import java.util.List;
import org.apache.log4j.Logger;
+import org.springframework.dao.DataIntegrityViolationException;
import com.datastax.driver.core.Row;
import com.datastax.driver.core.Session;
import com.datastax.driver.core.ResultSet;
+import com.datastax.driver.core.exceptions.QueryExecutionException;
+import com.datastax.driver.core.exceptions.QueryValidationException;
import compbio.data.sequence.FastaSequence;
import compbio.engine.JpredJob;
session = s;
}
+ private ResultSet execute(String command) {
+ try {
+ ResultSet results = session.execute(command);
+ return results;
+ } catch (QueryExecutionException e) {
+ String mess = "CassandraWriter: query execution exception...";
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ } catch (QueryValidationException e) {
+ String mess = "CassandraWriter: query validation exception... Command: " + command;
+ System.out.println(mess);
+ log.error(mess);
+ log.error(e.getLocalizedMessage(), e.getCause());
+ return null;
+ }
+ }
+
public boolean JobisNotInsterted(String jobid) {
- ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
- if (results1.isExhausted()) {
+ ResultSet results = execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
+ if (null != results && results.isExhausted()) {
return true;
}
return false;
}
public boolean JobisNotArchived(String jobid) {
- ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
- if (results1.isExhausted()) {
+ ResultSet results = execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
+ if (null != results && results.isExhausted()) {
return true;
}
return false;
String com1 = "INSERT INTO ProteinLog (JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein) VALUES ('" + id
+ "','" + job.getIP() + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus + "','"
+ execstatus + "','" + protein + "');";
- session.execute(com1);
+ ResultSet insert = execute(com1);
+ if (null == insert) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into ProteinLog");
+ // return 0;
+ }
if (finalstatus.equals("OK")) {
String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate()
+ ",'" + id + "'," + job.getExecutionTime() + ",'" + protein + "');";
- session.execute(com2);
+ if (null == execute(com2)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into ProteinData");
+ // return 0;
+ }
String allpredictions = "";
List<FastaSequence> pr = job.getPredictions();
final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
}
- ResultSet results2 = session.execute("SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';");
- if (results2.isExhausted()) {
+ ResultSet results2 = execute("SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';");
+ if (null != results2 && results2.isExhausted()) {
String com3 = "INSERT INTO ProteinRow (Protein, JobID, Predictions) VALUES ('" + protein + "','" + id + "',{"
+ final_prediction + "});";
- session.execute(com3);
+ if (null == execute(com3)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into ProteinRow");
+ return 0;
+ }
}
} else {
String com5 = "INSERT INTO FailLog (jobtime, JobID, ExecTime, ip, FinalStatus) VALUES (" + job.getStartingDate() + ",'"
+ id + "'," + job.getExecutionTime() + ",'" + job.getIP() + "', '" + finalstatus + "');";
- session.execute(com5);
+ if (null == execute(com5)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into FailLog");
+ return 0;
+ }
}
// update Main parameters if the job is the earliest job so far
- ResultSet results3 = session.execute("SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';");
+ ResultSet results3 = execute("SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';");
+ if (null == results3) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't get results from MainParameters");
+ // return 0;
+ }
boolean updateparameter = true;
if (!results3.isExhausted()) {
Row r = results3.one();
updateparameter = false;
}
if (updateparameter) {
- session.execute("INSERT INTO MainParameters (Name, Value) VALUES ('EarliestJobDate','" + job.getStartingDate() + "');");
+ String com6 = "INSERT INTO MainParameters (Name, Value) VALUES ('EarliestJobDate','" + job.getStartingDate() + "');";
+ if (null == execute(com6)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into MainParameters");
+ return 0;
+ }
}
// update internal job counts (used by the Daily Statistics
// requests)
- //TODO I don't like the bit of code. There should not be so many counters...
+ // TODO I don't like the bit of code. There should not be so many
+ // counters...
int njobsTotal = 1;
int njobsOk = 0;
int njobsStop = 0;
njobsError = 1;
else if (finalstatus.equals("STOPPED"))
njobsStop = 1;
- ResultSet results4 = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";");
+ ResultSet results4 = execute("SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";");
+ if (null == results4) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't get data from JobDateInfo");
+ // return 0;
+ }
if (!results4.isExhausted()) {
Row r = results4.one();
njobsTotal += r.getLong("Total");
String com = "INSERT INTO JobDateInfo " + "(jobday, Total, TotalOK, TotalStopped, TotalError, TotalTimeOut)" + " VALUES ("
+ job.getStartingDate() + "," + njobsTotal + "," + njobsOk + "," + njobsStop + "," + njobsError + "," + njobsTimeOut
+ ");";
- session.execute(com);
+ if (null == execute(com)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into JobDateInfo");
+ // return 0;
+ }
return 1;
}
return 0;
+ ","
+ job.getExecutionTime()
+ ",'" + job.getFinalStatus() + "','" + job.getExecutionStatus() + "','" + log + "','" + archivepath + "');";
- session.execute(com);
+ if (null == execute(com)) {
+ System.out.println("CassandraWriter.ArchiveData: couldn't insert into JpredArchive");
+ }
List<FastaSequence> predictions = job.getPredictions();
for (FastaSequence p : predictions) {
- session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
- + p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
+ if (null == execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
+ + p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';")) {
+ System.out.println("CassandraWriter.ArchiveData: couldn't update data in JpredArchive");
+ }
}
List<FastaSequence> seqs = job.getAlignment();
+
for (FastaSequence s : seqs) {
- session.execute("UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
- + s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
+ String com2 = "UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
+ + s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';";
+ if (null == execute(com2)) {
+ System.out.println("CassandraWriter.ArchiveData: couldn't update data in JpredArchive");
+ }
}
return 1;
}
git://source.jalview.org / proteocache.git / blobdiff