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.ProteinBean;
import compbio.cassandra.CassandraNativeConnector;
import compbio.cassandra.CassandraReader;
+import compbio.cassandra.DataBase;
import compbio.cassandra.Pair;
import compbio.cassandra.JobBean;
import compbio.cassandra.Total;
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 ArrayList<DataBase> query;
private static long currentDate = 0;
private static long earlestDate = 0;
private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
/*
* query: execution time for the period from date1 till date2
-
+ */
public List<DataBase> extractExecutionTime(String date1, String date2) {
if (null == date1) {
date1 = "1970/1/1";
db.setTimeTotalExec(totalTime);
query.add(db);
return query;
-<<<<<<< HEAD
- }*/
-
+ }
+
/*
* query: total number of jobs for the period from date1 till date2
*/
/*
* 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;
long day = DateParsing(date, formatDDMMYY);
if (day < earlestDate || day > currentDate)
return null;
- return db.ReadProteinData(day, date);
+
+ 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);
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
SimpleDateFormat datformat = new SimpleDateFormat("dd/MM/yyyy");
return datformat.format(new Date(inDate));
}
-
- // convert long to date in string format
- private static String DateFormatYYMMDD(long inDate) {
- SimpleDateFormat datformat = new SimpleDateFormat("yyyy/MM/dd");
- return datformat.format(new Date(inDate));
- }
/*
* set earlest date and current dates. earlestDate is static and should be
earlestDate = CassandraNativeConnector.getEarliestDateInDB();
return earlestDate;
}
-
- /*
- * find the earliest date in the database in String format
- */
- public String earliestDateString() {
- earlestDate = CassandraNativeConnector.getEarliestDateInDB();
- return DateFormatYYMMDD(earlestDate);
- }
-
+
}