package compbio.cassandra;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
import java.util.List;
import org.apache.log4j.Logger;
*/
public int FormQueryTables(JpredJob job) {
if (JobisNotInsterted(job.getJobID())) {
- int njobsOk = 0;
- int njobsStop = 0;
- int njobsError = 0;
- int njobsTimeOut = 0;
String id = job.getJobID();
- String ip = job.getIP();
String protein = job.getProtein();
String finalstatus = job.getFinalStatus();
String execstatus = job.getExecutionStatus();
- String com1 = "INSERT INTO ProteinLog " + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)"
- + " VALUES ('" + id + "','" + ip + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus
- + "','" + execstatus + "','" + protein + "');";
+
+ 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);
- if (execstatus.equals("OK")) {
- String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
- + "'," + job.getExecutionTime() + ",'" + protein + "');";
+ if (finalstatus.equals("OK")) {
+ String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate()
+ + ",'" + id + "'," + job.getExecutionTime() + ",'" + protein + "');";
session.execute(com2);
-
+
String allpredictions = "";
List<FastaSequence> pr = job.getPredictions();
for (FastaSequence pred : pr) {
final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
}
- String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';";
- ResultSet results2 = session.execute(check2);
+ ResultSet results2 = session.execute("SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';");
if (results2.isExhausted()) {
- String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + id + "',{"
+ String com3 = "INSERT INTO ProteinRow (Protein, JobID, Predictions) VALUES ('" + protein + "','" + id + "',{"
+ final_prediction + "});";
session.execute(com3);
}
- njobsOk = 1;
} else {
- String com5 = "INSERT INTO FailLog " + "(jobtime, JobID, ExecTime, ip, FinalStatus)" + " VALUES ("
- + job.getStartingDate() + ",'" + id
- + "'," + job.getExecutionTime() + ",'" + ip + "', '" + finalstatus + "');";
+ String com5 = "INSERT INTO FailLog (jobtime, JobID, ExecTime, ip, FinalStatus) VALUES (" + job.getStartingDate() + ",'"
+ + id + "'," + job.getExecutionTime() + ",'" + job.getIP() + "', '" + finalstatus + "');";
session.execute(com5);
- if (finalstatus.equals("TIMEDOUT"))
- njobsTimeOut = 1;
- else if (finalstatus.equals("JPREDERROR"))
- njobsError = 1;
- else if (finalstatus.equals("STOPPED"))
- njobsStop = 1;
}
- // update some internal query tables
- String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
- ResultSet results3 = session.execute(check3);
+
+ // update Main parameters if the job is the earliest job so far
+ ResultSet results3 = session.execute("SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';");
boolean updateparameter = true;
if (!results3.isExhausted()) {
- Row r = results3.one();
+ Row r = results3.one();
if (job.getStartingDate() >= Long.parseLong(r.getString("Value")))
updateparameter = false;
}
if (updateparameter) {
- String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + job.getStartingDate()
- + "');";
- session.execute(com);
+ session.execute("INSERT INTO MainParameters (Name, Value) VALUES ('EarliestJobDate','" + job.getStartingDate() + "');");
}
- String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";";
- ResultSet results4 = session.execute(check4);
- updateparameter = true;
- int njobs = 1;
+
+ // 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...
+ int njobsTotal = 1;
+ int njobsOk = 0;
+ int njobsStop = 0;
+ int njobsError = 0;
+ int njobsTimeOut = 0;
+ if (finalstatus.equals("OK"))
+ njobsOk = 1;
+ else if (finalstatus.equals("TIMEDOUT"))
+ njobsTimeOut = 1;
+ else if (finalstatus.equals("JPREDERROR"))
+ njobsError = 1;
+ else if (finalstatus.equals("STOPPED"))
+ njobsStop = 1;
+ ResultSet results4 = session.execute("SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";");
if (!results4.isExhausted()) {
Row r = results4.one();
- njobs += r.getLong("Total");
+ njobsTotal += r.getLong("Total");
njobsOk += r.getLong("TotalOK");
njobsError += r.getLong("TotalError");
njobsStop += r.getLong("TotalStopped");
njobsTimeOut += r.getLong("TotalTimeOut");
}
String com = "INSERT INTO JobDateInfo " + "(jobday, Total, TotalOK, TotalStopped, TotalError, TotalTimeOut)" + " VALUES ("
- + job.getStartingDate() + "," + njobs + "," + njobsOk + "," + njobsStop + "," + njobsError + "," + njobsTimeOut + ");";
+ + job.getStartingDate() + "," + njobsTotal + "," + njobsOk + "," + njobsStop + "," + njobsError + "," + njobsTimeOut
+ + ");";
session.execute(com);
return 1;
}
if (JobisNotArchived(job.getJobID())) {
String id = job.getJobID();
String log = job.getLog().replaceAll("'", "");
- String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, ExecutionStatus, LOG, ArchiveLink) VALUES ('" + id + "','"
- + job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + job.getFinalStatus() + "','"
- + job.getExecutionStatus() + "','" + log + "','" + archivepath + "');";
+ String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, ExecutionStatus, LOG, ArchiveLink) VALUES ('"
+ + id
+ + "','"
+ + job.getProtein()
+ + "','"
+ + job.getIP()
+ + "',"
+ + job.getStartingTime()
+ + ","
+ + job.getExecutionTime()
+ + ",'" + job.getFinalStatus() + "','" + job.getExecutionStatus() + "','" + log + "','" + archivepath + "');";
session.execute(com);
List<FastaSequence> predictions = job.getPredictions();
for (FastaSequence p : predictions) {
git://source.jalview.org / proteocache.git / blobdiff