eu.eubrazilcc.lvl.core.GbSeqXmlFileTest.java Source code

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Here is the source code for eu.eubrazilcc.lvl.core.GbSeqXmlFileTest.java

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/*
 * Copyright 2014 EUBrazilCC (EU?Brazil Cloud Connect)
 * 
 * Licensed under the EUPL, Version 1.1 or - as soon they will be approved by 
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at:
 * 
 *   http://ec.europa.eu/idabc/eupl
 * 
 * Unless required by applicable law or agreed to in writing, software 
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing permissions and 
 * limitations under the Licence.
 * 
 * This product combines work with different licenses. See the "NOTICE" text
 * file for details on the various modules and licenses.
 * The "NOTICE" text file is part of the distribution. Any derivative works
 * that you distribute must include a readable copy of the "NOTICE" text file.
 */

package eu.eubrazilcc.lvl.core;

import static com.google.common.collect.Lists.newArrayList;
import static eu.eubrazilcc.lvl.core.entrez.GbSeqXmlHelper.toFasta;
import static eu.eubrazilcc.lvl.core.util.TestUtils.getGBSeqXMLFiles;
import static java.lang.System.getProperty;
import static org.apache.commons.io.FileUtils.deleteQuietly;
import static org.apache.commons.io.FileUtils.readFileToString;
import static org.apache.commons.io.FilenameUtils.concat;
import static org.apache.commons.lang.RandomStringUtils.random;
import static org.apache.commons.lang.StringUtils.isNotBlank;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.notNullValue;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.Assert.fail;

import java.io.File;
import java.util.Collection;
import java.util.Collections;
import java.util.List;

import org.junit.After;
import org.junit.Before;
import org.junit.Test;

import eu.eubrazilcc.lvl.core.entrez.GbSeqXmlHelper;

/**
 * Tests GenBank sequence XML file helper class {@link GbSeqXmlHelper}.
 * @author Erik Torres <ertorser@upv.es>
 */
public class GbSeqXmlFileTest {

    private static final File TEST_OUTPUT_DIR = new File(concat(getProperty("java.io.tmpdir"),
            GbSeqXmlFileTest.class.getSimpleName() + "_" + random(8, true, true)));

    @Before
    public void setUp() {
        deleteQuietly(TEST_OUTPUT_DIR);
    }

    @Test
    public void test() {
        System.out.println("GbSeqXmlFileTest.test()");
        try {
            File output = null;
            String payload = null;

            // test writing individual FASTA files (uncompressed)
            final Collection<File> files = getGBSeqXMLFiles();
            for (final File file : files) {
                System.out.println(" >> Sequence file: " + file.getCanonicalPath());
                output = new File(TEST_OUTPUT_DIR, "sequence.fasta");
                toFasta(file, output.getCanonicalPath(), false);
                assertThat("fasta sequence file exists: " + output.getCanonicalPath(), output.canRead(),
                        equalTo(true));
                payload = readFileToString(output);
                assertThat("fasta sequence is not null", payload, notNullValue());
                assertThat("fasta sequence is not empty", isNotBlank(payload), equalTo(true));
                /* uncomment for additional output */
                System.out.println(" >> FASTA sequence \n" + payload);
            }

            // test writing a single FASTA file (uncompressed)
            output = new File(TEST_OUTPUT_DIR, "sequences.fasta");
            toFasta(files, output.getCanonicalPath(), false);
            assertThat("fasta sequences file exists: " + output.getCanonicalPath(), output.canRead(),
                    equalTo(true));
            payload = readFileToString(output);
            assertThat("fasta sequences is not null", payload, notNullValue());
            assertThat("fasta sequences is not empty", isNotBlank(payload), equalTo(true));
            /* uncomment for additional output */
            System.out.println(" >> FASTA sequences \n" + payload);

            // test writing a FASTA file (compressed)
            final List<File> list = newArrayList(files);
            Collections.shuffle(list);
            final File file = list.get(0);
            output = new File(TEST_OUTPUT_DIR, "sequence.fasta.gz");
            toFasta(file, output.getCanonicalPath(), false);
            assertThat("fasta GZIP compressed file exists: " + output.getCanonicalPath(), output.canRead(),
                    equalTo(true));
            assertThat("fasta GZIP compressed file is not empty", output.length() > 0l, equalTo(true));

        } catch (Exception e) {
            e.printStackTrace(System.err);
            fail("GbSeqXmlFileTest.test() failed: " + e.getMessage());
        } finally {
            System.out.println("GbSeqXmlFileTest.test() has finished");
        }
    }

    @After
    public void cleanUp() {
        deleteQuietly(TEST_OUTPUT_DIR);
    }

}