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

Introduction

Here is the source code for edu.emory.bmi.aiw.i2b2export.output.HeaderRowOutputFormatterTest.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.AggregationType;
import edu.emory.bmi.aiw.i2b2export.entity.DisplayFormat;
import edu.emory.bmi.aiw.i2b2export.entity.OutputColumnConfigurationEntity;
import edu.emory.bmi.aiw.i2b2export.entity.OutputConfigurationEntity;
import edu.emory.bmi.aiw.i2b2export.entity.RowDimension;
import java.io.IOException;
import java.sql.SQLException;
import org.junit.Assert;
import org.junit.Test;

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

/**
 *
 */
public class HeaderRowOutputFormatterTest extends AbstractRowOutputFormatterTest {

    @Test
    public void testFormatHeader() throws IOException, SQLException {
        OutputConfigurationEntity config = new OutputConfigurationEntity();
        config.setName("foo");
        config.setUsername("i2b2");
        config.setRowDimension(RowDimension.PATIENT);
        config.setSeparator(",");
        config.setMissingValue("(NULL)");
        config.setWhitespaceReplacement("_");
        config.setColumnConfigs(new ArrayList<OutputColumnConfigurationEntity>());

        OutputColumnConfigurationEntity colConfig1 = new OutputColumnConfigurationEntity();
        colConfig1.setOutputConfig(config);
        colConfig1.setColumnOrder(1);
        colConfig1.setColumnName("Concept FOO");
        colConfig1.setDisplayFormat(DisplayFormat.EXISTENCE);

        OutputColumnConfigurationEntity colConfig2 = new OutputColumnConfigurationEntity();
        colConfig2.setOutputConfig(config);
        colConfig2.setColumnOrder(2);
        colConfig2.setColumnName("Concept BAR 1");
        colConfig2.setDisplayFormat(DisplayFormat.VALUE);
        colConfig2.setHowMany(3);
        colConfig2.setIncludeTimeRange(true);
        colConfig2.setIncludeUnits(true);

        OutputColumnConfigurationEntity colConfig3 = new OutputColumnConfigurationEntity();
        colConfig3.setOutputConfig(config);
        colConfig3.setColumnOrder(3);
        colConfig3.setColumnName("ConceptAgg");
        colConfig3.setDisplayFormat(DisplayFormat.AGGREGATION);
        colConfig3.setAggregation(AggregationType.MAX);
        colConfig3.setIncludeUnits(true);

        OutputColumnConfigurationEntity colConfig4 = new OutputColumnConfigurationEntity();
        colConfig4.setOutputConfig(config);
        colConfig4.setColumnOrder(4);
        colConfig4.setColumnName("Concept BAZ");
        colConfig4.setDisplayFormat(DisplayFormat.VALUE);
        colConfig4.setHowMany(1);
        colConfig4.setIncludeUnits(false);
        colConfig4.setIncludeTimeRange(false);

        OutputColumnConfigurationEntity colConfig5 = new OutputColumnConfigurationEntity();
        colConfig5.setOutputConfig(config);
        colConfig5.setColumnOrder(5);
        colConfig5.setColumnName("ConceptAgg2");
        colConfig5.setDisplayFormat(DisplayFormat.AGGREGATION);
        colConfig5.setAggregation(AggregationType.AVG);
        colConfig5.setIncludeUnits(false);

        OutputColumnConfigurationEntity colConfig6 = new OutputColumnConfigurationEntity();
        colConfig6.setOutputConfig(config);
        colConfig6.setColumnOrder(6);
        colConfig6.setColumnName("Concept QUUX");
        colConfig6.setDisplayFormat(DisplayFormat.VALUE);
        colConfig6.setHowMany(1);
        colConfig6.setIncludeUnits(false);
        colConfig6.setIncludeTimeRange(true);

        config.getColumnConfigs().add(colConfig1);
        config.getColumnConfigs().add(colConfig3);
        config.getColumnConfigs().add(colConfig4);
        config.getColumnConfigs().add(colConfig5);
        config.getColumnConfigs().add(colConfig6);
        config.getColumnConfigs().add(colConfig2);

        HeaderRowOutputFormatter formatter = new HeaderRowOutputFormatter(config);
        Assert.assertEquals(
                "Patient_id,Concept_FOO,Concept_BAR_1_value,Concept_BAR_1_units,Concept_BAR_1_start,Concept_BAR_1_end,Concept_BAR_1_value,Concept_BAR_1_units,Concept_BAR_1_start,Concept_BAR_1_end,Concept_BAR_1_value,Concept_BAR_1_units,Concept_BAR_1_start,Concept_BAR_1_end,"
                        + "ConceptAgg_max,ConceptAgg_units,Concept_BAZ_value,ConceptAgg2_avg,Concept_QUUX_value,Concept_QUUX_start,Concept_QUUX_end"
                        + IOUtils.LINE_SEPARATOR,
                formatString(formatter));
    }
}