ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest.java Source code

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Here is the source code for ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceTest.java

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/*
 * The Gemma project
 *
 * Copyright (c) 2011 University of British Columbia
 *
 * 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.
 */
package ubic.gemma.core.analysis.preprocess.batcheffects;

import org.apache.commons.lang3.time.DateUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.junit.Test;

import java.util.*;

import static org.junit.Assert.assertEquals;

/**
 * Unit tests. Note that these depend on BatchInfoPopulationService.MAX_GAP_BETWEEN_SAMPLES_TO_BE_SAME_BATCH
 *
 * @author paul
 */
public class BatchInfoPopulationServiceTest {

    private static final Log log = LogFactory.getLog(BatchInfoPopulationServiceTest.class);

    @Test
    public void testDatesToBatchA() {
        BatchInfoPopulationHelperServiceImpl ser = new BatchInfoPopulationHelperServiceImpl();

        Calendar cal = Calendar.getInstance();
        cal.set(2004, Calendar.APRIL, 10, 10, 1, 1);
        Date d = cal.getTime();

        Collection<Date> dates = new HashSet<>();

        dates.add(d);
        dates.add(DateUtils.addHours(d, 1)); // first batch
        dates.add(DateUtils.addHours(d, 2)); // first batch
        dates.add(DateUtils.addHours(d, 3)); // first batch
        dates.add(DateUtils.addHours(d, 24)); // second batch
        dates.add(DateUtils.addHours(d, 25));// second batch
        dates.add(DateUtils.addHours(d, 26));// second batch
        dates.add(DateUtils.addHours(d, 27));// second batch

        Map<String, Collection<Date>> actual = ser.convertDatesToBatches(dates);

        /*
         * How many unique values?
         */
        Set<String> s = new HashSet<>(actual.keySet());
        assertEquals(2, s.size());
    }

    @Test
    public void testDatesToBatchB() {
        BatchInfoPopulationHelperServiceImpl ser = new BatchInfoPopulationHelperServiceImpl();
        Calendar cal = Calendar.getInstance();
        cal.set(2004, Calendar.APRIL, 10);
        Date d = cal.getTime();

        Collection<Date> dates = new HashSet<>();

        dates.add(d);

        dates.add(DateUtils.addSeconds(d, 3500));// first batch, all within two hours of each other.
        dates.add(DateUtils.addSeconds(d, 7000));// first batch, all within two hours of each other.
        dates.add(DateUtils.addSeconds(d, 8000));// first batch, all within two hours of each other.
        dates.add(DateUtils.addHours(d, 2226));// second batch, but singleton merged backwards

        dates.add(DateUtils.addHours(d, 11124));// third batch , but second was a singleton so we're only on #2.
        dates.add(DateUtils.addHours(d, 11125));// third batch, but gets merged in with second.
        dates.add(DateUtils.addHours(d, 11189)); // fourth batch, but gets merged in with second.

        Map<String, Collection<Date>> actual = ser.convertDatesToBatches(dates);

        /*
         * How many unique values?
         */
        Set<String> s = new HashSet<>(actual.keySet());
        assertEquals(2, s.size());

        this.debug(actual);
    }

    @Test
    public void testDatesToBatchC() {
        BatchInfoPopulationHelperServiceImpl ser = new BatchInfoPopulationHelperServiceImpl();
        Calendar cal = Calendar.getInstance();
        cal.set(2004, Calendar.APRIL, 10, 10, 1, 1);
        Date d = cal.getTime();

        Collection<Date> dates = new HashSet<>();

        dates.add(d);
        dates.add(DateUtils.addHours(d, 2)); // should be merged back.
        dates.add(DateUtils.addHours(d, 3)); // merged back.
        dates.add(DateUtils.addHours(d, 4)); // merged back.
        dates.add(DateUtils.addHours(d, 5)); // merged back.
        dates.add(DateUtils.addHours(d, 6)); // merged back.
        dates.add(DateUtils.addHours(d, 7)); // merged back.
        dates.add(DateUtils.addHours(d, 8)); // merged back.

        Map<String, Collection<Date>> actual = ser.convertDatesToBatches(dates);
        this.debug(actual);
        Set<String> s = new HashSet<>(actual.keySet());
        assertEquals(1, s.size());

    }

    @Test
    public void testDatesToBatchD() {
        BatchInfoPopulationHelperServiceImpl ser = new BatchInfoPopulationHelperServiceImpl();
        Calendar cal = Calendar.getInstance();
        cal.set(2004, Calendar.APRIL, 10, 10, 1, 1);
        Date d = cal.getTime();

        Collection<Date> dates = new HashSet<>();

        dates.add(d);
        dates.add(DateUtils.addHours(d, 200)); // merged back, even though gap is big.
        dates.add(DateUtils.addHours(d, 201)); // merge back
        dates.add(DateUtils.addHours(d, 202)); // merge back
        dates.add(DateUtils.addHours(d, 203)); // merge back
        dates.add(DateUtils.addHours(d, 301)); // new batch
        dates.add(DateUtils.addHours(d, 302)); // merge back
        dates.add(DateUtils.addHours(d, 402)); // singleton merged.

        Map<String, Collection<Date>> actual = ser.convertDatesToBatches(dates);
        this.debug(actual);
        Set<String> s = new HashSet<>(actual.keySet());
        assertEquals(2, s.size());

    }

    private void debug(Map<String, Collection<Date>> actual) {
        if (BatchInfoPopulationServiceTest.log.isDebugEnabled()) {
            for (String st : actual.keySet()) {
                BatchInfoPopulationServiceTest.log.debug(st + " " + actual.get(st).size() + " members.");
                for (Date da : actual.get(st)) {
                    BatchInfoPopulationServiceTest.log.debug(da);
                }
            }
        }
    }

}