X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraWriter.java;h=b12f59e1f0c5e0596c53de05c855061d00656bfd;hb=5fb4cb600b34a9b33e1a96aae9d66cdd1c3201dc;hp=15e30e888cb1d2fa4d4b547af1b487e447d1321c;hpb=bf5e83e2959a3b88963cb9a8da68fc50ce4329af;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java
index 15e30e8..b12f59e 100644
--- a/datadb/compbio/cassandra/CassandraWriter.java
+++ b/datadb/compbio/cassandra/CassandraWriter.java
@@ -7,6 +7,8 @@ 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.exceptions.QueryExecutionException;
+import com.datastax.driver.core.exceptions.QueryValidationException;
 
 import compbio.data.sequence.FastaSequence;
 import compbio.engine.JpredJob;
@@ -28,17 +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;
@@ -53,15 +74,32 @@ public class CassandraWriter {
 			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) VALUES ('" + id
-					+ "','" + job.getIP() + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus + "','"
-					+ execstatus + "','" + protein + "');";
-			session.execute(com1);
+			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;
+			}
 			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();
@@ -75,20 +113,30 @@ 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 +144,17 @@ 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 +168,11 @@ 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 +184,10 @@ 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;
@@ -141,7 +201,7 @@ public class CassandraWriter {
 		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 ('"
+			String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, ExecutionStatus, LOG, ArchiveLink, ProgramName, ProgramVersion) VALUES ('"
 					+ id
 					+ "','"
 					+ job.getProtein()
@@ -151,18 +211,35 @@ public class CassandraWriter {
 					+ job.getStartingTime()
 					+ ","
 					+ job.getExecutionTime()
-					+ ",'" + job.getFinalStatus() + "','" + job.getExecutionStatus() + "','" + log + "','" + archivepath + "');";
-			session.execute(com);
+					+ ",'"
+					+ 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 = '" + 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;
 		}