From 8f8d263a3c136f5cffab2fdf57f1c44b10d62ec2 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Thu, 9 Jan 2014 15:53:12 +0000 Subject: [PATCH] Add exceptions and internal checks for Cassandra requests --- datadb/compbio/cassandra/CassandraWriter.java | 99 ++++++++++++++++++++----- 1 file changed, 79 insertions(+), 20 deletions(-) diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java index 15e30e8..f20f457 100644 --- a/datadb/compbio/cassandra/CassandraWriter.java +++ b/datadb/compbio/cassandra/CassandraWriter.java @@ -3,10 +3,13 @@ package compbio.cassandra; 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; @@ -28,17 +31,36 @@ public class CassandraWriter { 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; @@ -57,11 +79,18 @@ public class CassandraWriter { 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 pr = job.getPredictions(); @@ -75,20 +104,30 @@ public class CassandraWriter { 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(); @@ -96,12 +135,17 @@ public class CassandraWriter { 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; @@ -115,7 +159,11 @@ public class CassandraWriter { 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"); @@ -127,7 +175,10 @@ public class CassandraWriter { 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; @@ -152,17 +203,25 @@ public class CassandraWriter { + "," + 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 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 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; } -- 1.7.10.2