org.bridgedb.rdb.construct.GdbConstructImpl3 Maven / Gradle / Ivy
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package org.bridgedb.rdb.construct;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Statement;
import org.bridgedb.IDMapperException;
import org.bridgedb.Xref;
public class GdbConstructImpl3 implements GdbConstruct
{
private static int GDB_COMPAT_VERSION = 3;
private final Connection con; //TODO: initialize
private final DBConnector dbConnector; //TODO
private String dbName; //TODO
private Exception recentException = null;
public GdbConstructImpl3(String dbName, DBConnector dbConnector, int props) throws IDMapperException
{
con = dbConnector.createConnection(dbName, props);
this.dbConnector = dbConnector;
this.dbName = dbName;
}
/**
compact the database.
@throws IDMapperException on failure
*/
final public void compact() throws IDMapperException
{
dbConnector.compact(con);
}
/**
finalize the database.
@throws IDMapperException on failure
*/
final public void finalize() throws IDMapperException
{
dbConnector.compact(con);
createGdbIndices();
dbConnector.closeConnection(con, DBConnector.PROP_FINALIZE);
String newDb = dbConnector.finalizeNewDatabase(dbName);
dbName = newDb;
recentException = null;
}
private PreparedStatement pstGene = null;
private PreparedStatement pstLink = null;
private PreparedStatement pstAttr = null;
/** {@inheritDoc} */
public int addGene(Xref ref)
{
recentException = null;
//TODO: bpText is unused
if (pstGene == null) throw new NullPointerException();
try
{
pstGene.setString(1, ref.getId());
pstGene.setString(2, ref.getDataSource().getSystemCode());
pstGene.executeUpdate();
}
catch (SQLException e)
{
recentException = e;
return 1;
}
return 0;
}
/** {@inheritDoc} */
public int addAttribute(Xref ref, String attr, String val)
{
recentException = null;
try {
pstAttr.setString(1, attr);
pstAttr.setString(2, val);
pstAttr.setString(3, ref.getId());
pstAttr.setString(4, ref.getDataSource().getSystemCode());
pstAttr.executeUpdate();
} catch (SQLException e) {
recentException = e;
return 1;
}
return 0;
}
/** {@inheritDoc} */
public int addLink(Xref left, Xref right)
{
if (pstLink == null) throw new NullPointerException();
recentException = null;
try
{
pstLink.setString(1, left.getId());
pstLink.setString(2, left.getDataSource().getSystemCode());
pstLink.setString(3, right.getId());
pstLink.setString(4, right.getDataSource().getSystemCode());
pstLink.executeUpdate();
}
catch (SQLException e)
{
recentException = e;
return 1;
}
return 0;
}
/**
prepare for inserting genes and/or links.
@throws IDMapperException on failure
*/
public void preInsert() throws IDMapperException
{
try
{
con.setAutoCommit(false);
pstGene = con.prepareStatement(
"INSERT INTO datanode " +
" (id, code)" +
"VALUES (?, ?)"
);
pstLink = con.prepareStatement(
"INSERT INTO link " +
" (idLeft, codeLeft," +
" idRight, codeRight)" +
"VALUES (?, ?, ?, ?)"
);
pstAttr = con.prepareStatement(
"INSERT INTO attribute " +
" (attrname, attrvalue, id, code)" +
"VALUES (?, ?, ?, ?)"
);
}
catch (SQLException e)
{
throw new IDMapperException (e);
}
}
public void setInfo(String key, String value) throws IDMapperException
{
try
{
/**
* This is a bit awkward because we store keys as columns.
* TODO: in a future schema version this should be a regular 2-column table.
*/
if (!key.matches("^\\w+$")) throw new IllegalArgumentException("key: '" + key + "' contains invalid characters");
PreparedStatement pstInfo1 = con.prepareStatement (
"ALTER TABLE info " +
"ADD COLUMN " + key + " VARCHAR (50)"
);
pstInfo1.execute();
PreparedStatement pstInfo2 = con.prepareStatement (
"UPDATE info SET " + key + " = ? " +
"WHERE schemaversion = " + GDB_COMPAT_VERSION
);
pstInfo2.setString(1, value);
pstInfo2.execute();
}
catch (SQLException ex)
{
throw new IDMapperException(ex);
}
}
/**
Create indices on the database
You can call this at any time after creating the tables,
but it is good to do it only after inserting all data.
@throws IDMapperException on failure
*/
public void createGdbIndices() throws IDMapperException
{
try
{
Statement sh = con.createStatement();
sh.execute(
"CREATE INDEX i_codeLeft" +
" ON link(codeLeft)"
);
sh.execute(
"CREATE INDEX i_idRight" +
" ON link(idRight)"
);
sh.execute(
"CREATE INDEX i_codeRight" +
" ON link(codeRight)"
);
sh.execute(
"CREATE INDEX i_code" +
" ON " + "datanode" + "(code)"
);
}
catch (SQLException e)
{
throw new IDMapperException (e);
}
}
/**
* Executes several SQL statements to create the tables and indexes in the database the given
* connection is connected to
* Note: Official GDB's are created by AP, not with this code.
* This is just here for testing purposes.
* @throws IDMapperException
*/
public void createGdbTables() throws IDMapperException
{
// Logger.log.info("Info: Creating tables");
try
{
Statement sh = con.createStatement();
// sh.execute("DROP TABLE info");
// sh.execute("DROP TABLE link");
// sh.execute("DROP TABLE datanode");
// sh.execute("DROP TABLE attribute");
// sh.close();
// sh = con.createStatement();
sh.execute(
"CREATE TABLE " +
" info " +
"( schemaversion INTEGER PRIMARY KEY " +
")");
// Logger.log.info("Info table created");
sh.execute( //Add compatibility version of GDB
"INSERT INTO info VALUES ( " + GDB_COMPAT_VERSION + ")");
// Logger.log.info("Version stored in info");
sh.execute(
"CREATE TABLE " +
" link " +
" ( idLeft VARCHAR(50) NOT NULL, " +
" codeLeft VARCHAR(50) NOT NULL, " +
" idRight VARCHAR(50) NOT NULL, " +
" codeRight VARCHAR(50) NOT NULL, " +
" bridge VARCHAR(50), " +
" PRIMARY KEY (idLeft, codeLeft, " +
" idRight, codeRight) " +
" ) ");
// Logger.log.info("Link table created");
sh.execute(
"CREATE TABLE " +
" datanode " +
" ( id VARCHAR(50), " +
" code VARCHAR(50), " +
" PRIMARY KEY (id, code) " +
" ) ");
// Logger.log.info("DataNode table created");
sh.execute(
"CREATE TABLE " +
" attribute " +
" ( id VARCHAR(50), " +
" code VARCHAR(50), " +
" attrname VARCHAR(50), " +
" attrvalue VARCHAR(255) " +
" ) ");
// Logger.log.info("Attribute table created");
}
catch (SQLException e)
{
throw new IDMapperException (e);
}
}
/**
commit inserted data.
@throws IDMapperException on failure
*/
final public void commit() throws IDMapperException
{
try
{
con.commit();
}
catch (SQLException e)
{
throw new IDMapperException (e);
}
}
/**
* Older method to open a connection to a Gene database
* using a DBConnector to handle differences
* between different RDBMS-es. The other createInstance() is preferred.
*
* Use this instead of constructor to create an instance of SimpleGdb that matches the schema version.
* @param dbName The file containing the Gene Database.
* @param newDbConnector handles the differences between types of RDBMS.
* A new instance of DbConnector class is instantiated automatically.
* @param props PROP_RECREATE if you want to create a new database, overwriting any existing ones. Otherwise, PROP_NONE.
* @return a new Gdb
* @throws IDMapperException on failure
*/
public static GdbConstruct createInstance(String dbName, DBConnector newDbConnector, int props) throws IDMapperException
{
try
{
// create a fresh db connector of the correct type.
DBConnector dbConnector = newDbConnector.getClass().newInstance();
return new GdbConstructImpl3(dbName, dbConnector, props);
}
catch (InstantiationException e)
{
throw new IDMapperException (e);
}
catch (IllegalAccessException e)
{
throw new IDMapperException (e);
}
}
@Override
public Exception recentException() {
return recentException;
}
}