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.StructureJobLog;
  16 import compbio.cassandra.StructureProteinPrediction;
  17
  18 public class CassandraRequester {
  19         private CassandraNativeConnector DBInstance = new CassandraNativeConnector();
  20         private ArrayList<DataBase> query;
  21         private static long currentDate = 0;
  22         private static long earlestDate = 0;
  23
  24         /*
  25          * query: execution time for the period from date1 till date2
  26          */
  27         public List<DataBase> extractExecutionTime(String date1, String date2) {
  28                 if (null == date1) {
  29                         date1 = "1970/1/1";
  30                 }
  31                 if (null == date2) {
  32                         date1 = "2100/1/1";
  33                 }
  34                 if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
  35                         System.out.println("Wrong date: point 3");
  36                         return null;
  37                 }
  38                 SetDateRange();
  39                 int nbins = 5;
  40                 long dateStart = DateParsing(date1);
  41                 long dateEnd = DateParsing(date2);
  42                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
  43                         return null;
  44                 if (dateStart < earlestDate)
  45                         dateStart = earlestDate;
  46                 if (dateEnd > currentDate)
  47                         dateStart = currentDate;
  48
  49                 Calendar start = Calendar.getInstance();
  50                 start.setTime(new Date(dateStart));
  51                 Calendar end = Calendar.getInstance();
  52                 end.setTime(new Date(dateEnd));
  53                 query = new ArrayList<DataBase>();
  54                 List<Integer> totalTime = new ArrayList<Integer>();
  55                 for (int i = 0; i < nbins; i++)
  56                         totalTime.add(i, 0);
  57                 List<Pair<String, String>> res = DBInstance.ReadProteinDataTable();
  58                 List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
  59
  60                 for (Pair<String, String> entry : res) {
  61                         SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
  62                         try {
  63                                 Date jobstartdate = dateformatter.parse(entry.getElement0());
  64                                 long date = jobstartdate.getTime();
  65                                 if (dateStart <= date && date <= dateEnd) {
  66                                         SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
  67                                         Date jobstarttime = datetimeformatter.parse(entry.getElement0());
  68                                         Date jobendtime = datetimeformatter.parse(entry.getElement1());
  69                                         long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
  70                                         Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
  71                                         numres.add(pair);
  72                                 }
  73                         } catch (ParseException e) {
  74                                 e.printStackTrace();
  75                         }
  76                 }
  77
  78                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
  79                         List<Integer> timeResult = new ArrayList<Integer>();
  80                         for (int i = 0; i < nbins; i++)
  81                                 timeResult.add(i, 0);
  82                         for (Pair<Date, Long> p : numres) {
  83                                 if (date.equals(p.getElement0())) {
  84                                         long lenResult = p.getElement1().longValue();
  85                                         if (lenResult <= 30)
  86                                                 timeResult.set(0, timeResult.get(0) + 1);
  87                                         else if (lenResult > 30 && lenResult <= 60)
  88                                                 timeResult.set(1, timeResult.get(1) + 1);
  89                                         else if (lenResult > 60 && lenResult <= 120)
  90                                                 timeResult.set(2, timeResult.get(2) + 1);
  91                                         else if (lenResult > 120 && lenResult <= 600)
  92                                                 timeResult.set(3, timeResult.get(3) + 1);
  93                                         else {
  94                                                 timeResult.set(4, timeResult.get(4) + 1);
  95                                         }
  96                                 }
  97                         }
  98                         for (int i = 0; i < nbins; i++)
  99                                 totalTime.set(i, totalTime.get(i) + timeResult.get(i));
 100                         DataBase db = new DataBase();
 101                         db.setTimeRez(timeResult);
 102                         db.setDate(DateFormat(date.getTime()));
 103                         query.add(db);
 104                 }
 105
 106                 DataBase db = new DataBase();
 107                 db.setTimeTotalExec(totalTime);
 108                 query.add(db);
 109                 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 110                 return query;
 111         }
 112
 113         /*
 114          * query: total number of jobs  for the period from date1 till date2
 115          */
 116         public List<DataBase> countJobs(String date1, String date2) {
 117                 if (null == date1) {
 118                         date1 = "1970/1/1";
 119                 }
 120                 if (null == date2) {
 121                         date1 = "2100/1/1";
 122                 }
 123                 if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
 124                         System.out.println("Wrong date: point 3");
 125                         return null;
 126                 }
 127                 SetDateRange();
 128                 long dateStart = DateParsing(date1);
 129                 long dateEnd = DateParsing(date2);
 130                 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
 131                         return null;
 132                 if (dateStart < earlestDate)
 133                         dateStart = earlestDate;
 134                 if (dateEnd > currentDate)
 135                         dateStart = currentDate;
 136
 137                 Calendar start = Calendar.getInstance();
 138                 start.setTime(new Date(dateStart));
 139                 Calendar end = Calendar.getInstance();
 140                 end.setTime(new Date(dateEnd));
 141                 query = new ArrayList<DataBase>();
 142                 for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
 143                         Integer res = DBInstance.ReadDateTable(date.getTime());
 144                         if (res == null)
 145                                 continue;
 146                         DataBase db = new DataBase();
 147                         db.setTotal(res);
 148                         db.setDate(DateFormat(date.getTime()));
 149                         query.add(db);
 150                 }
 151                 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
 152                 return query;
 153         }
 154         /*
 155          * query: protein sequence
 156          * */
 157         public List<DataBase> readProteins(String protIn, String flag) {
 158                 query = new ArrayList<DataBase>();
 159                 List<StructureProteinPrediction> res;
 160                 if (flag.equals("whole"))
 161                         res = DBInstance.ReadWholeSequence(protIn);
 162                  else
 163                         res = DBInstance.ReadPartOfSequence(protIn);
 164                 for (StructureProteinPrediction entry : res) {
 165                         Map<String,String> pred = entry.getPrediction();
 166                         Iterator it = pred.entrySet().iterator();
 167                         while (it.hasNext()) {
 168                                 DataBase db = new DataBase();
 169                                 db.setProt(entry.getSequence());
 170                                 Map.Entry pairs = (Map.Entry)it.next();
 171                                 db.setId(entry.getJobid());
 172                                 db.setJpred(pairs.getValue().toString());
 173                                 if (flag.equals("part"))
 174                                         db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
 175                                 query.add(db);
 176                         }
 177                 }
 178                 return query;
 179         }
 180
 181         /*
 182          * query  protein sequences with number of jobs
 183          * */
 184         public List<DataBase> readProteinByCounter(int counter) {
 185                 query = new ArrayList<DataBase>();
 186                 Map<String, Integer> map = DBInstance.ReadProteinDataByCounter();
 187                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 188                         if (entry.getValue() > counter) {
 189                                 DataBase db = new DataBase();
 190                                 db.setTotalId(entry.getValue());
 191                                 db.setProt(entry.getKey());
 192                                 query.add(db);
 193                         }
 194                 }
 195                 return query;
 196         }
 197
 198         /*
 199          * query jobs log info
 200          */
 201         public DataBase readJobLog(String jobid) {
 202         //      query = new ArrayList<DataBase>();
 203                 StructureJobLog res = DBInstance.ReadJobLog(jobid);
 204                 DataBase query = new DataBase();
 205                 query.setLogInfo(res);
 206         //      query.setres);
 207                 return query;
 208         }
 209         /*
 210          * create list of parts of protein sequence;
 211          */
 212         private static List<String> CreateSubprot (String protein, String subprot) {
 213                 List<String> sub = new ArrayList<String>();
 214                 String subStr = protein;
 215                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 216                         String first = subStr.substring(0, subStr.indexOf(subprot));
 217                         if (first.length() > 0)
 218                                 sub.add(first);
 219                         sub.add(subprot);
 220                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 221                 }
 222                 if (subStr.length() > 0)
 223                         sub.add(subStr);
 224                 return sub;
 225         }
 226         /*
 227          * convert String date into long date (miliseconds since the epoch start)
 228          */
 229         private static long DateParsing(String datInput) {
 230                 if (datInput == null) {
 231                         return 0;
 232                 }
 233                 long dateWorkSt = 0;
 234                 SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
 235                 try {
 236                         dateWorkSt = formatter.parse(datInput).getTime();
 237                 } catch (ParseException e) {
 238                         e.printStackTrace();
 239                 }
 240                 return dateWorkSt;
 241         }
 242
 243         // convert long to date in string format
 244         private static String DateFormat(long inDate) {
 245                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 246                 return datformat.format(new Date(inDate));
 247         }
 248
 249         /*
 250          * set earlest date and current dates. earlestDate is static and should be
 251          * set at the 1st call currentDate should be re-calculated every time
 252          */
 253         private static void SetDateRange() {
 254                 Calendar cal = Calendar.getInstance();
 255                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
 256                 if (0 == earlestDate) {
 257                         CassandraRequester cr = new CassandraRequester();
 258                         earlestDate = cr.earliestDate();
 259                         System.out.println("Set earlest Date = " + earlestDate);
 260                 }
 261         }
 262
 263         public boolean isThisDateValid(String dateToValidate) {
 264                 if (dateToValidate == null || dateToValidate.equals("")) {
 265                         System.out.println("Undefined date");
 266                         return false;
 267                 }
 268                 SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
 269                 try {
 270                         // if not valid, this will throw ParseException
 271                         sdf.setLenient(false);
 272                         Date date = sdf.parse(dateToValidate);
 273                 } catch (ParseException e) {
 274                         e.printStackTrace();
 275                         return false;
 276                 }
 277                 return true;
 278         }
 279
 280         /*
 281          * find the earliest date in the database
 282          */
 283         public long earliestDate() {
 284                 earlestDate =  DBInstance.getEarliestDateInDB();
 285                 return earlestDate;
 286         }
 287
 288 }