X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraWriter.java;h=48bbda7a361cb1756511b72c3ba114a7cbaff9b9;hb=52edb573d0491d34b3951c18bced4c3e00a58d13;hp=c478d6829c756dc9327989bafefb2525b966b0f6;hpb=5b33e8d273539ac860bb2db853b47b5e7de0280e;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java
index c478d68..48bbda7 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 +7,8 @@ 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.PreparedStatement;
-import com.datastax.driver.core.BoundStatement;
 
+import compbio.engine.JpredJob;
 import compbio.engine.ProteoCachePropertyHelperManager;
 import compbio.util.PropertyHelper;
 
@@ -48,20 +46,25 @@ 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<FastaSequence> predictions) {
-		if (JobisNotInsterted(jobid)) {
+	public int FormQueryTables(JpredJob job) {
+		if (JobisNotInsterted(job.getJobID())) {
+			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 ('" + jobid + "','" + ip + "','" + startdate + "','" + enddate + "','" + statusFinal + "','" + statusEx
-					+ "','" + protein + "');";
+					+ " VALUES ('" + id + "','" + ip + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus
+					+ "','" + execstatus + "','" + protein + "');";
 			session.execute(com1);
 
-			String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + jobtime + ",'" + jobid + "','" + protein
-					+ "');";
+			String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
+					+ "','" + protein + "');";
 			session.execute(com2);
 
 			String allpredictions = "";
-			for (FastaSequence pred : predictions) {
+			List<FastaSequence> pr = job.getPredictions();
+			for (FastaSequence pred : pr) {
 				String predictionname = pred.getId();
 				String prediction = pred.getSequence().replaceAll("\n", "");
 				allpredictions += "'" + predictionname + "':'" + prediction + "',";
@@ -71,10 +74,10 @@ public class CassandraWriter {
 				final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
 			}
 
-			String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "';";
+			String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + job.getJobID() + "';";
 			ResultSet results2 = session.execute(check2);
 			if (results2.isExhausted()) {
-				String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + jobid + "',{"
+				String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + id + "',{"
 						+ final_prediction + "});";
 				session.execute(com3);
 			}
@@ -85,15 +88,15 @@ public class CassandraWriter {
 			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)
+				String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + job.getStartingDateStr()
 						+ "');";
 				session.execute(com);
 			}
-			String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + jobtime + ";";
+			String check4 = "SELECT * FROM JobDateInfo WHERE jobday = " + job.getStartingDate() + ";";
 			ResultSet results4 = session.execute(check4);
 			updateparameter = true;
 			int njobs = 1;
@@ -101,7 +104,7 @@ public class CassandraWriter {
 				Row r = results4.one();
 				njobs += r.getLong("Total");
 			}
-			String com = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + jobtime + "," + njobs + ");";
+			String com = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + job.getStartingDate() + "," + njobs + ");";
 			session.execute(com);
 
 			return 1;
@@ -113,26 +116,25 @@ 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<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,LOG, ArchiveLink) VALUES ('" + id + "','"
+					+ job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + log
+					+ "','" + archivepath + "');";
+			session.execute(com);
 
+			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 + "';");
+						+ p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 			}
 
+			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 + "';");
+						+ s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + id + "';");
 			}
 			return 1;
 		}