corpora.DataSaver Maven / Gradle / Ivy

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package corpora;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import utils.DBUtils;

import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.Statement;

/**
 *
 * @author Chinh
 * @Date: Aug 30, 2010
 */
public class DataSaver {
	private static final Logger log = LoggerFactory.getLogger(DataSaver.class);
	Statement stmt;
	ResultSet rs;
	PreparedStatement ps_pro, ps_event, ps_trigger, ps_modify, ps_equiv, ps_abstract;
	Connection con;
	// SenSimplifier simp;

	public DataSaver(DBUtils db) {
		// init database
		try {
			// simp = new SenSimplifier(db);
			con = db.getConnection();
			stmt = con.createStatement();
			// preparing tables - DROPPING TABLES
			stmt.executeUpdate("DROP TABLE PROTEIN IF EXISTS");
			stmt.executeUpdate("DROP TABLE TRIGGERS IF EXISTS");
			stmt.executeUpdate("DROP TABLE EVENT IF EXISTS");
			stmt.executeUpdate("DROP TABLE MODIFY IF EXISTS");
			stmt.executeUpdate("DROP TABLE EQUIV IF EXISTS");
			stmt.executeUpdate("DROP TABLE ABSTRACT IF EXISTS");

			// CREATING TABLES
			// stmt.executeUpdate("create cached table PROTEIN(PMID VARCHAR(80),
			// TID VARCHAR(15), POS1 INT, POS2 INT, TXT VARCHAR(120))");
			stmt.executeUpdate(
					"create cached table PROTEIN(PMID VARCHAR(80), TID VARCHAR(15), POS1 INT, POS2 INT, TXT CLOB)");
			stmt.executeUpdate(
					"create cached table TRIGGERS(PMID VARCHAR(80), TID VARCHAR(15), T_TYPE VARCHAR(30), POS1 INT, POS2 INT, TXT VARCHAR(80))");
			stmt.executeUpdate(
					"create cached table EVENT(PMID VARCHAR(80), EID VARCHAR(15), T_TYPE VARCHAR(30), TRIG_ID VARCHAR(5), THEME1 VARCHAR(5),THEME2 VARCHAR(5) ,CAUSE VARCHAR(5))");
			stmt.executeUpdate(
					"create cached table MODIFY(PMID VARCHAR(80), MID VARCHAR(15), T_TYPE VARCHAR(30), THEME VARCHAR(5))");
			stmt.executeUpdate("create cached table EQUIV(PMID VARCHAR(80), TID1 VARCHAR(15),  TID2 VARCHAR(50))");
			// stmt.executeUpdate("create cached table ABSTRACT(PMID
			// VARCHAR(80), TEXT VARCHAR(25000))");
			stmt.executeUpdate("create cached table ABSTRACT(PMID VARCHAR(80), TEXT CLOB)");

			// DROPPING INDEXES
			stmt.executeUpdate("DROP index PRO_idx  IF EXISTS");
			stmt.executeUpdate("DROP index TRIG_idx  IF EXISTS");
			stmt.executeUpdate("DROP index EVENT_idx  IF EXISTS");
			stmt.executeUpdate("DROP index MODIFY_idx  IF EXISTS");
			stmt.executeUpdate("DROP index ABSTRACT_idx  IF EXISTS");
			stmt.executeUpdate("DROP index EQUIV_idx  IF EXISTS");

			// CREATING INDEXES
			stmt.executeUpdate("create index PRO_idx on Protein (pmid,tid)");
			stmt.executeUpdate("create index TRIG_idx on Triggers (pmid,tid)");
			stmt.executeUpdate("create index EVENT_idx on Event (pmid,eid)");
			stmt.executeUpdate("create index MODIFY_idx on Modify (pmid,mid)");
			stmt.executeUpdate("create index EQUIV_idx on EQUIV (pmid,tid1)");
			stmt.executeUpdate("create index ABSTRACT_idx on ABSTRACT (pmid)");

			// prepare statements
			ps_pro = con.prepareStatement("Insert into PROTEIN(PMID, TID, POS1, POS2,TXT) VALUES(?,?,?,?,?)");
			ps_trigger = con
					.prepareStatement("Insert into TRIGGERS(PMID, TID, T_TYPE, POS1, POS2,TXT) VALUES(?,?,?,?,?,?)");
			ps_event = con.prepareStatement(
					"Insert into EVENT(PMID,EID,T_TYPE,TRIG_ID,THEME1,THEME2,CAUSE) VALUES(?,?,?,?,?,?,?)");
			ps_modify = con.prepareStatement("Insert into MODIFY(PMID, MID, T_TYPE, THEME) VALUES(?,?,?,?)");
			ps_equiv = con.prepareStatement("Insert into EQUIV(PMID, TID1, TID2) VALUES(?,?,?)");
			ps_abstract = con.prepareStatement("Insert into ABSTRACT(PMID, TEXT) VALUES(?,?)");
			stmt.close();
		} catch (Exception e) {
			throw new RuntimeException(e);
		}
	}

	/*
	 * Store protein data into Protein table
	 */
	public void saveProtein(String pmid, String tid, int p1, int p2, String value) {
		try {
			ps_pro.setString(1, pmid);
			ps_pro.setString(2, tid);
			ps_pro.setInt(3, p1);
			ps_pro.setInt(4, p2);
			ps_pro.setString(5, value);
			ps_pro.executeUpdate();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	/*
	 * Store protein data into Protein table
	 */
	public void saveAbstract(String pmid, String txt) {
		try {
			ps_abstract.setString(1, pmid);
			ps_abstract.setString(2, txt);
			ps_abstract.executeUpdate();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	/**
	 * Store trigger into Trigger table
	 */
	public void saveTrigger(String pmid, String tid, String type, int p1, int p2, String value) {
		try {
			ps_trigger.setString(1, pmid);
			ps_trigger.setString(2, tid);
			ps_trigger.setString(3, type);
			ps_trigger.setInt(4, p1);
			ps_trigger.setInt(5, p2);
			ps_trigger.setString(6, value);
			ps_trigger.executeUpdate();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	/*
	 * Store event into event table
	 */
	public void saveEvent(String pmid, String eid, String type1, String trig_id, String theme1, String theme2,
			String cause) {
		try {
			ps_event.setString(1, pmid);
			ps_event.setString(2, eid);
			ps_event.setString(3, type1);
			ps_event.setString(4, trig_id);
			ps_event.setString(5, theme1);
			ps_event.setString(6, theme2);
			ps_event.setString(7, cause);
			ps_event.executeUpdate();

		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	/**
	 * Store modified values
	 */
	public void saveModify(String pmid, String mid, String type, String theme) {
		try {
			ps_modify.setString(1, pmid);
			ps_modify.setString(2, mid);
			ps_modify.setString(3, type);
			ps_modify.setString(4, theme);
			ps_modify.executeUpdate();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	/**
	 * Store modified values
	 */
	public void saveEquiv(String pmid, String tid, String tid2) {
		try {
			ps_equiv.setString(1, pmid);
			ps_equiv.setString(2, tid);
			ps_equiv.setString(3, tid2);
			ps_equiv.executeUpdate();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	public void close() {
		try {
			log.debug("Closing database connection {}", con);
			con.close();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}
}