package compbio.cassandra;
-import java.io.IOException;
import java.util.List;
import org.apache.log4j.Logger;
import com.datastax.driver.core.Row;
import com.datastax.driver.core.Session;
import com.datastax.driver.core.ResultSet;
-import com.datastax.driver.core.PreparedStatement;
-import com.datastax.driver.core.BoundStatement;
+import com.datastax.driver.core.exceptions.QueryExecutionException;
+import com.datastax.driver.core.exceptions.QueryValidationException;
+import compbio.data.sequence.FastaSequence;
+import compbio.engine.JpredJob;
import compbio.engine.ProteoCachePropertyHelperManager;
import compbio.util.PropertyHelper;
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;
/*
* inserting data into the tables for queries
*/
- public int FormQueryTables(long jobtime, String startdate, String enddate, String ip, String jobid, String statusEx,
- String statusFinal, String protein, List<FastaSequence> predictions) {
- if (JobisNotInsterted(jobid)) {
- String com1 = "INSERT INTO ProteinLog " + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)"
- + " VALUES ('" + jobid + "','" + ip + "','" + startdate + "','" + enddate + "','" + statusFinal + "','" + statusEx
- + "','" + protein + "');";
- session.execute(com1);
-
- String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + jobtime + ",'" + jobid + "','" + protein
- + "');";
- session.execute(com2);
-
- String allpredictions = "";
- for (FastaSequence pred : predictions) {
- String predictionname = pred.getId();
- String prediction = pred.getSequence().replaceAll("\n", "");
- allpredictions += "'" + predictionname + "':'" + prediction + "',";
+ public int FormQueryTables(JpredJob job) {
+ if (JobisNotInsterted(job.getJobID())) {
+ String id = job.getJobID();
+ String protein = job.getProtein();
+ String finalstatus = job.getFinalStatus();
+ String execstatus = job.getExecutionStatus();
+ String ProgramName = job.getProgramName();
+ String ProgramVersion = job.getProgramVersion();
+
+ String com1 = "INSERT INTO ProteinLog (JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein, ProgramName, ProgramVersion) VALUES ('"
+ + id
+ + "','"
+ + job.getIP()
+ + "','"
+ + job.getStartingTimeStr()
+ + "','"
+ + job.getEndTimeStr()
+ + "','"
+ + finalstatus
+ + "','" + execstatus + "','" + protein + "','" + ProgramName + "','" + ProgramVersion + "');";
+ ResultSet insert = execute(com1);
+ if (null == insert) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into ProteinLog");
+ // return 0;
}
- String final_prediction = "";
- if (!allpredictions.equals("")) {
- final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
+ if (finalstatus.equals("OK")) {
+ String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate()
+ + ",'" + id + "'," + job.getExecutionTime() + ",'" + protein + "');";
+ if (null == execute(com2)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into ProteinData");
+ // return 0;
+ }
+
+ String allpredictions = "";
+ List<FastaSequence> pr = job.getPredictions();
+ for (FastaSequence pred : pr) {
+ String predictionname = pred.getId();
+ String prediction = pred.getSequence().replaceAll("\n", "");
+ allpredictions += "'" + predictionname + "':'" + prediction + "',";
+ }
+ String final_prediction = "";
+ if (!allpredictions.equals("")) {
+ final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
+ }
+
+ 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 + "});";
+ 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 + "');";
+ if (null == execute(com5)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into FailLog");
+ return 0;
+ }
}
- String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "';";
- ResultSet results2 = session.execute(check2);
- if (results2.isExhausted()) {
- String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + jobid + "',{"
- + final_prediction + "});";
- session.execute(com3);
+ // update Main parameters if the job is the earliest job so far
+ 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;
}
-
- // update some internal query tables
- String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
- ResultSet results3 = session.execute(check3);
boolean updateparameter = true;
if (!results3.isExhausted()) {
Row r = results3.one();
- if (jobtime >= Long.parseLong(r.getString("Value")))
+ if (job.getStartingDate() >= Long.parseLong(r.getString("Value")))
updateparameter = false;
}
if (updateparameter) {
- String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + String.valueOf(jobtime)
- + "');";
- session.execute(com);
+ 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...
+ 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 = execute("SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";");
+ if (null == results4) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't get data from JobDateInfo");
+ // return 0;
}
- String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + jobtime + ";";
- ResultSet results4 = session.execute(check4);
- updateparameter = true;
- int njobs = 1;
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() + "," + njobsTotal + "," + njobsOk + "," + njobsStop + "," + njobsError + "," + njobsTimeOut
+ + ");";
+ if (null == execute(com)) {
+ System.out.println("CassandraWriter.FormQueryTables: couldn't insert into JobDateInfo");
+ // return 0;
}
- String com = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + jobtime + "," + njobs + ");";
- session.execute(com);
-
return 1;
}
return 0;
* insert data from a real Jpred job: timing+IP, Execution Status, Final
* status, protein sequence, predictions, alignment, LOG and tar.gz files
*/
- public int ArchiveData(long starttime, long exectime, String ip, String jobid, String statusEx, String statusFinal, String protein,
- List<FastaSequence> predictions, List<FastaSequence> seqs, String LogFile, String archivepath) {
- if (JobisNotArchived(jobid)) {
- String log = LogFile.replaceAll("'", "");
- session.execute("INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime,LOG) VALUES ('" + jobid + "','" + protein
- + "','" + ip + "'," + starttime + "," + exectime + ",'" + log + "');");
- if (false) {
- PreparedStatement statement = session.prepare("INSERT INTO JpredArchive (JobID, archive) VALUES (?,?);");
- BoundStatement boundStatement = new BoundStatement(statement);
- session.execute(boundStatement.bind(jobid, archivepath));
+ public int ArchiveData(JpredJob job, String archivepath) {
+ 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, ProgramName, ProgramVersion) VALUES ('"
+ + id
+ + "','"
+ + job.getProtein()
+ + "','"
+ + job.getIP()
+ + "',"
+ + job.getStartingTime()
+ + ","
+ + job.getExecutionTime()
+ + ",'"
+ + job.getFinalStatus()
+ + "','"
+ + job.getExecutionStatus()
+ + "','"
+ + log
+ + "','"
+ + archivepath
+ + "','"
+ + job.getProgramName() + "','" + job.getProgramVersion() + "');";
+ 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 = '" + jobid + "';");
+ 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 = '" + jobid + "';");
+ 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