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

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

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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.I2b2ConceptEntity;
import edu.emory.bmi.aiw.i2b2export.entity.OutputConfigurationEntity;
import java.io.BufferedWriter;
import java.io.IOException;
import java.sql.Connection;
import java.sql.SQLException;

import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.eurekaclinical.i2b2.client.pdo.Event;
import org.eurekaclinical.i2b2.client.pdo.Observation;
import org.eurekaclinical.i2b2.client.pdo.Patient;

/**
 * Output formatter for a patient row.
 *
 * @author Michel Mansour
 * @since 1.0
 */
final class PatientDataRowOutputFormatter extends DataRowOutputFormatter {

    private final Patient patient;
    private final Map<String, List<Observation>> keyToObx;

    PatientDataRowOutputFormatter(OutputConfigurationEntity config, Patient patient, Connection con) {
        super(con, config);
        this.patient = patient;
        this.keyToObx = new HashMap<>();
        for (Event e : patient.getEvents()) {
            for (Observation o : e.getObservations()) {
                org.arp.javautil.collections.Collections.putList(this.keyToObx, o.getConceptPath(), o);
            }
        }
    }

    @Override
    protected int rowPrefix(BufferedWriter writer) throws IOException {
        write(patient.getPatientId(), writer, 0);
        return 1;
    }

    @Override
    protected Collection<Observation> matchingObservations(I2b2ConceptEntity i2b2Concept) throws SQLException {
        switch (StringUtils.upperCase(i2b2Concept.getTableName())) {
        case "CONCEPT_DIMENSION":
            List<Observation> obxs = this.keyToObx.get(i2b2Concept.getI2b2Key());
            if (obxs != null) {
                return Collections.unmodifiableCollection(obxs);
            } else {
                return Collections.emptyList();
            }
        case "PATIENT_DIMENSION":
            if (compareDimensionColumnValue(i2b2Concept, patient)) {
                Observation.Builder b = new Observation.Builder(null).tval(getParam(patient, i2b2Concept));
                Collection<Observation> o = Collections.singleton(b.build());
                return o;
            } else {
                return Collections.emptyList();
            }
        default:
            return Collections.emptyList();
        }
    }

}