X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fstatistic%2FCassandraRequester.java;h=afba67b4304fc042e5bea1b7f1babb2cf1dbcc1c;hb=8a0caa40d0fa288a0ad23f6af2aab1b0de0d50cd;hp=b7f83a803455f5d8b24fdf5e8c2a418f4c6eecf7;hpb=efa31207c6ba71709270a30aa04145a59a659a4e;p=proteocache.git diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java index b7f83a8..afba67b 100755 --- a/server/compbio/statistic/CassandraRequester.java +++ b/server/compbio/statistic/CassandraRequester.java @@ -10,15 +10,19 @@ import java.util.List; import java.util.Map; import compbio.cassandra.CassandraNativeConnector; +import compbio.cassandra.CassandraReader; import compbio.cassandra.DataBase; import compbio.cassandra.Pair; +import compbio.cassandra.StructureJobLog; import compbio.cassandra.StructureProteinPrediction; public class CassandraRequester { - private CassandraNativeConnector DBInstance = new CassandraNativeConnector(); + 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 @@ -30,14 +34,14 @@ public class CassandraRequester { if (null == date2) { date1 = "2100/1/1"; } - if (!isThisDateValid(date1) || !isThisDateValid(date2)) { + if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) { System.out.println("Wrong date: point 3"); 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) @@ -53,7 +57,7 @@ public class CassandraRequester { List totalTime = new ArrayList(); for (int i = 0; i < nbins; i++) totalTime.add(i, 0); - List> res = DBInstance.ReadProteinDataTable(); + List> res = db.ReadProteinDataTable(); List> numres = new ArrayList>(); for (Pair entry : res) { @@ -119,13 +123,13 @@ public class CassandraRequester { if (null == date2) { date1 = "2100/1/1"; } - if (!isThisDateValid(date1) || !isThisDateValid(date2)) { + if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) { System.out.println("Wrong date: point 3"); 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) @@ -139,14 +143,50 @@ public class CassandraRequester { end.setTime(new Date(dateEnd)); query = new ArrayList(); for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) { - Integer res = DBInstance.ReadDateTable(date.getTime()); + List res = db.ReadDateTable(date.getTime()); if (res == null) continue; - DataBase db = new DataBase(); - db.setTotal(res); - db.setDate(DateFormat(date.getTime())); - query.add(db); - } + 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); + } + System.out.println("StatisticsProt.readLength: total number of dates = " + query.size()); + return query; + } + + /* + * query: jobs and sequence at date + */ + public List readJobByDay (String date) { + System.out.println(date); + if (null == date) { + return null; + } + if (!isThisDateValid(date, formatDDMMYY)) { + System.out.println("Wrong date: point 3"); + return null; + } + SetDateRange(); + long day = DateParsing(date, formatDDMMYY); + System.out.println(day); + if (day < earlestDate || day > currentDate) + return null; + List> res = db.ReadProteinData(day); + if (res == null) + return null; + query = new ArrayList(); + for (Pair entry : res) { + DataBase bean = new DataBase(); + bean.setDate(date); + bean.setId(entry.getElement0()); + bean.setProt(entry.getElement1()); + query.add(bean); + } System.out.println("StatisticsProt.readLength: total number of dates = " + query.size()); return query; } @@ -154,40 +194,64 @@ public class CassandraRequester { * query: protein sequence * */ public List readProteins(String protIn, String flag) { + if (protIn == null) + return null; + System.out.println(protIn.length()); query = new ArrayList(); List res; if (flag.equals("whole")) - res = DBInstance.ReadWholeSequence(protIn); + res = db.ReadWholeSequence(protIn); else - res = DBInstance.ReadPartOfSequence(protIn); + res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null; + if (res == 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()); + DataBase bean = new DataBase(); + bean.setProt(entry.getSequence()); + bean.setId(entry.getJobid()); + bean.setJpred(entry.getJnetpred()); if (flag.equals("part")) - db.setSubProt(CreateSubprot (entry.getSequence(), protIn)); - query.add(db); - } + bean.setSubProt(CreateSubprot (entry.getSequence(), protIn)); + query.add(bean); + } return query; } /* - * query protein sequences with number of jobs - * */ - public List readProteinByCounter(int counter) { + * query protein sequences with number of jobs + */ + public List readProteinByCounter(int minimalcounter) { query = new ArrayList(); - // List> res = DBInstance.ReadProteinDataByCounter(counter); - + Map map = db.ReadProteinSequenceByCounter(); + 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()); + query.add(bean); + } + } return query; } + /* + * query jobs log info + */ + public DataBase readJobLog(String jobid) { + if (jobid == null) + return null; + StructureJobLog res = db.ReadJobLog(jobid); + if (res == null) + return null; + DataBase query = new DataBase(); + query.setLogInfo(res); + return query; + } + /* + * create list of parts of protein sequence; + */ private static List CreateSubprot (String protein, String subprot) { List sub = new ArrayList(); String subStr = protein; @@ -205,12 +269,12 @@ public class CassandraRequester { /* * 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) { @@ -231,7 +295,7 @@ 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(); @@ -239,12 +303,11 @@ public class CassandraRequester { } } - 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); @@ -260,7 +323,7 @@ public class CassandraRequester { * find the earliest date in the database */ public long earliestDate() { - earlestDate = DBInstance.getEarliestDateInDB(); + earlestDate = CassandraNativeConnector.getEarliestDateInDB(); return earlestDate; }