eu.eubrazilcc.lvl.core.util.TestUtils.java Source code

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Here is the source code for eu.eubrazilcc.lvl.core.util.TestUtils.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.util;

import static com.google.common.collect.Lists.newArrayList;
import static eu.eubrazilcc.lvl.core.AllTests.TEST_RESOURCES_PATH;
import static java.io.File.separator;
import static org.apache.commons.io.FileUtils.listFiles;
import static org.apache.commons.io.FilenameUtils.concat;

import java.io.File;
import java.net.URL;
import java.util.Collection;
import java.util.List;

/**
 * Test utilities.
 * @author Erik Torres <ertorser@upv.es>
 */
public class TestUtils {

    public static final String ANCHOR_FILENAME = "m2anchor";

    public static final String GENBANK_FOLDER = "genbank";
    public static final String GB_SETS_FOLDER = GENBANK_FOLDER + separator + "sets";
    public static final String GB_SEQUENCES_FOLDER = GENBANK_FOLDER + separator + "sequences";

    public static final String PUBMED_FOLDER = "pubmed";
    public static final String PM_SETS_FOLDER = PUBMED_FOLDER + separator + "sets";
    public static final String PM_ARTICLES_FOLDER = PUBMED_FOLDER + separator + "articles";

    public static final String TAXONOMY_FOLDER = "taxonomy";
    public static final String TAXONOMY_SETS_FOLDER = TAXONOMY_FOLDER + separator + "sets";

    public static final String GEOJSON_FOLDER = "geojson";

    public static final String RESOURCES_FOLDER;
    static {
        final URL anchorURL = TestUtils.class.getClassLoader().getResource(ANCHOR_FILENAME);
        File anchorFile = null;
        try {
            anchorFile = new File(anchorURL.toURI());
        } catch (Exception e) {
            anchorFile = new File(System.getProperty("user.dir"));
        }
        RESOURCES_FOLDER = anchorFile.getParent();
    }

    public static Collection<File> getGenBankFlatFiles() {
        final File dir = new File(concat(TEST_RESOURCES_PATH, GB_SEQUENCES_FOLDER));
        return listFiles(dir, new String[] { "gb" }, false);
    }

    public static Collection<File> getGBSeqXMLFiles() {
        final File dir = new File(concat(TEST_RESOURCES_PATH, GB_SEQUENCES_FOLDER));
        return listFiles(dir, new String[] { "xml" }, false);
    }

    public static Collection<File> getGBSeqXMLSetFiles() {
        final File dir = new File(concat(TEST_RESOURCES_PATH, GB_SETS_FOLDER));
        return listFiles(dir, new String[] { "xml" }, false);
    }

    public static Collection<File> getPubMedXMLFiles() {
        final File dir = new File(concat(TEST_RESOURCES_PATH, PM_ARTICLES_FOLDER));
        return listFiles(dir, new String[] { "xml" }, false);
    }

    public static Collection<File> getPubMedXMLSetFiles() {
        final File dir = new File(concat(TEST_RESOURCES_PATH, PM_SETS_FOLDER));
        return listFiles(dir, new String[] { "xml" }, false);
    }

    public static Collection<File> getTaxonomyXMLSetFiles() {
        final File dir = new File(concat(TEST_RESOURCES_PATH, TAXONOMY_SETS_FOLDER));
        return listFiles(dir, new String[] { "xml" }, false);
    }

    public static Collection<File> getGeoJsonFiles() {
        final File dir = new File(concat(TEST_RESOURCES_PATH, GEOJSON_FOLDER));
        return listFiles(dir, new String[] { "json" }, false);
    }

    public static Collection<File> getTextFiles() {
        final List<File> files = newArrayList();
        files.addAll(getGenBankFlatFiles());
        files.addAll(getGBSeqXMLFiles());
        files.addAll(getGBSeqXMLSetFiles());
        files.addAll(getPubMedXMLSetFiles());
        files.addAll(getGeoJsonFiles());
        return files;
    }

}