X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fstatistic%2FCassandraRequester.java;h=1bb0050944683a038a5e0cec7891feb5f21ec9ec;hb=025c55d49c191f24d0e06c5cbb69a9894c50af22;hp=ec74c6f8312944e5fae62a1d848418f1a8368a48;hpb=2664ee4e4eb002b7e8cd153b10ac7000c522af24;p=proteocache.git diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java index ec74c6f..1bb0050 100755 --- a/server/compbio/statistic/CassandraRequester.java +++ b/server/compbio/statistic/CassandraRequester.java @@ -5,22 +5,29 @@ import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Calendar; import java.util.Date; -import java.util.Iterator; import java.util.List; import java.util.Map; +import compbio.cassandra.DateBean; +import compbio.cassandra.ProteinBean; import compbio.cassandra.CassandraNativeConnector; import compbio.cassandra.CassandraReader; import compbio.cassandra.DataBase; import compbio.cassandra.Pair; -import compbio.cassandra.StructureJobLog; -import compbio.cassandra.StructureProteinPrediction; +import compbio.cassandra.JobBean; +import compbio.cassandra.Total; +import compbio.cassandra.TotalByCounterBean; +import compbio.cassandra.TotalJobsStatisticBean; +import compbio.cassandra.UserBean; +import compbio.engine.JobStatus; public class CassandraRequester { private CassandraReader db = new CassandraReader(); private ArrayList 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 @@ -32,14 +39,14 @@ public class CassandraRequester { if (null == date2) { date1 = "2100/1/1"; } - if (!isThisDateValid(date1) || !isThisDateValid(date2)) { - System.out.println("Wrong date: point 3"); + 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); - long dateEnd = DateParsing(date2); + long dateStart = DateParsing(date1, formatYYMMDD); + long dateEnd = DateParsing(date2, formatYYMMDD); if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd) return null; if (dateStart < earlestDate) @@ -107,27 +114,26 @@ public class CassandraRequester { DataBase db = new DataBase(); db.setTimeTotalExec(totalTime); query.add(db); - System.out.println("StatisticsProt.readLength: total number of dates = " + query.size()); return query; } - + /* - * query: total number of jobs for the period from date1 till date2 + * query: total number of jobs for the period from date1 till date2 */ - public List countJobs(String date1, String 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) || !isThisDateValid(date2)) { - System.out.println("Wrong date: point 3"); + 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); - long dateEnd = DateParsing(date2); + long dateStart = DateParsing(date1, formatYYMMDD); + long dateEnd = DateParsing(date2, formatYYMMDD); if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd) return null; if (dateStart < earlestDate) @@ -139,84 +145,129 @@ public class CassandraRequester { start.setTime(new Date(dateStart)); Calendar end = Calendar.getInstance(); end.setTime(new Date(dateEnd)); - query = new ArrayList(); + 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()) { - List res = db.ReadDateTable(date.getTime()); + Total res = db.ReadDateTable(date.getTime()); if (res == null) continue; - DataBase bean = new DataBase(); - bean.setTotal((int)(long)res.get(0)); - bean.setTotalOK((int)(long)res.get(1)); - bean.setTotalStopped((int)(long)res.get(2)); - bean.setTotalError((int)(long)res.get(3)); - bean.setTotalTimeOut((int)(long)res.get(4)); - bean.setDate(DateFormat(date.getTime())); - query.add(bean); + 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()); } - System.out.println("StatisticsProt.readLength: total number of dates = " + query.size()); + 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 readProteins(String protIn, String flag) { - query = new ArrayList(); - List res; - if (flag.equals("whole")) - res = db.ReadWholeSequence(protIn); - else - res = db.ReadPartOfSequence(protIn); - if (res == null) + */ + public List readProteins(String protIn, String searchtype) { + List result; + if (searchtype.equals("whole")) + result = db.ReadWholeSequence(protIn); + else + result = db.ReadPartOfSequence(protIn); + if (result == null) return null; - for (StructureProteinPrediction entry : res) { - Map pred = entry.getPrediction(); - Iterator it = pred.entrySet().iterator(); - while (it.hasNext()) { - DataBase db = new DataBase(); - db.setProt(entry.getSequence()); - Map.Entry pairs = (Map.Entry)it.next(); - db.setId(entry.getJobid()); - db.setJpred(pairs.getValue().toString()); - if (flag.equals("part")) - db.setSubProt(CreateSubprot (entry.getSequence(), protIn)); - query.add(db); + + if (searchtype.equals("partial")) { + for (ProteinBean entry : result) { + entry.setSubProt(CreateSubprot(entry.getSequence(), protIn)); } } - return query; + return result; } - - /* + + /* * query protein sequences with number of jobs */ - public List readProteinByCounter(int minimalcounter) { - query = new ArrayList(); + public List readProteinByCounter(int minimalcounter) { + List query = new ArrayList(); Map map = db.ReadProteinSequenceByCounter(); + if (map == null) + return null; for (Map.Entry entry : map.entrySet()) { - if (entry.getValue() > minimalcounter && entry.getKey().length() > 0) { - DataBase bean = new DataBase(); - bean.setTotalId(entry.getValue()); - bean.setProt(entry.getKey()); + 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 readIpByCounter(Integer minimalcounter) { + List query = new ArrayList(); + Map map = db.ReadIpByCounter(); + if (minimalcounter == null) + minimalcounter = 0; + if (map == null) + return null; + for (Map.Entry 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 DataBase readJobLog(String jobid) { - // query = new ArrayList(); - StructureJobLog res = db.ReadJobLog(jobid); - DataBase query = new DataBase(); - query.setLogInfo(res); - // query.setres); + 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 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 CreateSubprot (String protein, String subprot) { + private static List CreateSubprot(String protein, String subprot) { List sub = new ArrayList(); String subStr = protein; while (subStr.length() > 0 && subStr.contains(subprot)) { @@ -230,15 +281,16 @@ public class CassandraRequester { sub.add(subStr); return sub; } + /* * convert String date into long date (miliseconds since the epoch start) */ - private static long DateParsing(String datInput) { + private static long DateParsing(String datInput, SimpleDateFormat formatter) { if (datInput == null) { return 0; } long dateWorkSt = 0; - SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd"); + try { dateWorkSt = formatter.parse(datInput).getTime(); } catch (ParseException e) { @@ -259,20 +311,18 @@ public class CassandraRequester { */ 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)); + 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(); - System.out.println("Set earlest Date = " + earlestDate); } } - public boolean isThisDateValid(String dateToValidate) { + public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) { if (dateToValidate == null || dateToValidate.equals("")) { - System.out.println("Undefined date"); return false; } - SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd"); try { // if not valid, this will throw ParseException sdf.setLenient(false); @@ -291,5 +341,5 @@ public class CassandraRequester { earlestDate = CassandraNativeConnector.getEarliestDateInDB(); return earlestDate; } - + }