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