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.JobBean;
+import compbio.cassandra.Total;
+import compbio.cassandra.TotalByCounterBean;
+import compbio.cassandra.TotalJobsStatisticBean;
+import compbio.cassandra.UserBean;
public class CassandraRequester {
private CassandraReader db = new CassandraReader();
if (null == date2) {
date1 = "2100/1/1";
}
- if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
+ if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
System.out.println("CassandraRequester.extractExecutionTime: wrong format for date1 " + date1 + "or date2 " + date2);
return null;
}
query.add(db);
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<DataBase> countJobs(String date1, String date2) {
+ public TotalJobsStatisticBean countJobs(String date1, String date2) {
if (null == date1) {
date1 = "1970/1/1";
}
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());
}
+ query.setWholeTotal(wholeTotal);
return query;
}
/*
* query: jobs and sequence at date
*/
- public List<DataBase> readJobByDay (String date) {
- if (null == date) {
- return null;
- }
+ public DateBean readJobByDay(String date) {
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;
- List<Pair<String, String>> res = db.ReadProteinData(day);
- if (res == null)
return null;
- query = new ArrayList<DataBase>();
- for (Pair<String, String> entry : res) {
- DataBase bean = new DataBase();
- bean.setDate(date);
- bean.setId(entry.getElement0());
- bean.setProt(entry.getElement1());
- query.add(bean);
- }
- return query;
+ return db.ReadProteinData(day, date);
}
-
- /*
+ /*
* query: protein sequence
- * */
+ */
public List<ProteinBean> readProteins(String protIn, String flag) {
List<ProteinBean> result;
- if (flag.equals("whole"))
+ if (flag.equals("whole"))
result = db.ReadWholeSequence(protIn);
- else
- result = db.ReadPartOfSequence(protIn);
+ else
+ result = db.ReadPartOfSequence(protIn);
if (result == null)
return null;
-
+
if (flag.equals("part")) {
for (ProteinBean entry : result) {
entry.setSubProt(CreateSubprot(entry.getSequence(), protIn));
}
- }
+ }
return result;
}
-
- /*
+ /*
* 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<DataBase> readIpByCounter(Integer minimalcounter) {
- query = new ArrayList<DataBase>();
+ public List<TotalByCounterBean> readIpByCounter(Integer minimalcounter) {
+ List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
Map<String, Integer> map = db.ReadIpByCounter();
if (minimalcounter == null)
minimalcounter = 0;
return null;
for (Map.Entry<String, Integer> entry : map.entrySet()) {
if (entry.getValue() > minimalcounter) {
- DataBase bean = new DataBase();
- bean.setTotalId(entry.getValue());
- bean.setIp(entry.getKey());
+ 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);
- if (res == null)
- return null;
- DataBase query = new DataBase();
- query.setLogInfo(res);
- return query;
+ return db.ReadJobLog(jobid);
}
-
-
+
/*
* query jobs by ipStructureJobLog
*/
- public List<DataBase> readIp(String ip) {
+ public UserBean readIp(String ip) {
if (ip == null)
return null;
- List<Pair<String, String>> res = db.ReadIpWithJobs(ip);
- if (res == null)
+ Map<String, String[]> res = db.ReadIpWithJobs(ip);
+ if (res == null)
return null;
- query = new ArrayList<DataBase>();
- for (Pair<String, String> entry : res) {
- DataBase bean = new DataBase();
- bean.setIp(ip);
- bean.setId(entry.getElement0());
- bean.setProt(entry.getElement1());
- query.add(bean);
- }
+ 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();
earlestDate = CassandraNativeConnector.getEarliestDateInDB();
return earlestDate;
}
-
+
}
git://source.jalview.org / proteocache.git / blobdiff