+ "ExecutionStatus ascii, Protein ascii, PRIMARY KEY(JobID));");
session.execute("CREATE TABLE IF NOT EXISTS ProteinData "
- + "(jobtime bigint, JobID ascii, Protein ascii, PRIMARY KEY(JobID));");
+ + "(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, alignment map<ascii,ascii>, "
+ + "(JobID ascii, Protein varchar, IP ascii, StartTime bigint, ExecTime int, FinalStatus ascii, alignment map<ascii,ascii>, "
+ "predictions map<ascii,ascii>, ArchiveLink varchar, LOG varchar, PRIMARY KEY(JobID));");
session.execute("CREATE TABLE IF NOT EXISTS JobDateInfo "
+ "(jobday bigint, Total bigint, Program varchar, Version varchar, PRIMARY KEY(jobday));");
session.execute("CREATE INDEX IF NOT EXISTS ProteinSeq ON ProteinRow (protein);");
- session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinData (jobtime);");
+ session.execute("CREATE INDEX IF NOT EXISTS ProteinIp ON ProteinLog (ip);");
+ // session.execute("CREATE INDEX IF NOT EXISTS JobDateStamp ON ProteinData (jobtime);");
}
public void Closing() {
*/
public Map<String, Integer> ReadProteinSequenceByCounter() {
final long startTime = System.currentTimeMillis();
- String com = "SELECT Protein FROM ProteinRow;";
+ String com = "SELECT Protein, JobID FROM ProteinRow;";
System.out.println("Command: " + com);
ResultSet results = session.execute(com);
if (results.isExhausted())
int c = 0;
for (Row r : rows) {
String protein = r.getString("Protein");
+ String id = r.getString("JobID");
+ System.out.println(id + ", " + protein);
if (res.containsKey(protein))
res.put(protein, res.get(protein) + 1);
else
package compbio.cassandra;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
+
import org.apache.log4j.Logger;
import com.datastax.driver.core.ResultSet;
public class CassandraRemover {
private Session session;
+ static SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
public CassandraRemover() {
}
/*
- * getting a record from CF for current jobId
+ * delete a record from CF for current jobId
*/
- public StructureJobLog ReadJobLog(String jobid) {
- final long startTime = System.currentTimeMillis();
- String com = "SELECT Protein, StartTime FROM ProteinLog WHERE JobID = '" + jobid + "';";
+ private void RemoveJob(String jobid, long date) {
+ String com0 = "DELETE FROM ProteinLog WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com0);
+ session.execute(com0);
+ String com1 = "DELETE FROM ProteinRow WHERE JobID = '" + jobid + "';";
+ System.out.println("Command: " + com1);
+ session.execute(com1);
+ String com2 = "DELETE FROM ProteinData WHERE JobID = '" + jobid + "' AND jobtime = " + date + ";";
+ System.out.println("Command: " + com2);
+ session.execute(com2);
+ String com3 = "UPDATE jpredarchive SET finalstatus = 'DELETED' WHERE JobID = '" + jobid + "' ;";
+ System.out.println("Command: " + com3);
+ session.execute(com3);
+ String com = "SELECT total FROM JobDateInfo WHERE jobday = " + date + ";";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ long njobs = results.one().getLong("total");
+ System.out.println("njobs: " + njobs);
+ String com4 = "INSERT INTO JobDateInfo " + "(jobday, Total)" + " VALUES (" + date + "," + (njobs -1) + ");";
+ System.out.println("Command: " + com4);
+ session.execute(com4);
+ System.out.println("Remove jobs: " + jobid);
+ }
+
+ public void RemoveJobById (String jobid) {
+ if (jobid == null)
+ return;
+ Long date = FindDate(jobid);
+ if (date == null)
+ return;
+ RemoveJob(jobid, date);
+ }
+
+ public void RemoveJobByDate (String date1, String date2) {
+ System.out.println("Start " + date1 + ", " + date2);
+ if (date1 == null || date2 == null)
+ return;
+ Long dateBegin = convertDate(date1);
+ Long dateEnd = convertDate(date2);
+ System.out.println("Date to long done!: ");
+ if (dateBegin == null || dateEnd == null)
+ return;
+ Calendar start = Calendar.getInstance();
+ start.setTime(new Date(dateBegin));
+ Calendar end = Calendar.getInstance();
+ end.setTime(new Date(dateEnd));
+ System.out.println("Date to cal done!: ");
+ for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+ String com = "SELECT JobID FROM ProteinData WHERE jobtime = " + date.getTime() + ";";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (!results.isExhausted()) {
+ List<Row> rows = results.all();
+ for (Row r : rows) {
+ String jobid = r.getString("JobID");
+ if (jobid != null)
+ RemoveJob(jobid, date.getTime());
+ }
+ }
+ }
+ }
+
+
+ public void RemoveJobByIp (String ip) {
+ if (ip == null)
+ return;
+ String com = "SELECT databegin, JobID FROM ProteinLog WHERE ip = '" + ip + "';";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (!results.isExhausted()) {
+ List<Row> rows = results.all();
+ for (Row r : rows) {
+ Long date = convertDate(r.getString("databegin"));
+ String jobid = r.getString("JobID");
+ if (date == null || jobid == null)
+ continue;
+ RemoveJob(jobid, date);
+ }
+ }
+ }
+
+ public void RemoveJobBySequence (String seq) {
+ if (seq == null)
+ return;
+ String com = "SELECT JobID FROM ProteinRow WHERE Protein = '" + seq + "';";
+ System.out.println("Command: " + com);
+ ResultSet results = session.execute(com);
+ if (!results.isExhausted()) {
+ List<Row> rows = results.all();
+ for (Row r : rows) {
+ String jobid = r.getString("JobID");
+ if (jobid == null)
+ continue;
+ Long date = FindDate(jobid);
+ if (date == null)
+ continue;
+ RemoveJob(jobid, date);
+ }
+ }
+ }
+
+ private Long FindDate(String jobid) {
+ String com = "SELECT databegin FROM ProteinLog WHERE JobID = '" + jobid + "';";
System.out.println("Command: " + com);
ResultSet results = session.execute(com);
if (results.isExhausted())
return null;
- final long queryTime = System.currentTimeMillis();
- Row row = results.one();
- String com1 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "' ALLOW FILTERING;";
- System.out.println("Command: " + com1);
- ResultSet results1 = session.execute(com1);
- if (results1.isExhausted())
- return null;
- Row row1 = results1.one();
- StructureJobLog res = new StructureJobLog(row.getString("Protein"), row.getString("JobID"), row.getString("DataBegin"),
- row.getString("DataEnd"), row.getString("ip"), row1.getMap("Predictions", String.class, String.class));
- 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");
- return res;
+ Long date = convertDate(results.one().getString("databegin"));
+ return date;
}
+ protected long convertDate (String d) {
+ try {
+ if (null != d) {
+ Date startdate = dateformatter.parse(d);
+ return startdate.getTime();
+ }
+ } catch (ParseException e) {
+ e.printStackTrace();
+ }
+ return 0L;
+ }
}
+ "','" + execstatus + "','" + protein + "');";
session.execute(com1);
- String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
- + "','" + protein + "');";
+ String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, ExecTime, Protein)" + " VALUES (" + job.getStartingDate() + ",'" + id
+ + "'," + job.getExecutionTime() + ",'" + protein + "');";
session.execute(com2);
String allpredictions = "";
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
+ String com = "INSERT INTO JpredArchive (JobID, Protein, IP, StartTime, ExecTime, FinalStatus, LOG, ArchiveLink) VALUES ('" + id + "','"
+ + job.getProtein() + "','" + job.getIP() + "'," + job.getStartingTime() + "," + job.getExecutionTime() + ",'" + job.getFinalStatus() + "','" + log
+ "','" + archivepath + "');";
session.execute(com);
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
+import compbio.cassandra.CassandraRemover;
import compbio.statistic.CassandraRequester;
/**
* @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
*/
protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
- CassandraRequester cr = new CassandraRequester();
+ CassandraRemover cr = new CassandraRemover();
String flagId = request.getParameter("byId");
String jobId = request.getParameter("id");
+ String flagDate = request.getParameter("byDate");
String date1 = request.getParameter("date1");
String date2 = request.getParameter("date2");
- if (flagId.equals("on"))
- request.setAttribute("result", cr.countJobs(date1, date2));
- System.out.println(flagId);
+ String flagIp = request.getParameter("byIp");
+ String ip = request.getParameter("ip");
+ String flagSeq = request.getParameter("bySequence");
+ String seq = request.getParameter("seq");
+ if (flagId != null)
+ cr.RemoveJobById(jobId);
+ if (flagDate != null)
+ cr.RemoveJobByDate(date1, date2);
+ if (flagIp != null)
+ cr.RemoveJobByIp(ip);
+ if (flagSeq != null)
+ cr.RemoveJobBySequence(seq);
// request.setAttribute("IdJob", id);
// RequestDispatcher rd = request.getRequestDispatcher("/ReportLogInfo.jsp");
// rd.forward(request, response);
</div>
<input type="checkbox" name="byDate" onclick="show(this, 'date');">records for the period of dates
<div id='date' class="row" style="visibility:hidden;">
- from <input type="text" name="data1" value = <%= currentdate%> style=" width : 145px;"/>
- to <input type="text" name="data2" value = <%= currentdate%> />
+ from <input type="text" name="date1" value = <%= currentdate%> style=" width : 145px;"/>
+ to <input type="text" name="date2" value = <%= currentdate%> />
</div>
<input type="checkbox" name="byIp" onclick="show(this, 'ip');">records with ip
<div id='ip' class="row" style="visibility:hidden;">
git://source.jalview.org / proteocache.git / commitdiff