X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraWriter.java;h=b12f59e1f0c5e0596c53de05c855061d00656bfd;hb=5fb4cb600b34a9b33e1a96aae9d66cdd1c3201dc;hp=6ee62fd3add4b6421a5389a6c3ff9ea3d46bfbc3;hpb=c4aca39f2d4a49b34e7e0b564450d100f442f3bf;p=proteocache.git diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java index 6ee62fd..b12f59e 100644 --- a/datadb/compbio/cassandra/CassandraWriter.java +++ b/datadb/compbio/cassandra/CassandraWriter.java @@ -1,6 +1,5 @@ package compbio.cassandra; -import java.io.IOException; import java.util.List; import org.apache.log4j.Logger; @@ -8,9 +7,11 @@ 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; @@ -29,17 +30,36 @@ 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; @@ -48,62 +68,126 @@ public class CassandraWriter { /* * 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 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 (null != allpredictions) { - 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 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 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 MainParameters WHERE Name = 'TotalNumberOfJobs';"; - ResultSet results4 = session.execute(check4); - updateparameter = true; - int njobs = 1; if (!results4.isExhausted()) { Row r = results4.one(); - njobs += Integer.parseInt(r.getString("Value")); + 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 MainParameters " + "(Name, Value)" + " VALUES ('TotalNumberOfJobs','" + String.valueOf(njobs) + "');"; - session.execute(com); - return 1; } return 0; @@ -113,26 +197,49 @@ public class CassandraWriter { * 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 predictions, List 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 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 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; }