import com.datastax.driver.core.Row;
import com.datastax.driver.core.Session;
import com.datastax.driver.core.ResultSet;
+import compbio.engine.JobStatus;
public class CassandraReader {
private Session session;
public CassandraReader() {
Session inis = CassandraNativeConnector.getSession();
- setSession (inis);
+ setSession(inis);
}
public void setSession(Session s) {
* getting data from the db
*/
public DateBean ReadProteinData(long day, String date) {
- final long startTime = System.currentTimeMillis();
String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
System.out.println("Command: " + com);
ResultSet results = session.execute(com);
if (results.isExhausted())
return null;
- final long queryTime = System.currentTimeMillis();
List<Row> rows = results.all();
- System.out.println("Query time is " + (queryTime - startTime) + " msec");
DateBean res = new DateBean(date);
- int c = 0;
for (Row r : rows) {
res.setJobidAndSeq(r.getString("JobID"), r.getString("Protein"));
- ++c;
}
- final long endTime = System.currentTimeMillis();
- System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
return res;
}
+
+ /**
+ * getting data from the db
+ */
+ public DateBean ReadFailedJobs(long day, String date, JobStatus status) {
+ // FailLog (jobtime, JobID, ExecTime, ip, FinalStatus)
+ String com = "SELECT JobID FROM FailLog WHERE jobtime = " + day + " and FinalStatus = '" + status.name() + "';";
+ ResultSet results = session.execute(com);
+ if (results.isExhausted())
+ return null;
+ List<Row> rows = results.all();
+ DateBean res = new DateBean(date);
+ for (Row r : rows) {
+ String jobid = r.getString("JobID");
+ String com1 = "SELECT Protein FROM ProteinLog WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com1);
+ ResultSet results2 = session.execute(com1);
+ List<Row> jrows = results2.all();
+ if (1 == jrows.size()) {
+ String protein = jrows.get(0).getString("Protein");
+ res.setJobidAndSeq(jobid, protein);
+ }
+ }
+ return res;
+ }
+
/*
* getting data from the db JobDateInfo
*/
if (results.isExhausted())
return null;
Row therow = results.one();
- Total res = new Total(therow.getLong("Total"), therow.getLong("TotalOK"), therow.getLong("TotalStopped"),
+ Total res = new Total(therow.getLong("Total"), therow.getLong("TotalOK"), therow.getLong("TotalStopped"),
therow.getLong("TotalError"), therow.getLong("TotalTimeOut"));
if (!results.isExhausted()) {
- Date date = new Date (queryDate);
- log.warn("CassandraReader.ReadDateTable: date row for " + date.toString () + " ("+ queryDate + ") duplicated ");
+ Date date = new Date(queryDate);
+ log.warn("CassandraReader.ReadDateTable: date row for " + date.toString() + " (" + queryDate + ") duplicated ");
}
return res;
}
System.out.println("Query time is " + (queryTime - startTime) + " msec");
System.out.println(" rows analysed, " + rows.size());
List<ProteinBean> res = new ArrayList<ProteinBean>();
- ProteinBean structure = new ProteinBean(queryProtein, rows.get(0).getMap(
- "Predictions", String.class, String.class));
+ ProteinBean structure = new ProteinBean(queryProtein, rows.get(0).getMap("Predictions", String.class, String.class));
System.out.println("second size : " + rows.size());
int c = 0;
for (Row r : rows) {
- structure.setJobid(r.getString("JobID"));
+ structure.setJobid(r.getString("JobID"));
++c;
}
res.add(structure);
return res;
}
-
/*
* getting jobs by ip
*/
System.out.println(" rows analysed, " + rows.size());
int c = 0;
for (Row r : rows) {
- if (r.getString("FinalStatus").equals("OK")) {
+ if (r.getString("FinalStatus").equals("OK")) {
String date = r.getString("DataBegin");
- res.put(r.getString("JobID"), new String[] {date.substring(0, date.indexOf(":")), r.getString("Protein")});
+ res.put(r.getString("JobID"), new String[] { date.substring(0, date.indexOf(":")), r.getString("Protein") });
++c;
}
}
for (Row r : rows) {
String prot = r.getString("Protein");
if (prot.matches("(.*)" + queryProtein + "(.*)")) {
- ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
+ ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
structure.setJobid(r.getString("JobID"));
res.add(structure);
++c;
if (results1.isExhausted())
return null;
Row row1 = results1.one();
- JobBean res = new JobBean(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
- row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
+ JobBean res = new JobBean(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), row.getString("DataEnd"),
+ row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
System.out.println("Query time is " + (queryTime - startTime) + " msec");
final long endTime = System.currentTimeMillis();
System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");