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.CassandraReader;
  14 import compbio.cassandra.DataBase;
  15 import compbio.cassandra.Pair;
  16 import compbio.cassandra.StructureJobLog;
  17 import compbio.cassandra.StructureProteinPrediction;
  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          * query: protein sequence
 161          * */
 162         public List<DataBase> readProteins(String protIn, String flag) {
 163                 query = new ArrayList<DataBase>();
 164                 List<StructureProteinPrediction> res;
 165                 if (flag.equals("whole"))
 166                         res = db.ReadWholeSequence(protIn);
 167                  else
 168                         res = db.ReadPartOfSequence(protIn);
 169                 if (res == null)
 170                         return null;
 171                 for (StructureProteinPrediction entry : res) {
 172                         Map<String,String> pred = entry.getPrediction();
 173                         Iterator it = pred.entrySet().iterator();
 174                         while (it.hasNext()) {
 175                                 DataBase db = new DataBase();
 176                                 db.setProt(entry.getSequence());
 177                                 Map.Entry pairs = (Map.Entry)it.next();
 178                                 db.setId(entry.getJobid());
 179                                 db.setJpred(pairs.getValue().toString());
 180                                 if (flag.equals("part"))
 181                                         db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
 182                                 query.add(db);
 183                         }
 184                 }
 185                 return query;
 186         }
 187
 188         /*
 189          * query protein sequences with number of jobs
 190          */
 191         public List<DataBase> readProteinByCounter(int minimalcounter) {
 192                 query = new ArrayList<DataBase>();
 193                 Map<String, Integer> map = db.ReadProteinSequenceByCounter();
 194                 for (Map.Entry<String, Integer> entry : map.entrySet()) {
 195                         if (entry.getValue() > minimalcounter && entry.getKey().length() > 0) {
 196                                 DataBase bean = new DataBase();
 197                                 bean.setTotalId(entry.getValue());
 198                                 bean.setProt(entry.getKey());
 199                                 query.add(bean);
 200                         }
 201                 }
 202                 return query;
 203         }
 204
 205         /*
 206          * query jobs log info
 207          */
 208         public DataBase readJobLog(String jobid) {
 209         //      query = new ArrayList<DataBase>();
 210                 StructureJobLog res = db.ReadJobLog(jobid);
 211                 DataBase query = new DataBase();
 212                 query.setLogInfo(res);
 213         //      query.setres);
 214                 return query;
 215         }
 216         /*
 217          * create list of parts of protein sequence;
 218          */
 219         private static List<String> CreateSubprot (String protein, String subprot) {
 220                 List<String> sub = new ArrayList<String>();
 221                 String subStr = protein;
 222                 while (subStr.length() > 0 && subStr.contains(subprot)) {
 223                         String first = subStr.substring(0, subStr.indexOf(subprot));
 224                         if (first.length() > 0)
 225                                 sub.add(first);
 226                         sub.add(subprot);
 227                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
 228                 }
 229                 if (subStr.length() > 0)
 230                         sub.add(subStr);
 231                 return sub;
 232         }
 233         /*
 234          * convert String date into long date (miliseconds since the epoch start)
 235          */
 236         private static long DateParsing(String datInput) {
 237                 if (datInput == null) {
 238                         return 0;
 239                 }
 240                 long dateWorkSt = 0;
 241                 SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
 242                 try {
 243                         dateWorkSt = formatter.parse(datInput).getTime();
 244                 } catch (ParseException e) {
 245                         e.printStackTrace();
 246                 }
 247                 return dateWorkSt;
 248         }
 249
 250         // convert long to date in string format
 251         private static String DateFormat(long inDate) {
 252                 SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
 253                 return datformat.format(new Date(inDate));
 254         }
 255
 256         /*
 257          * set earlest date and current dates. earlestDate is static and should be
 258          * set at the 1st call currentDate should be re-calculated every time
 259          */
 260         private static void SetDateRange() {
 261                 Calendar cal = Calendar.getInstance();
 262                 currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
 263                 if (0 == earlestDate) {
 264                         CassandraRequester cr = new CassandraRequester();
 265                         earlestDate = cr.earliestDate();
 266                         System.out.println("Set earlest Date = " + earlestDate);
 267                 }
 268         }
 269
 270         public boolean isThisDateValid(String dateToValidate) {
 271                 if (dateToValidate == null || dateToValidate.equals("")) {
 272                         System.out.println("Undefined date");
 273                         return false;
 274                 }
 275                 SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
 276                 try {
 277                         // if not valid, this will throw ParseException
 278                         sdf.setLenient(false);
 279                         Date date = sdf.parse(dateToValidate);
 280                 } catch (ParseException e) {
 281                         e.printStackTrace();
 282                         return false;
 283                 }
 284                 return true;
 285         }
 286
 287         /*
 288          * find the earliest date in the database
 289          */
 290         public long earliestDate() {
 291                 earlestDate = CassandraNativeConnector.getEarliestDateInDB();
 292                 return earlestDate;
 293         }
 294
 295 }