edu.emory.bmi.aiw.i2b2export.output.PatientDataOutputFormatter.java Source code

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Here is the source code for edu.emory.bmi.aiw.i2b2export.output.PatientDataOutputFormatter.java

Source

package edu.emory.bmi.aiw.i2b2export.output;

/*
 * #%L
 * i2b2 Export Service
 * %%
 * Copyright (C) 2013 Emory University
 * %%
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 * #L%
 */
import edu.emory.bmi.aiw.i2b2export.entity.OutputConfigurationEntity;
import java.io.BufferedWriter;
import java.io.IOException;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;

import java.util.Collection;
import org.apache.commons.io.IOUtils;
import org.eurekaclinical.i2b2.client.pdo.Patient;

/**
 * Output formatter for when each row represents a patient. Uses an h2
 * in-memory database called PatientDataOutputFormatter.
 *
 * @author Michel Mansour
 * @since 1.0
 */
final class PatientDataOutputFormatter extends AbstractFormatter {

    private final Collection<Patient> patients;

    PatientDataOutputFormatter(OutputConfigurationEntity config, Collection<Patient> patients) {
        super(config);
        this.patients = patients;
    }

    public void format(BufferedWriter writer) throws IOException {
        try {
            Class.forName("org.h2.Driver");
        } catch (ClassNotFoundException ex) {
            throw new AssertionError("Error parsing i2b2 metadata: " + ex);
        }
        try (Connection con = DriverManager.getConnection("jdbc:h2:mem:PatientDataOutputFormatter")) {
            for (Patient patient : this.patients) {
                new PatientDataRowOutputFormatter(getOutputConfiguration(), patient, con).format(writer);
                writer.write(IOUtils.LINE_SEPARATOR);
            }
        } catch (SQLException ex) {
            throw new IOException("Error parsing i2b2 metadata: " + ex.getMessage());
        }
    }
}