com.cloudera.science.quince.LoadVariantsToolIT.java Source code

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Here is the source code for com.cloudera.science.quince.LoadVariantsToolIT.java

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/*
 * Copyright (c) 2015, Cloudera, Inc. All Rights Reserved.
 *
 * Cloudera, Inc. licenses this file to you 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
 *
 * This software 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 com.cloudera.science.quince;

import java.io.File;
import java.io.FileFilter;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileUtil;
import org.junit.Before;
import org.junit.Test;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;

public class LoadVariantsToolIT {

    LoadVariantsTool tool;

    @Before
    public void setUp() {
        tool = new LoadVariantsTool();
        Configuration conf = new Configuration();
        tool.setConf(conf);
    }

    @Test
    public void testMissingPaths() throws Exception {
        int exitCode = tool.run(new String[0]);
        assertEquals(1, exitCode);
        // TODO: verify output
    }

    @Test
    public void testInvalidOption() throws Exception {
        int exitCode = tool.run(new String[] { "--invalid", "blah", "foo", "bar" });
        assertEquals(1, exitCode);
        // TODO: verify output
    }

    @Test
    public void testSmallAvro() throws Exception {

        String baseDir = "target/datasets";

        FileUtil.fullyDelete(new File(baseDir));

        String sampleGroup = "sample1";
        String input = "datasets/variants_avro";
        String output = "dataset:file:target/datasets/variants_flat_locuspart";

        int exitCode = tool.run(new String[] { "--sample-group", sampleGroup, input, output });

        assertEquals(0, exitCode);
        File partition = new File(baseDir, "variants_flat_locuspart/chr=1/pos=0/sample_group=sample1");
        assertTrue(partition.exists());

        File[] dataFiles = partition.listFiles(new FileFilter() {
            @Override
            public boolean accept(File pathname) {
                return !pathname.getName().startsWith(".");
            }
        });

        assertEquals(1, dataFiles.length);
        assertTrue(dataFiles[0].getName().endsWith(".parquet"));

        // loading into the same sample group again should fail
        exitCode = tool.run(new String[] { "--sample-group", sampleGroup, input, output });
        assertEquals(1, exitCode);

        // unless the overwrite option is specified
        exitCode = tool.run(new String[] { "--overwrite", "--sample-group", sampleGroup, input, output });
        assertEquals(0, exitCode);

        // loading into a new sample group should always succeed
        exitCode = tool.run(new String[] { "--sample-group", "sample2", input, output });
        assertEquals(0, exitCode);

    }

    @Test
    public void testSmallVCF() throws Exception {

        String baseDir = "target/datasets";

        FileUtil.fullyDelete(new File(baseDir));

        String sampleGroup = "sample1";
        String input = "datasets/variants_vcf/small.vcf";
        String output = "dataset:file:target/datasets/variants_flat_locuspart";

        int exitCode = tool.run(new String[] { "--sample-group", sampleGroup, input, output });

        assertEquals(0, exitCode);
        File partition = new File(baseDir, "variants_flat_locuspart/chr=1/pos=0/sample_group=sample1");
        assertTrue(partition.exists());

        File[] dataFiles = partition.listFiles(new FileFilter() {
            @Override
            public boolean accept(File pathname) {
                return !pathname.getName().startsWith(".");
            }
        });

        assertEquals(1, dataFiles.length);
        assertTrue(dataFiles[0].getName().endsWith(".parquet"));
    }
}