public HashSet<OWLClass> getTransitiveAnnotations(String entity) throws SQLException {
HashSet<OWLClass> result = new HashSet<>();
getTransitiveAnnotations.setString(1, entity);
try (ResultSet resultSet = getTransitiveAnnotations.executeQuery()) {
while (resultSet.next()) {
result.add(utils.getEntity(resultSet.getInt(1)).asOWLClass());
}
}
return result;
}
@Override
protected void cache() throws SQLException {
// We read the file line by line, split each line on whitespace into three parts and use each
// triplet to create
// an annotation in the database.
try (Statement statement = getConnection().createStatement()) {
statement.execute(
""
+ "CREATE TABLE IF NOT EXISTS annotations ("
+ " id INT PRIMARY KEY AUTO_INCREMENT,"
+ " entity VARCHAR(256),"
+ " annotation INT,"
+ " corpus VARCHAR(256),"
+ " INDEX (entity),"
+ " INDEX (annotation),"
+ " INDEX (corpus))");
if (wipe) statement.execute("TRUNCATE TABLE annotations");
}
@SuppressWarnings("resource")
PreparedStatement insertAnnotation =
getConnection()
.prepareStatement(
"INSERT INTO annotations (entity, annotation, corpus) VALUES (?, ?, ?)");
insertAnnotation.setString(3, corpus);
String line;
int lineNum = 0;
int counter = 0;
try {
while ((line = fileReader.readLine()) != null) {
line = line.trim();
if (line.length() == 0 || line.startsWith("#")) continue;
lineNum++;
String[] parts = line.split("\\s+", 3); // Ignore everything from the third column onwards!
if (parts.length < 2) {
System.err.println(
"Ignoring line " + lineNum + ": expecting 2 columns; got " + parts.length);
continue;
}
String entity = parts[0];
if (entity.length() > 256) {
System.err.println(
"Ignoring line "
+ lineNum
+ ": can only use entities whose name does not have more than 256 characters");
continue;
}
int annotationID = utils.getID(factory.getOWLClass(IRI.create(parts[1])));
if (annotationID == -1) {
System.err.println("Ignoring line " + lineNum + ": unknown ontology term");
continue;
}
insertAnnotation.setString(1, entity);
insertAnnotation.setInt(2, annotationID);
insertAnnotation.addBatch();
counter++;
if (counter % 1000 == 0) {
System.out.println("... " + counter + " annotations found ...");
insertAnnotation.executeBatch();
}
}
} catch (IOException e) {
throw new RuntimeException(e);
} finally {
insertAnnotation.executeBatch();
insertAnnotation.close();
}
}
