * query ip with number of jobs
 240          */
 241         public List<DataBase> readIpByCounter(Integer minimalcounter) {
 242                 query = new ArrayList<DataBase>();
 243                 Map<String, Integer> map = db.ReadIpByCounter();
 244                 if (minimalcounter == null)
 245                         minimalcounter = 0;
 246                 if (map == null)
 247                         return null;
 248                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 249                         if (entry.getValue() > minimalcounter) {
 250                                 DataBase bean = new DataBase();
 251                                 bean.setTotalId(entry.getValue());
 252                                 bean.setIp(entry.getKey());
 253                                 query.add(bean);
 254                         }
 255                 }
 256                 return query;
 257         }
 258         /*
 259          * query jobs log info
 260          */
 261         public DataBase readJobLog(String jobid) {
 262                 if (jobid == null)
 263                         return null;
 264                 StructureJobLog res = db.ReadJobLog(jobid);
 265                 if (res == null)
 266                         return null;
 267                 DataBase query = new DataBase();
 268                 query.setLogInfo(res);
 269                 return query;
 270         }
 271
 272
 273         /*
 274          * query jobs by ipStructureJobLog
 275          */
 276         public List<DataBase> readIp(String ip) {
 277                 if (ip == null)
 278                         return null;
 279                 List<Pair<String, String>> res = db.ReadIpWithJobs(ip);
 280         //      System.out.println(res.size());
 281                 if (res == null)
 282                         return null;
 283                 query = new ArrayList<DataBase>();
 284                 for (Pair<String, String> entry : res) {
 285                         System.out.println("ip " + ip);
 286                         System.out.println("id " + entry.getElement0());
 287                         DataBase bean = new DataBase();
 288                         bean.setIp(ip);
 289                         bean.setId(entry.getElement0());
 290                         bean.setProt(entry.getElement1());
 291                         query.add(bean);
 292                 }
 293                 System.out.println(query.size());
 294                 return query;
 295         }
 296
 297         /*
 298          * create list of parts of protein sequence;
 299          */
 300         private static List<String> CreateSubprot (String protein, String subprot) {
 301                 List<String> sub = new ArrayList<String>();
 302                 String subStr = protein;
 303                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 304                         String first = subStr.substring(0, subStr.indexOf(subprot));
 305                         if (first.length() > 0)
 306                                 sub.add(first);
 307                         sub.add(subprot);
 308                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 309                 }
 310                 if (subStr.length() > 0)
 311                         sub.add(subStr);
 312                 return sub;
 313         }
 314         /*
 315          * convert String date into long date (miliseconds since the epoch start)
 316          */
 317         private static long DateParsing(String datInput, SimpleDateFormat formatter) {
 318                 if (datInput == null) {
 319                         return 0;
 320                 }
 321                 long dateWorkSt = 0;
 322
 323                 try {
 324                         dateWorkSt = formatter.parse(datInput).getTime();
 325                 } catch (ParseException e) {
 326                         e.printStackTrace();
 327                 }
 328                 return dateWorkSt;
 329         }
 330
 331         // convert long to date in string format
 332         private static String DateFormat(long inDate) {
 333                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 334                 return datformat.format(new Date(inDate));
 335         }
 336
 337         /*
 338          * set earlest date and current dates. earlestDate is static and should be
 339          * set at the 1st call currentDate should be re-calculated every time
 340          */
 341         private static void SetDateRange() {
 342                 Calendar cal = Calendar.getInstance();
 343                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH), formatYYMMDD);
 344                 if (0 == earlestDate) {
 345                         CassandraRequester cr = new CassandraRequester();
 346                         earlestDate = cr.earliestDate();
 347                         System.out.println("Set earlest Date = " + earlestDate);
 348                 }
 349         }
 350
 351         public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
 352                 if (dateToValidate == null || dateToValidate.equals("")) {
 353                         System.out.println("Undefined date");
 354                         return false;
 355                 }
 356                 try {
 357                         // if not valid, this will throw ParseException
 358                         sdf.setLenient(false);
 359                         Date date = sdf.parse(dateToValidate);
 360                 } catch (ParseException e) {
 361                         e.printStackTrace();
 362                         return false;
 363                 }
 364                 return true;
 365         }
 366
 367         /*
 368          * find the earliest date in the database
 369          */
 370         public long earliestDate() {
 371                 earlestDate = CassandraNativeConnector.getEarliestDateInDB();
 372                 return earlestDate;
 373         }
 374
 375 }