import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
-import java.util.Iterator;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import compbio.cassandra.AnnotatedProteinSequenceBean;
+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.CassandraReader;
+import compbio.cassandra.CassandraReaderOld;
import compbio.cassandra.DataBase;
import compbio.cassandra.Pair;
-import compbio.cassandra.StructureJobLog;
+import compbio.engine.JobStatus;
public class CassandraRequester {
- private CassandraReader db = new CassandraReader();
+ private CassandraReaderOld db = new CassandraReaderOld();
private ArrayList<DataBase> query;
private static long currentDate = 0;
private static long earlestDate = 0;
if (null == date2) {
date1 = "2100/1/1";
}
- if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
- 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();
query.add(db);
}
+ /* ???? Very strange code...
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
- */
- public List<DataBase> 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("Wrong date: point 3");
- return null;
- }
+ * 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;
-
+ /*
+ * 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>();
+ 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<Long> 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<DataBase> readProteins(String protIn, String flag) {
- if (protIn == null)
+ */
+ 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;
- System.out.println(protIn.length());
- query = new ArrayList<DataBase>();
- List<AnnotatedProteinSequenceBean> res;
- if (flag.equals("whole"))
- res = db.ReadWholeSequence(protIn);
- else
- res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null;
- if (res == 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;
- for (AnnotatedProteinSequenceBean entry : res) {
- DataBase db = new DataBase();
- db.setProt(entry.getSequence());
- db.setPredictions(entry);
- db.setId(entry.getJobid());
- if (flag.equals("part")) {
- db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
+ 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);
}
- query.add(db);
}
return query;
}
- /*
+ /*
* query protein sequences with number of jobs
*/
- public List<DataBase> readProteinByCounter(int minimalcounter) {
- query = new ArrayList<DataBase>();
+ 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 && 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<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 DataBase readJobLog(String jobid) {
+ public JobBean readJobLog(String jobid) {
if (jobid == null)
return null;
- StructureJobLog res = db.ReadJobLog(jobid);
+ 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;
- DataBase query = new DataBase();
- query.setLogInfo(res);
+ 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) {
+ 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)) {
sub.add(subStr);
return sub;
}
+
/*
* convert String date into long date (miliseconds since the epoch start)
*/
return 0;
}
long dateWorkSt = 0;
-
+
try {
dateWorkSt = formatter.parse(datInput).getTime();
} catch (ParseException e) {
*/
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);
+ 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, SimpleDateFormat sdf) {
if (dateToValidate == null || dateToValidate.equals("")) {
- System.out.println("Undefined date");
return false;
}
try {
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