/*
* #%L
* NICTA t3as UMLS CUI to SNOMED CT Lookup
* %%
* Copyright (C) 2014 NICTA
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
*
* Additional permission under GNU GPL version 3 section 7
*
* If you modify this Program, or any covered work, by linking or combining
* it with H2, GWT, or JavaBeans Activation Framework (JAF) (or a
* modified version of those libraries), containing parts covered by the
* terms of the H2 License, the GWT Terms, or the Common Development and
* Distribution License (CDDL) version 1.0 ,the licensors of this Program
* grant you additional permission to convey the resulting work.
* #L%
*/
package org.t3as.snomedct.lookup;
import org.h2.jdbcx.JdbcConnectionPool;
import org.t3as.metamap.jaxb.Candidate;
import org.t3as.metamap.jaxb.MMO;
import org.t3as.metamap.jaxb.MMOs;
import org.t3as.metamap.jaxb.Mapping;
import org.t3as.metamap.jaxb.Phrase;
import org.t3as.metamap.jaxb.SemType;
import org.t3as.metamap.jaxb.Utterance;
import java.io.Closeable;
import java.io.File;
import java.io.IOException;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collection;
public final class SnomedLookup implements Closeable {
private static final String SELECT_SQL =
"select top 1 snomedId, termType from snomed " + // only return 1 result
"where cui = ? and description = ? " + // unfortunately we must filter on description
"order by mrrank, snomedId desc"; // order first by rank, then by highest SNOMED code
private static final String FROM_SNOMEDID_SELECT_SQL =
"select cui, description, termType from snomed " +
"where snomedid = ?";
private final JdbcConnectionPool connectionPool;
private final Connection conn;
private final PreparedStatement fromCuiPrepStmt;
private final PreparedStatement fromSnomedIdPrepStmt;
public SnomedLookup(final File dbFile) throws SQLException {
// open the database in readonly mode, and fail if it does not exist
connectionPool = JdbcConnectionPool.create(
"jdbc:h2:" + dbFile.getAbsoluteFile() + ";IFEXISTS=TRUE;ACCESS_MODE_DATA=r", "foo", "bar");
conn = connectionPool.getConnection();
fromCuiPrepStmt = conn.prepareStatement(SELECT_SQL);
fromSnomedIdPrepStmt = conn.prepareStatement(FROM_SNOMEDID_SELECT_SQL);
}
/**
* Tries to look up each Mapping Candidate in the SNOMED CT db to add more data.
* @return the number of Candidates that were enriched
*/
public int enrichXml(final MMOs root) throws SQLException {
int count = 0;
// TODO: take out the print statements
for (final MMO mmo : root.getMMO()) {
for (final Utterance utterance : mmo.getUtterances().getUtterance()) {
for (final Phrase phrase : utterance.getPhrases().getPhrase()) {
System.out.printf("Phrase: %s\n", phrase.getPhraseText());
for (final Mapping mapping : phrase.getMappings().getMapping()) {
System.out.printf("Score: %s\n", mapping.getMappingScore());
for (final Candidate candidate : mapping.getMappingCandidates().getCandidate()) {
final Collection<String> semTypes = new ArrayList<>();
for (final SemType st : candidate.getSemTypes().getSemType()) {
semTypes.add(st.getvalue());
}
// the actual line of work
count += addSnomedId(candidate) ? 1 : 0;
System.out.printf(" %-5s %-9s %s %s %s %s\n",
candidate.getCandidateScore(),
candidate.getCandidateCUI(),
candidate.getSnomedId(),
candidate.getCandidatePreferred(),
semTypes,
candidate.getSources().getSource());
}
}
System.out.println();
}
}
}
return count;
}
/**
* Tries to find this candidate in the SNOMED CT database, and if found adds the SNOMED id and term type to the
* instance.
*/
public boolean addSnomedId(final Candidate candidate) throws SQLException {
final SnomedTerm result = findFromCuiAndDesc(candidate.getCandidateCUI(), candidate.getCandidatePreferred());
if (result != null) {
candidate.setSnomedId(result.snomedId);
candidate.setTermType(result.termType);
return true;
}
else {
// TODO: log this somewhere?
System.err.printf("WARNING! Could not find the SNOMED CT concept id for UMLS CUI: %s: '%s'\n",
candidate.getCandidateCUI(), candidate.getCandidatePreferred());
return false;
}
}
public SnomedTerm findFromCuiAndDesc(final String cui, final String description) throws SQLException {
//noinspection JpaQueryApiInspection
fromCuiPrepStmt.setString(1, cui);
//noinspection JpaQueryApiInspection
fromCuiPrepStmt.setString(2, description);
final ResultSet resultSet = fromCuiPrepStmt.executeQuery();
SnomedTerm t = null;
if (resultSet.first()) {
t = new SnomedTerm(cui, resultSet.getString("snomedId"), resultSet.getString("termType"),
description);
}
resultSet.close();
return t;
}
public SnomedTerm findFromSnomedId(final String snomedId) throws SQLException {
//noinspection JpaQueryApiInspection
fromSnomedIdPrepStmt.setString(1, snomedId);
final ResultSet resultSet = fromSnomedIdPrepStmt.executeQuery();
SnomedTerm t = null;
if (resultSet.first()) {
t = new SnomedTerm(resultSet.getString("cui"), snomedId, resultSet.getString("termType"),
resultSet.getString("description"));
}
resultSet.close();
return t;
}
@Override
public void close() throws IOException {
try {
fromCuiPrepStmt.close();
fromSnomedIdPrepStmt.close();
conn.close();
connectionPool.dispose();
}
catch (final SQLException e) {
throw new IOException("Could not close SQL connection: " + e.getMessage(), e);
}
}
}