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.CassandraNativeConnector;
  13 import compbio.cassandra.DataBase;
  14 import compbio.cassandra.Pair;
  15 import compbio.cassandra.StructureProteinPrediction;
  16
  17 public class CassandraRequester {
  18         private CassandraNativeConnector DBInstance = new CassandraNativeConnector();
  19         private ArrayList<DataBase> query;
  20         private static long currentDate = 0;
  21         private static long earlestDate = 0;
  22
  23         /*
  24          * query: execution time for the period from date1 till date2
  25          */
  26         public List<DataBase> extractExecutionTime(String date1, String date2) {
  27                 if (null == date1) {
  28                         date1 = "1970/1/1";
  29                 }
  30                 if (null == date2) {
  31                         date1 = "2100/1/1";
  32                 }
  33                 if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
  34                         System.out.println("Wrong date: point 3");
  35                         return null;
  36                 }
  37                 SetDateRange();
  38                 int nbins = 5;
  39                 long dateStart = DateParsing(date1);
  40                 long dateEnd = DateParsing(date2);
  41                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
  42                         return null;
  43                 if (dateStart < earlestDate)
  44                         dateStart = earlestDate;
  45                 if (dateEnd > currentDate)
  46                         dateStart = currentDate;
  47
  48                 Calendar start = Calendar.getInstance();
  49                 start.setTime(new Date(dateStart));
  50                 Calendar end = Calendar.getInstance();
  51                 end.setTime(new Date(dateEnd));
  52                 query = new ArrayList<DataBase>();
  53                 List<Integer> totalTime = new ArrayList<Integer>();
  54                 for (int i = 0; i < nbins; i++)
  55                         totalTime.add(i, 0);
  56                 List<Pair<String, String>> res = DBInstance.ReadProteinDataTable();
  57                 List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
  58
  59                 for (Pair<String, String> entry : res) {
  60                         SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
  61                         try {
  62                                 Date jobstartdate = dateformatter.parse(entry.getElement0());
  63                                 long date = jobstartdate.getTime();
  64                                 if (dateStart <= date && date <= dateEnd) {
  65                                         SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
  66                                         Date jobstarttime = datetimeformatter.parse(entry.getElement0());
  67                                         Date jobendtime = datetimeformatter.parse(entry.getElement1());
  68                                         long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
  69                                         Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
  70                                         numres.add(pair);
  71                                 }
  72                         } catch (ParseException e) {
  73                                 e.printStackTrace();
  74                         }
  75                 }
  76
  77                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
  78                         List<Integer> timeResult = new ArrayList<Integer>();
  79                         for (int i = 0; i < nbins; i++)
  80                                 timeResult.add(i, 0);
  81                         for (Pair<Date, Long> p : numres) {
  82                                 if (date.equals(p.getElement0())) {
  83                                         long lenResult = p.getElement1().longValue();
  84                                         if (lenResult <= 30)
  85                                                 timeResult.set(0, timeResult.get(0) + 1);
  86                                         else if (lenResult > 30 && lenResult <= 60)
  87                                                 timeResult.set(1, timeResult.get(1) + 1);
  88                                         else if (lenResult > 60 && lenResult <= 120)
  89                                                 timeResult.set(2, timeResult.get(2) + 1);
  90                                         else if (lenResult > 120 && lenResult <= 600)
  91                                                 timeResult.set(3, timeResult.get(3) + 1);
  92                                         else {
  93                                                 timeResult.set(4, timeResult.get(4) + 1);
  94                                         }
  95                                 }
  96                         }
  97                         for (int i = 0; i < nbins; i++)
  98                                 totalTime.set(i, totalTime.get(i) + timeResult.get(i));
  99                         DataBase db = new DataBase();
 100                         db.setTimeRez(timeResult);
 101                         db.setDate(DateFormat(date.getTime()));
 102                         query.add(db);
 103                 }
 104
 105                 DataBase db = new DataBase();
 106                 db.setTimeTotalExec(totalTime);
 107                 query.add(db);
 108                 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 109                 return query;
 110         }
 111
 112         /*
 113          * query: total number of jobs  for the period from date1 till date2
 114          */
 115         public List<DataBase> countJobs(String date1, String date2) {
 116                 if (null == date1) {
 117                         date1 = "1970/1/1";
 118                 }
 119                 if (null == date2) {
 120                         date1 = "2100/1/1";
 121                 }
 122                 if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
 123                         System.out.println("Wrong date: point 3");
 124                         return null;
 125                 }
 126                 SetDateRange();
 127                 long dateStart = DateParsing(date1);
 128                 long dateEnd = DateParsing(date2);
 129                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 130                         return null;
 131                 if (dateStart < earlestDate)
 132                         dateStart = earlestDate;
 133                 if (dateEnd > currentDate)
 134                         dateStart = currentDate;
 135
 136                 Calendar start = Calendar.getInstance();
 137                 start.setTime(new Date(dateStart));
 138                 Calendar end = Calendar.getInstance();
 139                 end.setTime(new Date(dateEnd));
 140                 query = new ArrayList<DataBase>();
 141                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
 142                         Integer res = DBInstance.ReadDateTable(date.getTime());
 143                         if (res == null)
 144                                 continue;
 145                         DataBase db = new DataBase();
 146                         db.setTotal(res);
 147                         db.setDate(DateFormat(date.getTime()));
 148                         query.add(db);
 149                 }
 150                 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 151                 return query;
 152         }
 153         /*
 154          * query: protein sequence
 155          * */
 156         public List<DataBase> readProteins(String protIn, String flag) {
 157                 query = new ArrayList<DataBase>();
 158                 List<StructureProteinPrediction> res;
 159                 if (flag.equals("whole"))
 160                         res = DBInstance.ReadWholeSequence(protIn);
 161                  else
 162                         res = DBInstance.ReadPartOfSequence(protIn);
 163                 for (StructureProteinPrediction entry : res) {
 164                         Map<String,String> pred = entry.getPrediction();
 165                         Iterator it = pred.entrySet().iterator();
 166                         while (it.hasNext()) {
 167                                 DataBase db = new DataBase();
 168                                 db.setProt(entry.getSequence());
 169                                 Map.Entry pairs = (Map.Entry)it.next();
 170                                 db.setId(entry.getJobid());
 171                                 db.setJpred(pairs.getValue().toString());
 172                                 if (flag.equals("part"))
 173                                         db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
 174                                 query.add(db);
 175                         }
 176                 }
 177                 return query;
 178         }
 179
 180         /*
 181          * query  protein sequences with number of jobs
 182          * */
 183         public List<DataBase> readProteinByCounter(int counter) {
 184                 query = new ArrayList<DataBase>();
 185         //      List<Pair<String, String>> res = DBInstance.ReadProteinDataByCounter(counter);
 186
 187                 return query;
 188         }
 189
 190
 191         private static List<String> CreateSubprot (String protein, String subprot) {
 192                 List<String> sub = new ArrayList<String>();
 193                 String subStr = protein;
 194                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 195                         String first = subStr.substring(0, subStr.indexOf(subprot));
 196                         if (first.length() > 0)
 197                                 sub.add(first);
 198                         sub.add(subprot);
 199                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 200                 }
 201                 if (subStr.length() > 0)
 202                         sub.add(subStr);
 203                 return sub;
 204         }
 205         /*
 206          * convert String date into long date (miliseconds since the epoch start)
 207          */
 208         private static long DateParsing(String datInput) {
 209                 if (datInput == null) {
 210                         return 0;
 211                 }
 212                 long dateWorkSt = 0;
 213                 SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
 214                 try {
 215                         dateWorkSt = formatter.parse(datInput).getTime();
 216                 } catch (ParseException e) {
 217                         e.printStackTrace();
 218                 }
 219                 return dateWorkSt;
 220         }
 221
 222         // convert long to date in string format
 223         private static String DateFormat(long inDate) {
 224                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 225                 return datformat.format(new Date(inDate));
 226         }
 227
 228         /*
 229          * set earlest date and current dates. earlestDate is static and should be
 230          * set at the 1st call currentDate should be re-calculated every time
 231          */
 232         private static void SetDateRange() {
 233                 Calendar cal = Calendar.getInstance();
 234                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
 235                 if (0 == earlestDate) {
 236                         CassandraRequester cr = new CassandraRequester();
 237                         earlestDate = cr.earliestDate();
 238                         System.out.println("Set earlest Date = " + earlestDate);
 239                 }
 240         }
 241
 242         public boolean isThisDateValid(String dateToValidate) {
 243                 if (dateToValidate == null || dateToValidate.equals("")) {
 244                         System.out.println("Undefined date");
 245                         return false;
 246                 }
 247                 SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
 248                 try {
 249                         // if not valid, this will throw ParseException
 250                         sdf.setLenient(false);
 251                         Date date = sdf.parse(dateToValidate);
 252                 } catch (ParseException e) {
 253                         e.printStackTrace();
 254                         return false;
 255                 }
 256                 return true;
 257         }
 258
 259         /*
 260          * find the earliest date in the database
 261          */
 262         public long earliestDate() {
 263                 earlestDate = DBInstance.getEarliestDateInDB();
 264                 return earlestDate;
 265         }
 266
 267 }