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

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Here is the source code for edu.emory.bmi.aiw.i2b2export.output.HeaderRowOutputFormatter.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.OutputColumnConfigurationEntity;
import edu.emory.bmi.aiw.i2b2export.entity.OutputConfigurationEntity;
import java.io.BufferedWriter;
import java.io.IOException;

import java.util.Collections;
import org.apache.commons.io.IOUtils;

/**
 * Formatter for the header row of an entire result set.
 *
 * @author Michel Mansour
 * @since 1.0
 */
public final class HeaderRowOutputFormatter extends AbstractFormatter implements RowOutputFormatter {

    private final OutputConfigurationEntity outputConfiguration;

    /**
     * Default constructor. Accepts the output configuration to use to format
     * the header.
     *
     * @param outputConfiguration the {@link OutputConfigurationEntity} to use to
     * format the header
     */
    public HeaderRowOutputFormatter(OutputConfigurationEntity outputConfiguration) {
        super(outputConfiguration);
        this.outputConfiguration = outputConfiguration;
    }

    /**
     * Formats the header row according to the instance's output configuration.
     * The row is returned as an array of strings that will be joined later
     * using the correct delimiter.
     *
     * @param writer the stream to which the results will go.
     * @throws java.io.IOException if an error occurred writing the results.
     */
    @Override
    public void format(BufferedWriter writer) throws IOException {
        int colNum = 0;
        switch (outputConfiguration.getRowDimension()) {
        case PROVIDER:
            write("Provider_name", writer, colNum++);
            break;
        case VISIT:
            write("Patient_id", writer, colNum++);
            write("Visit_id", writer, colNum++);
            write("Visit_start", writer, colNum++);
            write("Visit_end", writer, colNum++);
            break;
        case PATIENT:
            write("Patient_id", writer, colNum++);
            break;
        default:
            throw new RuntimeException("row dimension not provided: user:" + " " + outputConfiguration.getUsername()
                    + ", " + "name: " + outputConfiguration.getName());
        }
        Collections.sort(outputConfiguration.getColumnConfigs());
        for (int i = 0; i < outputConfiguration.getColumnConfigs().size(); i++) {
            OutputColumnConfigurationEntity colConfig = outputConfiguration.getColumnConfigs().get(i);
            String baseColName = colConfig.getColumnName();
            if (outputConfiguration.getWhitespaceReplacement() != null
                    && !outputConfiguration.getWhitespaceReplacement().isEmpty()) {
                baseColName = colConfig.getColumnName().replaceAll("\\s",
                        outputConfiguration.getWhitespaceReplacement());
            }
            switch (colConfig.getDisplayFormat()) {
            case EXISTENCE:
                write(baseColName, writer, colNum++);
                break;
            case VALUE:
                for (int j = 0; j < colConfig.getHowMany(); j++) {
                    write(baseColName + "_value", writer, colNum++);
                    if (colConfig.getIncludeUnits()) {
                        write(baseColName + "_units", writer, colNum++);
                    }
                    if (colConfig.getIncludeTimeRange()) {
                        write(baseColName + "_start", writer, colNum++);
                        write(baseColName + "_end", writer, colNum++);
                    }
                }
                break;
            case AGGREGATION:
                switch (colConfig.getAggregation()) {
                case MIN:
                    write(baseColName + "_min", writer, colNum++);
                    break;
                case MAX:
                    write(baseColName + "_max", writer, colNum++);
                    break;
                case AVG:
                    write(baseColName + "_avg", writer, colNum++);
                    break;
                default:
                    continue;
                }
                if (colConfig.getIncludeUnits()) {
                    write(baseColName + "_units", writer, colNum++);
                }
                break;
            default:
                break;
            }
        }
        writer.write(IOUtils.LINE_SEPARATOR);
    }

}