From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 20 Jan 2014 16:03:46 +0000 (+0000)
Subject: Fix problem with new table column names: ProgrammeName -> ProgramName, Version -... 
X-Git-Url: http://source.jalview.org/gitweb/?p=proteocache.git;a=commitdiff_plain;h=5fb4cb600b34a9b33e1a96aae9d66cdd1c3201dc

Fix problem with new table column names: ProgrammeName -> ProgramName, Version -> ProgramVersion
---

diff --git a/datadb/compbio/beans/JobBean.java b/datadb/compbio/beans/JobBean.java
index 05c798a..ec1f030 100644
--- a/datadb/compbio/beans/JobBean.java
+++ b/datadb/compbio/beans/JobBean.java
@@ -11,14 +11,14 @@ public class JobBean implements PredictionIndex {
 	private String dateEnd;
 	private String sequence;
 	private String ip;
-	private String programmeName;
-	private String version;
+	private String ProgramName;
+	private String ProgramVersion;
 	private LinkedHashMap<String, String> predictions;
 
-	public JobBean(String seq, String id, String dateStart, String dateEnd, String ip, Map<String, String> pred, String prog, String version) {
+	public JobBean(String seq, String id, String dateStart, String dateEnd, String ip, Map<String, String> pred, String program, String version) {
 		this.sequence = seq;
-		this.programmeName = prog;
-		this.version = version;
+		this.ProgramName = program;
+		this.ProgramVersion = version;
 		this.jobid = id;
 		this.dateStart = dateStart;
 		this.dateEnd = dateEnd;
@@ -55,12 +55,12 @@ public class JobBean implements PredictionIndex {
 		return ip;
 	}
 	
-	public String getProgrammeName() {
-		return programmeName;
+	public String getProgramName() {
+		return ProgramName;
 	}
 	
-	public String getVersion() {
-		return version;
+	public String getProgramVersion() {
+		return ProgramVersion;
 	}
 
 	public Map<String, String> getPrediction() {
diff --git a/datadb/compbio/cassandra/CassandraNativeConnector.java b/datadb/compbio/cassandra/CassandraNativeConnector.java
index beb83c4..3360ad1 100644
--- a/datadb/compbio/cassandra/CassandraNativeConnector.java
+++ b/datadb/compbio/cassandra/CassandraNativeConnector.java
@@ -73,7 +73,7 @@ public class CassandraNativeConnector {
 
 		session.execute("CREATE TABLE IF NOT EXISTS ProteinLog "
 				+ "(JobID ascii, DataBegin ascii, DataEnd ascii, ip ascii, FinalStatus ascii, "
-				+ "ExecutionStatus ascii, Protein ascii, ProgrammeName ascii, Version ascii, PRIMARY KEY(JobID));");
+				+ "ExecutionStatus ascii, Protein ascii, ProgramName ascii, ProgramVersion ascii, PRIMARY KEY(JobID));");
 
 		session.execute("CREATE TABLE IF NOT EXISTS ProteinData "
 				+ "(jobtime bigint, JobID ascii, ExecTime int, Protein ascii, PRIMARY KEY(jobtime, JobID));");
@@ -83,7 +83,7 @@ public class CassandraNativeConnector {
 
 		session.execute("CREATE TABLE IF NOT EXISTS JpredArchive "
 				+ "(JobID ascii, Protein varchar, IP ascii, StartTime bigint, ExecTime int, FinalStatus ascii, ExecutionStatus ascii, alignment map<ascii,ascii>, "
-				+ "predictions map<ascii,ascii>, ArchiveLink varchar, LOG varchar, ProgrammeName ascii, Version ascii, PRIMARY KEY(JobID));");
+				+ "predictions map<ascii,ascii>, ArchiveLink varchar, LOG varchar, ProgramName ascii, ProgramVersion ascii, PRIMARY KEY(JobID));");
 
 		session.execute("CREATE TABLE IF NOT EXISTS JobDateInfo "
 				+ "(jobday bigint, Total bigint,  TotalOK bigint, TotalStopped bigint, TotalError bigint, TotalTimeOut bigint, Program varchar, Version varchar, PRIMARY KEY(jobday));");
@@ -91,13 +91,11 @@ public class CassandraNativeConnector {
 		String com = "CREATE TABLE IF NOT EXISTS Users "
 				+ "(name varchar, id bigint, email varchar, password varchar, organisation varchar, position varchar, signedtolist boolean, registrationdate bigint, PRIMARY KEY(id));";
 
-		
-	
-	//	session.execute("ALTER TABLE ProteinLog ADD ProgrammeName ascii;");
-	//	session.execute("ALTER TABLE ProteinLog ADD Version ascii;");
-	//	session.execute("ALTER TABLE JpredArchive ADD ProgrammeName ascii;");
-	//	session.execute("ALTER TABLE JpredArchive ADD Version ascii;");
-		
+		// session.execute("ALTER TABLE ProteinLog ADD ProgramName ascii;");
+		// session.execute("ALTER TABLE ProteinLog ADD ProgramVersion ascii;");
+		// session.execute("ALTER TABLE JpredArchive ADD ProgramName ascii;");
+		// session.execute("ALTER TABLE JpredArchive ADD ProgramVersion ascii;");
+
 		session.execute("CREATE INDEX IF NOT EXISTS ProteinSeq ON ProteinRow (protein);");
 		session.execute("CREATE INDEX IF NOT EXISTS ProteinIp ON ProteinLog (ip);");
 		session.execute("CREATE INDEX IF NOT EXISTS ON ProteinLog (ExecutionStatus);");
diff --git a/datadb/compbio/cassandra/CassandraNewTableWriter.java b/datadb/compbio/cassandra/CassandraNewTableWriter.java
index 6cb9c98..4ee10c8 100644
--- a/datadb/compbio/cassandra/CassandraNewTableWriter.java
+++ b/datadb/compbio/cassandra/CassandraNewTableWriter.java
@@ -45,7 +45,7 @@ public class CassandraNewTableWriter {
 		}
 		return false;
 	}
-	
+
 	/*
 	 * update programme name and version
 	 */
@@ -68,8 +68,10 @@ public class CassandraNewTableWriter {
 				List<Row> rows = results.all();
 				System.out.println(rows.size());
 				for (Row r : rows) {
-					session.execute("UPDATE  ProteinLog SET ProgrammeName = 'Jpred', Version = '3.0.1' WHERE JobID = '" + r.getString("JobID") + "';");
-					session.execute("UPDATE  JpredArchive SET ProgrammeName = 'Jpred', Version = '3.0.1' WHERE JobID = '" + r.getString("JobID") + "';");					
+					session.execute("UPDATE  ProteinLog SET ProgramName = 'Jpred', ProgramVersion = '3.0.1' WHERE JobID = '"
+							+ r.getString("JobID") + "';");
+					session.execute("UPDATE  JpredArchive SET ProgramName = 'Jpred', ProgramVersion = '3.0.1' WHERE JobID = '"
+							+ r.getString("JobID") + "';");
 				}
 			} catch (QueryExecutionException e) {
 				e.printStackTrace();
@@ -78,7 +80,6 @@ public class CassandraNewTableWriter {
 		System.out.println("Table ProteinLog filled: total time is " + (System.currentTimeMillis() - StartTime) + " msec");
 	}
 
-
 	/*
 	 * fill new table
 	 */
diff --git a/datadb/compbio/cassandra/CassandraReaderOld.java b/datadb/compbio/cassandra/CassandraReaderOld.java
index 62979ad..e08b39c 100644
--- a/datadb/compbio/cassandra/CassandraReaderOld.java
+++ b/datadb/compbio/cassandra/CassandraReaderOld.java
@@ -314,7 +314,8 @@ public class CassandraReaderOld {
 			return null;
 		Row row1 = results1.one();
 		JobBean res = new JobBean(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), row.getString("DataEnd"),
-				row.getString("ip"), row1.getMap("Predictions", String.class, String.class), row.getString("ProgrammeName"), row.getString("Version"));
+				row.getString("ip"), row1.getMap("Predictions", String.class, String.class), row.getString("ProgramName"),
+				row.getString("ProgramVersion"));
 		System.out.println("Query time is " + (queryTime - startTime) + " msec");
 		final long endTime = System.currentTimeMillis();
 		System.out.println(" rows analysed, execution time is " + (endTime - startTime) + " msec");
diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java
index 05a03f0..b12f59e 100644
--- a/datadb/compbio/cassandra/CassandraWriter.java
+++ b/datadb/compbio/cassandra/CassandraWriter.java
@@ -74,12 +74,20 @@ public class CassandraWriter {
 			String protein = job.getProtein();
 			String finalstatus = job.getFinalStatus();
 			String execstatus = job.getExecutionStatus();
-			String programmeName = job.getProgrammeName();
-			String version = job.getVersion();
+			String ProgramName = job.getProgramName();
+			String ProgramVersion = job.getProgramVersion();
 
-			String com1 = "INSERT INTO ProteinLog (JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein, ProgrammeName, Version) VALUES ('" + id
-					+ "','" + job.getIP() + "','" + job.getStartingTimeStr() + "','" + job.getEndTimeStr() + "','" + finalstatus + "','"
-					+ execstatus + "','" + protein + "','" + programmeName + "','" + version + "');";
+			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");
@@ -193,7 +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, ProgrammeName, Version) VALUES ('"
+			String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, ExecutionStatus, LOG, ArchiveLink, ProgramName, ProgramVersion) VALUES ('"
 					+ id
 					+ "','"
 					+ job.getProtein()
@@ -203,7 +211,16 @@ public class CassandraWriter {
 					+ job.getStartingTime()
 					+ ","
 					+ job.getExecutionTime()
-					+ ",'" + job.getFinalStatus() + "','" + job.getExecutionStatus() + "','" + log + "','" + archivepath + "','" + job.getProgrammeName() + "','" + job.getVersion() + "');";
+					+ ",'"
+					+ job.getFinalStatus()
+					+ "','"
+					+ job.getExecutionStatus()
+					+ "','"
+					+ log
+					+ "','"
+					+ archivepath
+					+ "','"
+					+ job.getProgramName() + "','" + job.getProgramVersion() + "');";
 			if (null == execute(com)) {
 				System.out.println("CassandraWriter.ArchiveData: couldn't insert into JpredArchive");
 			}
diff --git a/datadb/compbio/cassandra/JpredParserHTTP.java b/datadb/compbio/cassandra/JpredParserHTTP.java
index 1d888e4..825689e 100644
--- a/datadb/compbio/cassandra/JpredParserHTTP.java
+++ b/datadb/compbio/cassandra/JpredParserHTTP.java
@@ -115,7 +115,7 @@ public class JpredParserHTTP implements JpredParser {
 		if (null != (out = buffer.readLine()) && (out.contains("version"))) {
 			Matcher matcher = Pattern.compile("((\\d|\\.)+)").matcher(out);
 			if (matcher.find())
-				job.setVersion(matcher.group(0));
+				job.setProgramVersion(matcher.group(0));
 		}
 		while (null != (line = buffer.readLine())) {
 			out += line;		
@@ -131,6 +131,7 @@ public class JpredParserHTTP implements JpredParser {
 		boolean LogfileExists = false;
 		JpredJob job = new JpredJob(jobinfo[jobinfo.length - 1], jobinfo[0], jobinfo[1]);
 		job.setIP(jobinfo[2]);
+		job.setProgramName("Jpred");
 		Date currDate = new Date();
 		String maindir = dirprefix + "/" + job.getJobID() + "/";
 
@@ -158,7 +159,6 @@ public class JpredParserHTTP implements JpredParser {
 			}
 			if (199 < httpConnection_logurl.getResponseCode() && httpConnection_logurl.getResponseCode() < 300) {
 				LogfileExists = true;
-				job.setProgrammeName("Jpred");
 				job.setLog(parseLogFile(logurl.openStream(), job));
 			} else {
 				// The job has not been started at all...
diff --git a/datadb/compbio/cassandra/readers/JobReader.java b/datadb/compbio/cassandra/readers/JobReader.java
index c632542..a525a56 100644
--- a/datadb/compbio/cassandra/readers/JobReader.java
+++ b/datadb/compbio/cassandra/readers/JobReader.java
@@ -29,7 +29,8 @@ public class JobReader extends CassandraReader {
 			return null;
 		Row row1 = results1.one();
 		JobBean res = new JobBean(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"), row.getString("DataEnd"),
-				row.getString("ip"), row1.getMap("Predictions", String.class, String.class), row.getString("ProgrammeName"), row.getString("Version"));
+				row.getString("ip"), row1.getMap("Predictions", String.class, String.class), row.getString("ProgramName"),
+				row.getString("ProgramVersion"));
 		return res;
 	}
 }
diff --git a/engine/compbio/engine/Job.java b/engine/compbio/engine/Job.java
index 162a246..31309e5 100644
--- a/engine/compbio/engine/Job.java
+++ b/engine/compbio/engine/Job.java
@@ -10,8 +10,8 @@ public class Job {
 	private String FinalStatus;
 	private String IP;
 	private String Email;
-	private String programmeName;
-	private String version;
+	private String ProgramName;
+	private String ProgramVersion;
 
 	private String StartingDateStr;
 	private long StartingDate;
@@ -29,8 +29,8 @@ public class Job {
 		ExecutionStatus = "OK";
 		FinalStatus = "OK";
 		jobid = "";
-		programmeName ="";
-		version = "";
+		ProgramName ="";
+		ProgramVersion = "";
 
 		StartingDateStr = "1970/1/1";
 		StartingTimeStr = "1970/1/1:0:0:0";
@@ -172,19 +172,19 @@ public class Job {
 		return jobid;
 	}
 	
-	public void setProgrammeName(String prog) {
-		this.programmeName = prog;
+	public void setProgramName(String prog) {
+		this.ProgramName = prog;
 	}
 
-	public String getProgrammeName() {
-		return programmeName;
+	public String getProgramName() {
+		return ProgramName;
 	}
 	
-	public void setVersion(String ver) {
-		this.version = ver;
+	public void setProgramVersion(String ver) {
+		this.ProgramVersion = ver;
 	}
 
-	public String getVersion() {
-		return version;
+	public String getProgramVersion() {
+		return ProgramVersion;
 	}
 }
diff --git a/webapp/view/reports/Job.jsp b/webapp/view/reports/Job.jsp
index dd0b1dd..2dd4e82 100644
--- a/webapp/view/reports/Job.jsp
+++ b/webapp/view/reports/Job.jsp
@@ -21,8 +21,10 @@
 		<div class="panel-body">
 			<p>Start timestamp : ${result.dateStart}</p>
 			<p>End timestamp : ${result.dateEnd}</p>
-			<p>Run : ${result.programmeName} server</p>
-			<p>Version : ${result.version}</p>
+			<c:if test='${jobarchive != null}'>
+				<p>Program name : ${result.programName}</p>
+				<p>Program version : ${result.programVersion}</p>
+			</c:if>
 <sec:authorize access="hasRole('ROLE_ADMIN')">
 			<p>IP: <a title="Click to view other jobs" href="${ip_query}?ip=${result.ip}">${result.ip}</a></p>
 </sec:authorize>