X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=datadb%2Fcompbio%2Fcassandra%2FCassandraWriter.java;fp=datadb%2Fcompbio%2Fcassandra%2FCassandraWriter.java;h=6ee62fd3add4b6421a5389a6c3ff9ea3d46bfbc3;hb=c4aca39f2d4a49b34e7e0b564450d100f442f3bf;hp=0000000000000000000000000000000000000000;hpb=53e189c6ddaf7833fd8d8d7a51606d3e020e2eaf;p=proteocache.git

diff --git a/datadb/compbio/cassandra/CassandraWriter.java b/datadb/compbio/cassandra/CassandraWriter.java
new file mode 100644
index 0000000..6ee62fd
--- /dev/null
+++ b/datadb/compbio/cassandra/CassandraWriter.java
@@ -0,0 +1,142 @@
+package compbio.cassandra;
+
+import java.io.IOException;
+import java.util.List;
+
+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.ProteoCachePropertyHelperManager;
+import compbio.util.PropertyHelper;
+
+public class CassandraWriter {
+	private Session session;
+	private static final PropertyHelper ph = ProteoCachePropertyHelperManager.getPropertyHelper();
+	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+
+	CassandraWriter() {
+		Session inis = CassandraNativeConnector.getSession();
+		setSession(inis);
+	}
+
+	public void setSession(Session s) {
+		assert s != null;
+		session = s;
+	}
+
+	public boolean JobisNotInsterted(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM ProteinLog WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	public boolean JobisNotArchived(String jobid) {
+		ResultSet results1 = session.execute("SELECT * FROM JpredArchive WHERE JobID = '" + jobid + "';");
+		if (results1.isExhausted()) {
+			return true;
+		}
+		return false;
+	}
+
+	/*
+	 * 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)) {
+			String com1 = "INSERT INTO ProteinLog " + "(JobID, IP, DataBegin, DataEnd, FinalStatus, ExecutionStatus, Protein)"
+					+ " VALUES ('" + jobid + "','" + ip + "','" + startdate + "','" + enddate + "','" + statusFinal + "','" + statusEx
+					+ "','" + protein + "');";
+			session.execute(com1);
+
+			String com2 = "INSERT INTO ProteinData " + "(jobtime, JobID, Protein)" + " VALUES (" + jobtime + ",'" + jobid + "','" + protein
+					+ "');";
+			session.execute(com2);
+
+			String allpredictions = "";
+			for (FastaSequence pred : predictions) {
+				String predictionname = pred.getId();
+				String prediction = pred.getSequence().replaceAll("\n", "");
+				allpredictions += "'" + predictionname + "':'" + prediction + "',";
+			}
+			String final_prediction = "";
+			if (null != allpredictions) {
+				final_prediction = allpredictions.substring(0, allpredictions.length() - 1);
+			}
+
+			String check2 = "SELECT * FROM ProteinRow WHERE JobID = '" + jobid + "';";
+			ResultSet results2 = session.execute(check2);
+			if (results2.isExhausted()) {
+				String com3 = "INSERT INTO ProteinRow " + "(Protein, JobID, Predictions)" + " VALUES ('" + protein + "','" + jobid + "',{"
+						+ final_prediction + "});";
+				session.execute(com3);
+			}
+
+			// update some internal tables 
+			String check3 = "SELECT * FROM MainParameters WHERE Name = 'EarliestJobDate';";
+			ResultSet results3 = session.execute(check3);
+			boolean updateparameter = true;
+			if (!results3.isExhausted()) {
+				Row r = results3.one();
+				if (jobtime >= Long.parseLong(r.getString("Value")))
+					updateparameter = false;
+			}
+			if (updateparameter) {
+				String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('EarliestJobDate','" + String.valueOf(jobtime)
+						+ "');";
+				session.execute(com);
+			}
+			String check4 = "SELECT * FROM MainParameters WHERE Name = 'TotalNumberOfJobs';";
+			ResultSet results4 = session.execute(check4);
+			updateparameter = true;
+			int njobs = 1;
+			if (!results4.isExhausted()) {
+				Row r = results4.one();
+				njobs += Integer.parseInt(r.getString("Value"));
+			}
+			String com = "INSERT INTO MainParameters " + "(Name, Value)" + " VALUES ('TotalNumberOfJobs','" + String.valueOf(njobs) + "');";
+			session.execute(com);
+
+			return 1;
+		}
+		return 0;
+	}
+
+	/*
+	 * 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));
+			}
+
+			for (FastaSequence p : predictions) {
+				session.execute("UPDATE JpredArchive SET predictions = predictions + {'" + p.getId() + "':'"
+						+ p.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + jobid + "';");
+			}
+
+			for (FastaSequence s : seqs) {
+				session.execute("UPDATE JpredArchive SET alignment = alignment + {'" + s.getId() + "':'"
+						+ s.getSequence().replaceAll("\n", "") + "'} WHERE JobID = '" + jobid + "';");
+			}
+			return 1;
+		}
+		return 0;
+	}
+
+}