+++ /dev/null
-package compbio.statistic;
-
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import compbio.beans.DateBean;
-import compbio.beans.JobBean;
-import compbio.beans.ProteinBean;
-import compbio.beans.Total;
-import compbio.beans.TotalByCounterBean;
-import compbio.beans.TotalJobsStatisticBean;
-import compbio.beans.UserBean;
-import compbio.cassandra.CassandraNativeConnector;
-import compbio.cassandra.CassandraReaderOld;
-import compbio.cassandra.DataBase;
-import compbio.cassandra.Pair;
-import compbio.engine.JobStatus;
-
-public class CassandraRequester {
- private CassandraReaderOld db = new CassandraReaderOld();
- private ArrayList<DataBase> query;
- private static long currentDate = 0;
- private static long earlestDate = 0;
- private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
- private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
-
- /*
- * query: execution time for the period from date1 till date2
- */
- public List<DataBase> extractExecutionTime(String date1, String date2) {
- if (null == date1) {
- date1 = "1970/1/1";
- }
- if (null == date2) {
- date1 = "2100/1/1";
- }
- if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
- System.out.println("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2);
- return null;
- }
- SetDateRange();
- int nbins = 5;
- long dateStart = DateParsing(date1, formatYYMMDD);
- long dateEnd = DateParsing(date2, formatYYMMDD);
- if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
- return null;
- if (dateStart < earlestDate)
- dateStart = earlestDate;
- if (dateEnd > currentDate)
- dateStart = currentDate;
-
- Calendar start = Calendar.getInstance();
- start.setTime(new Date(dateStart));
- Calendar end = Calendar.getInstance();
- end.setTime(new Date(dateEnd));
- query = new ArrayList<DataBase>();
- List<Integer> totalTime = new ArrayList<Integer>();
- for (int i = 0; i < nbins; i++)
- totalTime.add(i, 0);
- List<Pair<String, String>> res = db.ReadProteinDataTable();
- List<Pair<Date, Long>> numres = new ArrayList<Pair<Date, Long>>();
-
- for (Pair<String, String> entry : res) {
- SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
- try {
- Date jobstartdate = dateformatter.parse(entry.getElement0());
- long date = jobstartdate.getTime();
- if (dateStart <= date && date <= dateEnd) {
- SimpleDateFormat datetimeformatter = new SimpleDateFormat("yyyy/MM/dd:H:m:s");
- Date jobstarttime = datetimeformatter.parse(entry.getElement0());
- Date jobendtime = datetimeformatter.parse(entry.getElement1());
- long diff = (jobendtime.getTime() - jobstarttime.getTime()) / 1000;
- Pair<Date, Long> pair = new Pair<Date, Long>(jobstartdate, Long.valueOf(diff));
- numres.add(pair);
- }
- } catch (ParseException e) {
- e.printStackTrace();
- }
- }
-
- for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
- List<Integer> timeResult = new ArrayList<Integer>();
- for (int i = 0; i < nbins; i++)
- timeResult.add(i, 0);
- for (Pair<Date, Long> p : numres) {
- if (date.equals(p.getElement0())) {
- long lenResult = p.getElement1().longValue();
- if (lenResult <= 30)
- timeResult.set(0, timeResult.get(0) + 1);
- else if (lenResult > 30 && lenResult <= 60)
- timeResult.set(1, timeResult.get(1) + 1);
- else if (lenResult > 60 && lenResult <= 120)
- timeResult.set(2, timeResult.get(2) + 1);
- else if (lenResult > 120 && lenResult <= 600)
- timeResult.set(3, timeResult.get(3) + 1);
- else {
- timeResult.set(4, timeResult.get(4) + 1);
- }
- }
- }
- for (int i = 0; i < nbins; i++)
- totalTime.set(i, totalTime.get(i) + timeResult.get(i));
- DataBase db = new DataBase();
- db.setTimeRez(timeResult);
- db.setDate(DateFormat(date.getTime()));
- query.add(db);
- }
-
- /* ???? Very strange code...
- DataBase db = new DataBase();
- db.setTimeTotalExec(totalTime);
- query.add(db);
- */
- return query;
- }
-
- /*
- * query: total number of jobs for the period from date1 till date2
- */
- public TotalJobsStatisticBean countJobs(String date1, String date2) {
- /*
- * if (null == date1) { date1 = "1970/1/1"; } if (null == date2) { date1
- * = "2100/1/1"; } if (!isThisDateValid(date1, formatYYMMDD) ||
- * !isThisDateValid(date2, formatYYMMDD)) { System.out.println(
- * "CassandraRequester.countJobs: wrong format for date1 " + date1 +
- * "or date2 " + date2); return null; }
- */
- SetDateRange();
- long dateStart = DateParsing(date1, formatYYMMDD);
- long dateEnd = DateParsing(date2, formatYYMMDD);
- /*
- * if (dateEnd < earlestDate || dateStart > currentDate || dateStart >
- * dateEnd) return null; if (dateStart < earlestDate) dateStart =
- * earlestDate; if (dateEnd > currentDate) dateStart = currentDate;
- */
- Calendar start = Calendar.getInstance();
- start.setTime(new Date(dateStart));
- Calendar end = Calendar.getInstance();
- end.setTime(new Date(dateEnd));
- TotalJobsStatisticBean query = new TotalJobsStatisticBean();
- Total wholeTotal = new Total(0, 0, 0, 0, 0);
- for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
- Total res = db.ReadDateTable(date.getTime());
- if (res == null)
- continue;
- query.setDateTotal(DateFormat(date.getTime()), res);
- wholeTotal.setTotal(res.getTotal() + wholeTotal.getTotal());
- wholeTotal.setTotalOK(res.getTotalOK() + wholeTotal.getTotalOK());
- wholeTotal.setTotalStopped(res.getTotalStopped() + wholeTotal.getTotalStopped());
- wholeTotal.setTotalError(res.getTotalError() + wholeTotal.getTotalError());
- wholeTotal.setTotalTimeOut(res.getTotalTimeOut() + wholeTotal.getTotalTimeOut());
- }
- query.setWholeTotal(wholeTotal);
- return query;
- }
-
- /*
- * query: jobs and sequence at date
- */
- public DateBean readJobByDay(String date, JobStatus status) {
- if (!isThisDateValid(date, formatDDMMYY)) {
- System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
- return null;
- }
- SetDateRange();
- long day = DateParsing(date, formatDDMMYY);
- if (day < earlestDate || day > currentDate)
- return null;
-
- if (status == JobStatus.OK) {
- return db.ReadProteinData(day, date);
- }
- return db.ReadFailedJobs(day, date, status);
- }
-
- /*
- * query: protein sequence
- */
- public List<ProteinBean> readProteins(String protIn, String searchtype) {
- List<ProteinBean> result;
- if (searchtype.equals("whole"))
- result = db.ReadWholeSequence(protIn);
- else
- result = db.ReadPartOfSequence(protIn);
- if (result == null)
- return null;
-
- if (searchtype.equals("partial")) {
- for (ProteinBean entry : result) {
- entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
- }
- }
- return result;
- }
-
- /*
- * query: protein feature
- */
- public Map<String, String> readProteinsPrediction(String feature, int percent) {
- Map<String, String> result = db.ReadProtein();
- ;
- if (result == null)
- return null;
- Map<String, String> query = new HashMap<String, String>();
- for (Map.Entry<String, String> entry : result.entrySet()) {
- String pred = entry.getValue();
- if (pred.replaceAll("[^" + feature + "]", "").length() > pred.length() * percent / 100 && (!entry.getKey().equals(""))) {
- // if (!entry.getKey().equals(""))
- query.put(entry.getKey(), pred);
- }
- }
- return query;
- }
-
- /*
- * query protein sequences with number of jobs
- */
- public List<TotalByCounterBean> readProteinByCounter(int minimalcounter) {
- List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
- Map<String, Integer> map = db.ReadProteinSequenceByCounter();
- if (map == null)
- return null;
- for (Map.Entry<String, Integer> entry : map.entrySet()) {
- if (entry.getValue() > minimalcounter) {
- TotalByCounterBean bean = new TotalByCounterBean();
- bean.setTotaljobs(entry.getValue());
- bean.setName(entry.getKey());
- query.add(bean);
- }
- }
- return query;
- }
-
- /*
- * query ip with number of jobs
- */
- public List<TotalByCounterBean> readIpByCounter(Integer minimalcounter) {
- List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
- Map<String, Integer> map = db.ReadIpByCounter();
- if (minimalcounter == null)
- minimalcounter = 0;
- if (map == null)
- return null;
- for (Map.Entry<String, Integer> entry : map.entrySet()) {
- if (entry.getValue() > minimalcounter) {
- TotalByCounterBean bean = new TotalByCounterBean();
- bean.setTotaljobs(entry.getValue());
- bean.setName(entry.getKey());
- query.add(bean);
- }
- }
- return query;
- }
-
- /*
- * query jobs log info
- */
- public JobBean readJobLog(String jobid) {
- if (jobid == null)
- return null;
- return db.ReadJobLog(jobid);
- }
-
- /*
- * query jobs by ipStructureJobLog
- */
- public UserBean readIp(String ip) {
- if (ip == null)
- return null;
- Map<String, String[]> res = db.ReadIpWithJobs(ip);
- if (res == null)
- return null;
- UserBean query = new UserBean(ip);
- query.setMainInfo(res);
- return query;
- }
-
- /*
- * create list of parts of protein sequence;
- */
- private static List<String> CreateSubprot(String protein, String subprot) {
- List<String> sub = new ArrayList<String>();
- String subStr = protein;
- while (subStr.length() > 0 && subStr.contains(subprot)) {
- String first = subStr.substring(0, subStr.indexOf(subprot));
- if (first.length() > 0)
- sub.add(first);
- sub.add(subprot);
- subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
- }
- if (subStr.length() > 0)
- sub.add(subStr);
- return sub;
- }
-
- /*
- * convert String date into long date (miliseconds since the epoch start)
- */
- private static long DateParsing(String datInput, SimpleDateFormat formatter) {
- if (datInput == null) {
- return 0;
- }
- long dateWorkSt = 0;
-
- try {
- dateWorkSt = formatter.parse(datInput).getTime();
- } catch (ParseException e) {
- e.printStackTrace();
- }
- return dateWorkSt;
- }
-
- // convert long to date in string format
- private static String DateFormat(long inDate) {
- SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
- return datformat.format(new Date(inDate));
- }
-
- /*
- * set earlest date and current dates. earlestDate is static and should be
- * set at the 1st call currentDate should be re-calculated every time
- */
- private static void SetDateRange() {
- Calendar cal = Calendar.getInstance();
- currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH),
- formatYYMMDD);
- if (0 == earlestDate) {
- CassandraRequester cr = new CassandraRequester();
- earlestDate = cr.earliestDate();
- }
- }
-
- public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
- if (dateToValidate == null || dateToValidate.equals("")) {
- return false;
- }
- try {
- // if not valid, this will throw ParseException
- sdf.setLenient(false);
- Date date = sdf.parse(dateToValidate);
- } catch (ParseException e) {
- e.printStackTrace();
- return false;
- }
- return true;
- }
-
- /*
- * find the earliest date in the database
- */
- public long earliestDate() {
- earlestDate = CassandraNativeConnector.getEarliestDateInDB();
- return earlestDate;
- }
-
- /**
- * prepares an example of either job id or IP for the DB
- *
- * @param exampletype
- * defines which example you need (an existing job from the DB -
- * jobid, an IP - "ip")
- * @return a string representation of the requested example, if the example
- * type is not known empty string is returned
- */
- public String getExample(String exampletype) {
- if (exampletype.equals("jobid")) {
- return "jp_NzBOJKo";
- } else if (exampletype.equals("ip")) {
- return "127.0.0.1";
- }
- return "";
- }
-
-}
git://source.jalview.org / proteocache.git / blobdiff