X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraRemover.java;h=dbad0180234525c4b42ee94a43ce4c467aa65989;hb=5e76924c64903dd27013651144b1b7e2fcfc7c27;hp=d066d8201c54f098327842fd1264cd9d6e319bcb;hpb=d4eea7f5a8fea637ab742ce69c84a0f835266567;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraRemover.java b/datadb/compbio/cassandra/CassandraRemover.java
index d066d82..dbad018 100644
--- a/datadb/compbio/cassandra/CassandraRemover.java
+++ b/datadb/compbio/cassandra/CassandraRemover.java
@@ -1,51 +1,261 @@
 package compbio.cassandra;
 
-import org.apache.log4j.Logger;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.List;
 
 import com.datastax.driver.core.ResultSet;
 import com.datastax.driver.core.Row;
-import com.datastax.driver.core.Session;
+import compbio.cassandra.readers.CassandraReader;
 
-public class CassandraRemover {
-	private Session session;
-	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+/**
+ * The class removes jobs from the cassandra database. 4 different strategies
+ * are possiable: 1. remove 1 job with given job ID 2. remove jobs launched from
+ * an IP 3. remove jobs with particular protein sequence 4. remove jobs launched
+ * within a time range (date1, data2)
+ * 
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * @version 1.0
+ * @since Nov 2013
+ */
+public class CassandraRemover extends CassandraReader {
+	static SimpleDateFormat dateformatter = new SimpleDateFormat("yyyy/MM/dd");
 
-	public CassandraRemover() {
-		Session inis = CassandraNativeConnector.getSession();
-		setSession (inis);
+	/**
+	 * private method for real deleting one job
+	 * 
+	 * @param jobid
+	 *            job ID
+	 * @param date
+	 *            job execution date
+	 * 
+	 * @return nothing
+	 */
+	private int RemoveJob(String jobid, long date) {
+
+		if (date < 0L) {
+			log.error("CassandraRemover error: job " + jobid + " with date " + date
+					+ " can not be deleted in JobDateInfo. Daily statistics is inconsistent");
+			return 0;
+		}
+
+		String status = FindStatus(jobid);
+		String com1 = "DELETE FROM ProteinLog WHERE JobID = '" + jobid + "';";
+		System.out.println("Command: " + com1);
+		CassandraQuery(com1);
+
+		String com2 = "UPDATE jpredarchive SET finalstatus = 'DELETED'  WHERE JobID = '" + jobid + "' ;";
+		System.out.println("Command: " + com2);
+		CassandraQuery(com2);
+
+		String com3 = "SELECT * FROM JobDateInfo WHERE jobday = " + date + ";";
+		System.out.println("Command: " + com3);
+		ResultSet results = CassandraQuery(com3);
+		if (results.isExhausted()) {
+			log.error("CassandraRemover error: job " + jobid + " with date " + date
+					+ " can not be deleted in JobDateInfo. Daily statistics is inconsistent");
+			return 0;
+		}
+		Row row = results.one();
+		if (status.equals("OK")) {
+			long njobsOK = row.getLong("TotalOK") - 1;
+			String com4 = "DELETE FROM ProteinRow WHERE JobID = '" + jobid + "';";
+			System.out.println("Command: " + com4);
+			CassandraQuery(com4);
+
+			String com5 = "DELETE FROM ProteinData WHERE JobID = '" + jobid + "' AND jobtime = " + date + ";";
+			System.out.println("Command: " + com5);
+			CassandraQuery(com5);
+			UpdateJobDateInfo(date, "TotalOK", njobsOK);
+		} else {
+			String com6 = "DELETE FROM FailLog WHERE JobID = '" + jobid + "' AND jobtime = " + date + ";";
+			System.out.println("Command: " + com6);
+			CassandraQuery(com6);
+			if (status.equals("STOPPED")) {
+				long njobsStopped = row.getLong("TotalStopped") - 1;
+				UpdateJobDateInfo(date, "TotalStopped", njobsStopped);
+			} else if (status.equals("ERROR")) {
+				long njobsError = row.getLong("TotalError") - 1;
+				UpdateJobDateInfo(date, "TotalError", njobsError);
+			} else if (status.equals("TIMEDOUT")) {
+				long njobsTimeOut = row.getLong("TotalTimeOut") - 1;
+				UpdateJobDateInfo(date, "TotalTimeOut", njobsTimeOut);
+			}
+		}
+		System.out.println("Job " + jobid + " removed...");
+		return 1;
 	}
 
-	public void setSession(Session s) {
-		assert s != null;
-		session = s;
+	/**
+	 * update a pariticular column in the JobDateInfo table
+	 * 
+	 * @param jobid
+	 *            job ID
+	 * 
+	 * @return nothing
+	 * 
+	 */
+	private void UpdateJobDateInfo(long date, String ColumnName, long totalcol) {
+		String com = "UPDATE JobDateInfo SET " + ColumnName + " = " + totalcol + " WHERE jobday = " + date + ";";
+		CassandraQuery(com);
+	}
+
+	/**
+	 * external method for deleting job with given job ID (strategy 1)
+	 * 
+	 * @param jobid
+	 *            job ID
+	 * 
+	 * @return a number of deleted jobs
+	 * 
+	 */
+	public int RemoveJobById(String jobid) {
+		if (jobid == null)
+			return 0;
+		long date = FindJobDate(jobid);
+		return RemoveJob(jobid, date);
 	}
-	
-	/*
-	 * getting a record from CF for current jobId
+
+	/**
+	 * external method for deleting jobs within a time range (strategy 4)
+	 * 
+	 * @param date1
+	 *            starting date
+	 * 
+	 * @param date2
+	 *            ending date
+	 * 
+	 * @return a number of deleted jobs
+	 * 
 	 */
-	public StructureJobLog ReadJobLog(String jobid) {
-		final long startTime = System.currentTimeMillis();
-		String com = "SELECT Protein, StartTime FROM ProteinLog WHERE JobID = '" + jobid + "';";
+	public int RemoveJobByDate(String date1, String date2) {
+		if (date1 == null || date2 == null)
+			return 0;
+
+		int njobs = 0;
+		Long dateBegin = convertDate(date1);
+		Long dateEnd = convertDate(date2);
+		Calendar start = Calendar.getInstance();
+		start.setTime(new Date(dateBegin));
+		Calendar end = Calendar.getInstance();
+		end.setTime(new Date(dateEnd));
+
+		for (Date date = start.getTime(); !start.after(end); start.add(Calendar.DATE, 1), date = start.getTime()) {
+			String com1 = "SELECT JobID FROM ProteinData WHERE jobtime = " + date.getTime() + ";";
+			System.out.println("Command: " + com1);
+			ResultSet results = CassandraQuery(com1);
+			if (!results.isExhausted()) {
+				List<Row> rows = results.all();
+				for (Row r : rows) {
+					String jobid = r.getString("JobID");
+					if (jobid != null) {
+						njobs += RemoveJob(jobid, date.getTime());
+					}
+				}
+			}
+
+			String com2 = "SELECT JobID FROM FailLog WHERE jobtime = " + date.getTime() + ";";
+			ResultSet resultsfail = CassandraQuery(com2);
+			if (!resultsfail.isExhausted()) {
+				List<Row> rows = resultsfail.all();
+				for (Row r : rows) {
+					String jobid = r.getString("JobID");
+					if (jobid != null) {
+						njobs += RemoveJob(jobid, date.getTime());
+					}
+				}
+			}
+		}
+		return njobs;
+	}
+
+	/**
+	 * external method for deleting jobs launched from a particular IP (strategy
+	 * 2)
+	 * 
+	 * @param ip
+	 *            the IP
+	 * 
+	 * @return a number of deleted jobs
+	 * 
+	 */
+	public int RemoveJobByIp(String ip) {
+		int njobs = 0;
+		if (ip == null)
+			return 0;
+		String com = "SELECT databegin, JobID FROM ProteinLog WHERE ip = '" + ip + "';";
+		ResultSet results = CassandraQuery(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) {
+					njobs += RemoveJob(jobid, date);
+				}
+			}
+		}
+		return njobs;
+	}
+
+	/**
+	 * external method for deleting jobs with a protein sequence (strategy 3)
+	 * 
+	 * @param sequence
+	 *            the sequence
+	 * 
+	 * @return a number of deleted jobs
+	 * 
+	 */
+	public int RemoveJobBySequence(String sequence) {
+		int njobs = 0;
+		if (sequence == null)
+			return 0;
+		String com = "SELECT JobID FROM ProteinRow WHERE Protein = '" + sequence + "';";
+		ResultSet results = CassandraQuery(com);
+		if (!results.isExhausted()) {
+			List<Row> rows = results.all();
+			for (Row r : rows) {
+				String jobid = r.getString("JobID");
+				long date = FindJobDate(jobid);
+				njobs += RemoveJob(jobid, date);
+			}
+		}
+		return njobs;
+	}
+
+	private long FindJobDate(String jobid) {
+		String com = "SELECT databegin FROM ProteinLog WHERE JobID = '" + jobid + "';";
+		ResultSet results = CassandraQuery(com);
+		if (!results.isExhausted()) {
+			return convertDate(results.one().getString("databegin"));
+		}
+		return -1L;
+	}
+
+	private String FindStatus(String jobid) {
+		String com = "SELECT FinalStatus 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;
-	}
-	
-	
+		ResultSet results = CassandraQuery(com);
+		if (!results.isExhausted()) {
+			return results.one().getString("FinalStatus");
+		}
+		return "UNKNOWN";
+	}
+
+	protected long convertDate(String d) {
+		try {
+			if (null != d) {
+				Date startdate = dateformatter.parse(d);
+				return startdate.getTime();
+			}
+		} catch (ParseException e) {
+			e.printStackTrace();
+		}
+		return 0L;
+	}
 
 }