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;
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() {
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));");
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));");
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);");
}
return false;
}
-
+
/*
* update programme name and version
*/
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();
System.out.println("Table ProteinLog filled: total time is " + (System.currentTimeMillis() - StartTime) + " msec");
}
-
/*
* fill new table
*/
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");
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");
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()
+ 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");
}
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;
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() + "/";
}
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...
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;
}
}
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;
ExecutionStatus = "OK";
FinalStatus = "OK";
jobid = "";
- programmeName ="";
- version = "";
+ ProgramName ="";
+ ProgramVersion = "";
StartingDateStr = "1970/1/1";
StartingTimeStr = "1970/1/1:0:0:0";
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;
}
}
<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>