/**
* for term_info part, get the ontology match records for a given term
*
* @param term
* @param glossaryType
* @return
* @throws SQLException
*/
public ArrayList<TermGlossary> getOntologyMatchForTerm(String term, int glossaryType)
throws SQLException {
ArrayList<TermGlossary> glossies = new ArrayList<TermGlossary>();
Connection conn = null;
PreparedStatement pstmt = null;
ResultSet rset = null, rset2 = null;
try {
conn = getConnection();
String sql =
"select category, recordType, recordID "
+ "from selected_ontology_records "
+ "where glossaryType = ? and term = ?";
pstmt = conn.prepareStatement(sql);
pstmt.setInt(1, glossaryType);
pstmt.setString(2, term);
rset = pstmt.executeQuery();
while (rset.next()) {
String category = rset.getString("category");
// get id and definition
OntologyRecordType recordType = translateToOntologyRecordType(rset.getInt("recordType"));
String id_prefix = "Ontology ID: ";
if (recordType.equals(OntologyRecordType.SUBMISSION)) {
id_prefix = "Temporary ID: ";
sql = "select tmpID as id, definition from ontology_submissions where ID = ?";
} else {
sql = "select permanentID as id, definition from ontology_matches where ID = ?";
}
pstmt = conn.prepareStatement(sql);
pstmt.setInt(1, rset.getInt("recordID"));
rset2 = pstmt.executeQuery();
if (rset2.next()) {
String id = rset2.getString(1);
if (recordType.equals(OntologyRecordType.MATCH)) {
id = truncatePermanentID(id);
}
TermGlossary gloss = new TermGlossary(id_prefix + id, category, rset2.getString(2));
glossies.add(gloss);
}
}
} catch (SQLException e) {
e.printStackTrace();
throw e;
} finally {
close(rset);
close(pstmt);
closeConnection(conn);
}
return glossies;
}
// in db, couldn't save enum type, therefore translate it to integer values
private int translateOntologyRecordType(OntologyRecordType type) {
if (type.equals(OntologyRecordType.MATCH)) {
return 1;
} else {
return 2;
}
}
