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.DateBean;
import compbio.cassandra.ProteinBean;
import compbio.cassandra.CassandraNativeConnector;
-import compbio.cassandra.CassandraReader;
+import compbio.cassandra.CassandraReaderOld;
import compbio.cassandra.DataBase;
import compbio.cassandra.Pair;
import compbio.cassandra.JobBean;
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 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)) {
+ 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 TotalJobsStatisticBean countJobs(String date1, String date2) {
- if (null == date1) {
+ /* if (null == date1) {
date1 = "1970/1/1";
}
if (null == date2) {
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)
+/* if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
return null;
if (dateStart < earlestDate)
dateStart = earlestDate;
if (dateEnd > currentDate)
- dateStart = 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);
+ 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)
/*
* query: jobs and sequence at date
*/
- public DateBean readJobByDay (String 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;
- return db.ReadProteinData(day, date);
+ return null;
+
+ if (status == JobStatus.OK) {
+ return db.ReadProteinData(day, date);
+ }
+ return db.ReadFailedJobs(day, date, status);
}
-
- /*
+ /*
* query: protein sequence
- **/
- public List<ProteinBean> readProteins(String protIn, String flag) {
+ */
+ public List<ProteinBean> readProteins(String protIn, String searchtype) {
List<ProteinBean> result;
- if (flag.equals("whole"))
+ if (searchtype.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")) {
+
+ 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) {
+ public List<TotalByCounterBean> readProteinByCounter(int minimalcounter) {
List<TotalByCounterBean> query = new ArrayList<TotalByCounterBean>();
Map<String, Integer> map = db.ReadProteinSequenceByCounter();
if (map == null)
}
return query;
}
-
- /*
+
+ /*
* query ip with number of jobs
*/
public List<TotalByCounterBean> readIpByCounter(Integer minimalcounter) {
}
return query;
}
+
/*
* query jobs log info
*/
return null;
return db.ReadJobLog(jobid);
}
-
-
+
/*
* query jobs by ipStructureJobLog
*/
if (ip == null)
return null;
Map<String, String[]> res = db.ReadIpWithJobs(ip);
- if (res == null)
+ 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) {
+ 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