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("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2);
  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                 return query;
 113         }
 114
 115         /*
 116          * query: total number of jobs  for the period from date1 till date2
 117          */
 118         public List<DataBase> countJobs(String date1, String date2) {
 119                 if (null == date1) {
 120                         date1 = "1970/1/1";
 121                 }
 122                 if (null == date2) {
 123                         date1 = "2100/1/1";
 124                 }
 125                 if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
 126                         System.out.println("CassandraRequester.countJobs: wrong format for date1 " + date1 + "or date2 " + date2);
 127                         return null;
 128                 }
 129                 SetDateRange();
 130                 long dateStart = DateParsing(date1, formatYYMMDD);
 131                 long dateEnd = DateParsing(date2, formatYYMMDD);
 132                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 133                         return null;
 134                 if (dateStart < earlestDate)
 135                         dateStart = earlestDate;
 136                 if (dateEnd > currentDate)
 137                         dateStart = currentDate;
 138
 139                 Calendar start = Calendar.getInstance();
 140                 start.setTime(new Date(dateStart));
 141                 Calendar end = Calendar.getInstance();
 142                 end.setTime(new Date(dateEnd));
 143                 query = new ArrayList<DataBase>();
 144                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
 145                         List<Long> res = db.ReadDateTable(date.getTime());
 146                         if (res == null)
 147                                 continue;
 148                         DataBase bean = new DataBase();
 149                         bean.setTotal((int)(long)res.get(0));
 150                         bean.setTotalOK((int)(long)res.get(1));
 151                         bean.setTotalStopped((int)(long)res.get(2));
 152                         bean.setTotalError((int)(long)res.get(3));
 153                         bean.setTotalTimeOut((int)(long)res.get(4));
 154                         bean.setDate(DateFormat(date.getTime()));
 155                         query.add(bean);
 156                 }
 157                 return query;
 158         }
 159
 160         /*
 161          * query: jobs and sequence at date
 162          */
 163         public List<DataBase> readJobByDay (String date) {
 164                 if (null == date) {
 165                         return null;
 166                 }
 167                 if (!isThisDateValid(date, formatDDMMYY)) {
 168                         System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
 169                         return null;
 170                 }
 171                 SetDateRange();
 172                 long day = DateParsing(date, formatDDMMYY);
 173                 if (day < earlestDate || day > currentDate)
 174                         return null;
 175                 List<Pair<String, String>>      res = db.ReadProteinData(day);
 176                 if (res == null)
 177                         return null;
 178                 query = new ArrayList<DataBase>();
 179                 for (Pair<String, String> entry : res) {
 180                         DataBase bean = new DataBase();
 181                         bean.setDate(date);
 182                         bean.setId(entry.getElement0());
 183                         bean.setProt(entry.getElement1());
 184                         query.add(bean);
 185                 }
 186                 return query;
 187         }
 188
 189
 190         /*
 191          * query: protein sequence
 192          * */
 193         public List<DataBase> readProteins(String protIn, String flag) {
 194                 query = new ArrayList<DataBase>();
 195                 List<AnnotatedProteinSequenceBean> res;
 196                 if (flag.equals("whole"))
 197                         res = db.ReadWholeSequence(protIn);
 198                  else
 199                         res = db.ReadPartOfSequence(protIn);
 200                 if (res == null)
 201                         return null;
 202                 for (AnnotatedProteinSequenceBean entry : res) {
 203                         DataBase db = new DataBase();
 204                         db.setProt(entry.getSequence());
 205                         db.setPredictions(entry);
 206                         db.setId(entry.getJobid());
 207                         if (flag.equals("part")) {
 208                                 db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
 209                         }
 210                         query.add(db);
 211                 }
 212                 return query;
 213         }
 214
 215
 216         /*
 217          * query protein sequences with number of jobs
 218          */
 219         public List<DataBase> readProteinByCounter(int minimalcounter) {
 220                 query = new ArrayList<DataBase>();
 221                 Map<String, Integer> map = db.ReadProteinSequenceByCounter();
 222                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 223                         if (entry.getValue() > minimalcounter && entry.getKey().length() > 0) {
 224                                 DataBase bean = new DataBase();
 225                                 bean.setTotalId(entry.getValue());
 226                                 bean.setProt(entry.getKey());
 227                                 query.add(bean);
 228                         }
 229                 }
 230                 return query;
 231         }
 232
 233         /*
 234          * query ip with number of jobs
 235          */
 236         public List<DataBase> readIpByCounter(Integer minimalcounter) {
 237                 query = new ArrayList<DataBase>();
 238                 Map<String, Integer> map = db.ReadIpByCounter();
 239                 if (minimalcounter == null)
 240                         minimalcounter = 0;
 241                 if (map == null)
 242                         return null;
 243                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 244                         if (entry.getValue() > minimalcounter) {
 245                                 DataBase bean = new DataBase();
 246                                 bean.setTotalId(entry.getValue());
 247                                 bean.setIp(entry.getKey());
 248                                 query.add(bean);
 249                         }
 250                 }
 251                 return query;
 252         }
 253         /*
 254          * query jobs log info
 255          */
 256         public DataBase readJobLog(String jobid) {
 257                 if (jobid == null)
 258                         return null;
 259                 StructureJobLog res = db.ReadJobLog(jobid);
 260                 if (res == null)
 261                         return null;
 262                 DataBase query = new DataBase();
 263                 query.setLogInfo(res);
 264                 return query;
 265         }
 266
 267
 268         /*
 269          * query jobs by ipStructureJobLog
 270          */
 271         public List<DataBase> readIp(String ip) {
 272                 if (ip == null)
 273                         return null;
 274                 List<Pair<String, String>> res = db.ReadIpWithJobs(ip);
 275                 if (res == null)
 276                         return null;
 277                 query = new ArrayList<DataBase>();
 278                 for (Pair<String, String> entry : res) {
 279                         DataBase bean = new DataBase();
 280                         bean.setIp(ip);
 281                         bean.setId(entry.getElement0());
 282                         bean.setProt(entry.getElement1());
 283                         query.add(bean);
 284                 }
 285                 return query;
 286         }
 287
 288         /*
 289          * create list of parts of protein sequence;
 290          */
 291         private static List<String> CreateSubprot (String protein, String subprot) {
 292                 List<String> sub = new ArrayList<String>();
 293                 String subStr = protein;
 294                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 295                         String first = subStr.substring(0, subStr.indexOf(subprot));
 296                         if (first.length() > 0)
 297                                 sub.add(first);
 298                         sub.add(subprot);
 299                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 300                 }
 301                 if (subStr.length() > 0)
 302                         sub.add(subStr);
 303                 return sub;
 304         }
 305         /*
 306          * convert String date into long date (miliseconds since the epoch start)
 307          */
 308         private static long DateParsing(String datInput, SimpleDateFormat formatter) {
 309                 if (datInput == null) {
 310                         return 0;
 311                 }
 312                 long dateWorkSt = 0;
 313
 314                 try {
 315                         dateWorkSt = formatter.parse(datInput).getTime();
 316                 } catch (ParseException e) {
 317                         e.printStackTrace();
 318                 }
 319                 return dateWorkSt;
 320         }
 321
 322         // convert long to date in string format
 323         private static String DateFormat(long inDate) {
 324                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 325                 return datformat.format(new Date(inDate));
 326         }
 327
 328         /*
 329          * set earlest date and current dates. earlestDate is static and should be
 330          * set at the 1st call currentDate should be re-calculated every time
 331          */
 332         private static void SetDateRange() {
 333                 Calendar cal = Calendar.getInstance();
 334                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH), 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 }