import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Calendar;
-import java.util.Collections;
import java.util.Date;
-import java.util.Iterator;
+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 CassandraNativeConnector DBInstance = new CassandraNativeConnector();
+ 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 (!isThisDateValid(date1) || !isThisDateValid(date2)) {
- System.out.println("Wrong date: point 3");
+ 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);
- long dateEnd = DateParsing(date2);
- if ((dateStart < earlestDate && dateEnd < earlestDate) || (dateStart > currentDate && dateEnd > currentDate) || dateStart > dateEnd)
+ 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;
- System.out.println("CassandraRequester.extractExecutionTime: earlestDate = " + earlestDate + ", currentDate = " + currentDate);
-
Calendar start = Calendar.getInstance();
start.setTime(new Date(dateStart));
Calendar end = Calendar.getInstance();
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>();
- SliceQuery<Long, String, String> result = HFactory.createSliceQuery(DBInstance.GetKeyspace(), LongSerializer.get(),
- StringSerializer.get(), StringSerializer.get());
- result.setColumnFamily("ProteinData");
- result.setKey(date.getTime());
- result.setRange(null, null, false, Integer.MAX_VALUE);
- QueryResult<ColumnSlice<String, String>> columnSlice = result.execute();
- List<HColumn<String, String>> col = columnSlice.get().getColumns();
- if (!col.isEmpty()) {
- Iterator<HColumn<String, String>> itCol = col.iterator();
- for (int i = 0; i < nbins; i++)
- timeResult.add(i, 0);
- // split all jobs into nbins bins
- while (itCol.hasNext()) {
- String id = itCol.next().getName();
- long lenResult = CountID(id);
+ 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(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);
}
+ 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);
}
- */
+
DataBase db = new DataBase();
db.setTimeTotalExec(totalTime);
query.add(db);
- System.out.println("StatisticsProt.readLength: total number of dates = " + query.size());
return query;
}
- /*
- * convert String date into long date (miliseconds since the epoch start)
+ /*
+ * 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
*/
- private static long DateParsing(String datInput) {
- if (datInput == null) {
- return 0;
+ public DateBean readJobByDay(String date, JobStatus status) {
+ if (!isThisDateValid(date, formatDDMMYY)) {
+ System.out.println("CassandraRequester.readJobByDay: Wrong date format for " + date);
+ return null;
}
- long dateWorkSt = 0;
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
- try {
- dateWorkSt = formatter.parse(datInput).getTime();
- } catch (ParseException e) {
- e.printStackTrace();
+ SetDateRange();
+ long day = DateParsing(date, formatDDMMYY);
+ if (day < earlestDate || day > currentDate)
+ return null;
+
+ if (status == JobStatus.OK) {
+ return db.ReadProteinData(day, date);
}
- return dateWorkSt;
+ return db.ReadFailedJobs(day, date, status);
}
/*
- * convert String date:time into long date:time (miliseconds since the epoch start)
+ * query: protein sequence
*/
- private static long TimeConvert(String datInput) {
- long dateWorkSt = 0;
+ 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 dateWorkSt;
+ return 0;
}
- SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd:hh:mm:ss");
+ long dateWorkSt = 0;
+
try {
dateWorkSt = formatter.parse(datInput).getTime();
} catch (ParseException e) {
// convert long to date in string format
private static String DateFormat(long inDate) {
SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
- String dateString = datformat.format(new Date(inDate));
- return dateString;
+ return datformat.format(new Date(inDate));
}
/*
- * convert ???
- */
- public static String DateFormatYYMMDD(long indate) {
- SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
- String dateString = datformat.format(new Date(indate));
- return dateString;
- }
-
- /*
- * ???
- */
- public long CountID(String id) {
- /*
- SliceQuery<String, String, String> sliceQuery = HFactory.createSliceQuery(DBInstance.GetKeyspace(), StringSerializer.get(),
- StringSerializer.get(), StringSerializer.get());
- sliceQuery.setColumnFamily("ProteinLog").setKey(id).setRange("", "", false, 100);
- QueryResult<ColumnSlice<String, String>> result = sliceQuery.execute();
- String datBegin = result.get().getColumnByName("DataBegin").getValue();
- String datEnd = result.get().getColumnByName("DataEnd").getValue();
-
- long datBeginLong = TimeConvert(datBegin);
- long datEndLong = TimeConvert(datEnd);
- return (datEndLong - datBeginLong) / 1000;
- */
- return 0;
- }
-
- /*
- * set earlest date and current dates.
- * earlestDate is static and should be set at the 1st call
- * currentDate should be re-calculated every time
+ * 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) {
- StatisticsProt sp = new StatisticsProt();
- earlestDate = sp.earliestDate();
- System.out.println("Set earlest Date = " + earlestDate);
+ CassandraRequester cr = new CassandraRequester();
+ earlestDate = cr.earliestDate();
}
- Calendar cal = Calendar.getInstance();
- currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
}
- 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);
* find the earliest date in the database
*/
public long earliestDate() {
- /*
- ArrayList<Long> dateSort = new ArrayList<Long>();
- int row_count = 10000;
- RangeSlicesQuery<Long, String, String> result = HFactory.createRangeSlicesQuery(DBInstance.GetKeyspace(), LongSerializer.get(),
- StringSerializer.get(), StringSerializer.get());
- result.setColumnFamily("ProteinData");
- result.setRange(null, null, false, Integer.MAX_VALUE);
- result.setRowCount(row_count);
- Long last_key = null;
- while (true) {
- result.setKeys(last_key, null);
- QueryResult<OrderedRows<Long, String, String>> columnSlice = result.execute();
- OrderedRows<Long, String, String> rows = columnSlice.get();
- Iterator<Row<Long, String, String>> rowsIterator = rows.iterator();
- while (rowsIterator.hasNext()) {
- Row<Long, String, String> row = rowsIterator.next();
- last_key = row.getKey();
- dateSort.add(last_key);
- }
- if (rows.getCount() < row_count)
- break;
- }
- Collections.sort(dateSort);
- return dateSort.get(0);
- */
- return 0;
+ earlestDate = CassandraNativeConnector.getEarliestDateInDB();
+ return earlestDate;
}
+
}
git://source.jalview.org / proteocache.git / blobdiff