1 package compbio.statistic;
3 import java.text.ParseException;
4 import java.text.SimpleDateFormat;
5 import java.util.ArrayList;
6 import java.util.Calendar;
8 import java.util.Iterator;
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;
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;
26 * query: execution time for the period from date1 till date2
28 public List<DataBase> extractExecutionTime(String date1, String date2) {
35 if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
36 System.out.println("Wrong date: point 3");
41 long dateStart = DateParsing(date1);
42 long dateEnd = DateParsing(date2);
43 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
45 if (dateStart < earlestDate)
46 dateStart = earlestDate;
47 if (dateEnd > currentDate)
48 dateStart = currentDate;
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++)
58 List<Pair<String, String>> res = db.ReadProteinDataTable();
59 List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
61 for (Pair<String, String> entry : res) {
62 SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
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));
74 } catch (ParseException e) {
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++)
83 for (Pair<Date, Long> p : numres) {
84 if (date.equals(p.getElement0())) {
85 long lenResult = p.getElement1().longValue();
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);
95 timeResult.set(4, timeResult.get(4) + 1);
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()));
107 DataBase db = new DataBase();
108 db.setTimeTotalExec(totalTime);
110 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
115 * query: total number of jobs for the period from date1 till date2
117 public List<DataBase> countJobs(String date1, String date2) {
124 if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
125 System.out.println("Wrong date: point 3");
129 long dateStart = DateParsing(date1);
130 long dateEnd = DateParsing(date2);
131 if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
133 if (dateStart < earlestDate)
134 dateStart = earlestDate;
135 if (dateEnd > currentDate)
136 dateStart = currentDate;
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());
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()));
156 System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
161 * query: protein sequence
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);
169 res = db.ReadPartOfSequence(protIn);
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));
186 * query protein sequences with number of jobs
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());
203 * query jobs log info
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);
214 * create list of parts of protein sequence;
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)
224 subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
226 if (subStr.length() > 0)
231 * convert String date into long date (miliseconds since the epoch start)
233 private static long DateParsing(String datInput) {
234 if (datInput == null) {
238 SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
240 dateWorkSt = formatter.parse(datInput).getTime();
241 } catch (ParseException e) {
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));
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
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);
267 public boolean isThisDateValid(String dateToValidate) {
268 if (dateToValidate == null || dateToValidate.equals("")) {
269 System.out.println("Undefined date");
272 SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
274 // if not valid, this will throw ParseException
275 sdf.setLenient(false);
276 Date date = sdf.parse(dateToValidate);
277 } catch (ParseException e) {
285 * find the earliest date in the database
287 public long earliestDate() {
288 earlestDate = CassandraNativeConnector.getEarliestDateInDB();