/**
* load the temp file maintained by the MySQLbulkLoader into the DMBS. truncates the temp file,
* and leaves it open for more insertRecord() operations. returns number of records inserted.
*
* <p>TODO: perhaps instead of having each program that uses a DAO that uses bulk loading call
* 'completeInsert', get MySQLbulkLoader created by a factory, and have the factory remember to
* load all the tables from all the temp files before the program exits.
*
* @return number of records inserted
* @throws DaoException
* @throws IOException
*/
public int loadDataFromTempFileIntoDBMS() throws DaoException, IOException {
Connection con = null;
Statement stmt = null;
PreparedStatement pstmt = null;
ResultSet rs = null;
try {
try {
// close the file, flushing all buffers before loading the DBMS
tempFileWriter.close();
} catch (IOException e) {
throw new DaoException(e);
}
con = JdbcUtil.getDbConnection(MySQLbulkLoader.class);
stmt = con.createStatement();
// will throw error if attempts to overwrite primary keys in table
String command = "LOAD DATA LOCAL INFILE '" + tempFileName + "' INTO TABLE " + tableName;
long startTime = System.currentTimeMillis();
boolean rv = stmt.execute(command);
// TODO: throw exception if rv == true
int updateCount = stmt.getUpdateCount();
long duration = (System.currentTimeMillis() - startTime) / 1000;
// reopen empty temp file
this.tempFileWriter = new BufferedWriter(new FileWriter(this.tempFileHandle, false));
return updateCount;
} catch (SQLException e) {
throw new DaoException(e);
} finally {
JdbcUtil.closeAll(MySQLbulkLoader.class, con, pstmt, rs);
}
}
/**
* @param keywordS
* @return Map<keyword, List<cosmic>>
* @throws DaoException
*/
public static Map<String, Set<CosmicMutationFrequency>> getCosmicDataByKeyword(
Collection<String> keywordS) throws DaoException {
Connection con = null;
PreparedStatement pstmt = null;
ResultSet rs = null;
try {
con = JdbcUtil.getDbConnection(DaoCosmicData.class);
pstmt =
con.prepareStatement(
"SELECT * FROM cosmic_mutation "
+ " WHERE KEYWORD in ('"
+ StringUtils.join(keywordS, "','")
+ "')");
rs = pstmt.executeQuery();
Map<String, Set<CosmicMutationFrequency>> ret =
new HashMap<String, Set<CosmicMutationFrequency>>();
while (rs.next()) {
CosmicMutationFrequency cmf = extractCosmic(rs);
Set<CosmicMutationFrequency> cmfs = ret.get(cmf.getKeyword());
if (cmfs == null) {
cmfs = new HashSet<CosmicMutationFrequency>();
ret.put(cmf.getKeyword(), cmfs);
}
cmfs.add(cmf);
}
return ret;
} catch (SQLException e) {
throw new DaoException(e);
} finally {
JdbcUtil.closeAll(DaoCosmicData.class, con, pstmt, rs);
}
}
public static void deleteAllRecords() throws DaoException {
Connection con = null;
PreparedStatement pstmt = null;
ResultSet rs = null;
try {
con = JdbcUtil.getDbConnection(DaoCosmicData.class);
pstmt = con.prepareStatement("TRUNCATE TABLE cosmic_mutation");
pstmt.executeUpdate();
} catch (SQLException e) {
throw new DaoException(e);
} finally {
JdbcUtil.closeAll(DaoCosmicData.class, con, pstmt, rs);
}
}
