org.icgc.dcc.release.test.util.TestFiles.java Source code

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Here is the source code for org.icgc.dcc.release.test.util.TestFiles.java

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/*
 * Copyright (c) 2015 The Ontario Institute for Cancer Research. All rights reserved.                             
 *                                                                                                               
 * This program and the accompanying materials are made available under the terms of the GNU Public License v3.0.
 * You should have received a copy of the GNU General Public License along with                                  
 * this program. If not, see <http://www.gnu.org/licenses/>.                                                     
 *                                                                                                               
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY                           
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES                          
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT                           
 * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,                                
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED                          
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;                               
 * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER                              
 * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN                         
 * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package org.icgc.dcc.release.test.util;

import static com.fasterxml.jackson.core.JsonParser.Feature.AUTO_CLOSE_SOURCE;
import static com.google.common.base.Preconditions.checkState;

import java.io.File;
import java.io.PrintWriter;
import java.nio.charset.StandardCharsets;
import java.util.List;

import lombok.Cleanup;
import lombok.SneakyThrows;
import lombok.val;

import org.apache.commons.io.FileUtils;

import com.fasterxml.jackson.databind.MappingIterator;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;
import com.google.common.collect.Lists;

import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;

public class TestFiles {

    private static final ObjectMapper MAPPER = new ObjectMapper().configure(AUTO_CLOSE_SOURCE, false);

    @SneakyThrows
    public static void writeInputFile(File source, File target) {
        if (isCompressedFile(source)) {
            copyFiles(source, target);
        } else {
            writeTextInputFile(source, target);
        }
    }

    @SneakyThrows
    public static void writeTextInputFile(File source, File target) {
        val reader = MAPPER.reader(ObjectNode.class);

        @Cleanup
        val iterator = reader.readValues(source);

        @Cleanup
        val output = new PrintWriter(target, StandardCharsets.UTF_8.name());
        while (iterator.hasNext()) {
            val row = iterator.next();
            output.print(row.toString());
            output.println();
        }
    }

    @SneakyThrows
    public static void copyFiles(File source, File target) {
        FileUtils.copyFile(source, target);
    }

    @SneakyThrows
    public static void writeInputFile(List<ObjectNode> rows, File target) {
        @Cleanup
        val output = new PrintWriter(target, StandardCharsets.UTF_8.name());
        for (val row : rows) {
            output.print(row.toString());
            output.println();
        }
    }

    @SneakyThrows
    public static List<ObjectNode> readInputFile(File source) {
        if (source.isDirectory()) {
            return readInputDirectory(source);
        }

        val reader = MAPPER.reader(ObjectNode.class);

        @Cleanup
        MappingIterator<ObjectNode> iterator = reader.readValues(source);

        val rows = Lists.<ObjectNode>newArrayList();
        while (iterator.hasNext()) {
            val row = iterator.next();
            rows.add(row);
        }

        return rows;
    }

    @SuppressFBWarnings("NP_NULL_ON_SOME_PATH_FROM_RETURN_VALUE")
    public static List<ObjectNode> readInputDirectory(File sourceDir) {
        File[] files = sourceDir.listFiles(TestFiles::filterPartFiles);
        checkState(files != null, "Failed to resolve files in directory '%s'", sourceDir);
        val rows = Lists.<ObjectNode>newArrayList();
        for (val file : files) {
            rows.addAll(readInputFile(file));
        }

        return rows;
    }

    private static boolean filterPartFiles(File file) {
        return file.getName().startsWith("part-");
    }

    /**
     * This method is not reliable. It relies on the convention that {@code compressed} files are located in a
     * {@code compressed} directory.
     */
    private static boolean isCompressedFile(File source) {
        return source.getAbsolutePath().contains("compressed");
    }

}