gatk-3.8/java/test/org/broadinstitute/sting/WalkerTest.java

package org.broadinstitute.sting;

import junit.framework.Assert;
import org.broadinstitute.sting.gatk.CommandLineExecutable;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.junit.Before;
import org.junit.Test;
import org.apache.log4j.Appender;
import org.apache.log4j.WriterAppender;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.math.BigInteger;
import java.security.MessageDigest;
import java.util.*;

public class WalkerTest extends BaseTest {
    // the default output path for the integration test
    private File outputFileLocation = null;

    public void setOutputFileLocation(File outputFileLocation) {
        this.outputFileLocation = outputFileLocation;
    }

    public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
        try {
            byte[] bytesOfMessage = getBytesFromFile(resultsFile);
            byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytesOfMessage);
            BigInteger bigInt = new BigInteger(1, thedigest);
            String filemd5sum = bigInt.toString(16);
            while (filemd5sum.length() < 32) filemd5sum = "0" + filemd5sum; // pad to length 32
            if (parameterize() || expectedMD5.equals("")) {
                System.out.println(String.format("PARAMETERIZATION[%s]: file %s has md5 = %s, stated expectation is %s, equal? = %b",
                                                 name, resultsFile, filemd5sum, expectedMD5, filemd5sum.equals(expectedMD5)));
            } else {
                System.out.println(String.format("Checking MD5 for %s [calculated=%s, expected=%s]", resultsFile, filemd5sum, expectedMD5));
                System.out.flush();
                Assert.assertEquals(name + " Mismatching MD5s", expectedMD5, filemd5sum);
                System.out.println(String.format("  => %s PASSED", name));
            }

            return filemd5sum;
        } catch (Exception e) {
            throw new RuntimeException("Failed to read bytes from calls file: " + resultsFile);
        }
    }

    public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) {
        List<String> md5s = new ArrayList<String>();
        for (int i = 0; i < resultFiles.size(); i++) {
            String md5 = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i));
            md5s.add(i, md5);
        }

        return md5s;
    }


    public static byte[] getBytesFromFile(File file) throws IOException {
        InputStream is = new FileInputStream(file);

        // Get the size of the file
        long length = file.length();

        if (length > Integer.MAX_VALUE) {
            // File is too large
        }

        // Create the byte array to hold the data
        byte[] bytes = new byte[(int) length];

        // Read in the bytes
        int offset = 0;
        int numRead = 0;
        while (offset < bytes.length
                && (numRead = is.read(bytes, offset, bytes.length - offset)) >= 0) {
            offset += numRead;
        }

        // Ensure all the bytes have been read in
        if (offset < bytes.length) {
            throw new IOException("Could not completely read file " + file.getName());
        }

        // Close the input stream and return bytes
        is.close();
        return bytes;
    }

    public class WalkerTestSpec {
        String args = "";
        int nOutputFiles = -1;
        List<String> md5s = null;
        List<String> exts = null;

        protected Map<String, File> auxillaryFiles = new HashMap<String, File>();

        public WalkerTestSpec(String args, int nOutputFiles, List<String> md5s) {
            this.args = args;
            this.nOutputFiles = nOutputFiles;
            this.md5s = md5s;
        }

        public WalkerTestSpec(String args, int nOutputFiles, List<String> exts, List<String> md5s) {
            this.args = args;
            this.nOutputFiles = nOutputFiles;
            this.md5s = md5s;
            this.exts = exts;
        }

        public void addAuxFile(String expectededMD5sum, File outputfile) {
            auxillaryFiles.put(expectededMD5sum, outputfile);
        }
    }

    protected boolean parameterize() {
        return false;
    }

    protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec) {
        List<File> tmpFiles = new ArrayList<File>();
        for (int i = 0; i < spec.nOutputFiles; i++) {
            String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i);
            File fl = createTempFile(String.format("walktest.tmp_param.%d", i), ext);
            tmpFiles.add(fl);
        }

        final String args = String.format(spec.args, tmpFiles.toArray());
        System.out.println(Utils.dupString('-', 80));

        List<String> md5s = new LinkedList<String>();
        md5s.addAll(spec.md5s);

        // check to see if they included any auxillary files, if so add them to the list
        for (String md5 : spec.auxillaryFiles.keySet()) {
            md5s.add(md5);
            tmpFiles.add(spec.auxillaryFiles.get(md5));
        }

        return executeTest(name, md5s, tmpFiles, args);
    }

    public File createTempFile(String name, String extension) {
        try {
            File fl = File.createTempFile(name, extension);
            //fl.deleteOnExit();
            return fl;
        } catch (IOException ex) {
            throw new StingException("Cannot create temp file: " + ex.getMessage(), ex);
        }
    }

    /**
     * execute the test, given the following:
     * @param name     the name of the test
     * @param md5s     the list of md5s
     * @param tmpFiles the temp file corresponding to the md5 list
     * @param args     the argument list
     * @return a pair of file and string lists
     */
    private Pair<List<File>, List<String>> executeTest(String name, List<String> md5s, List<File> tmpFiles, String args) {
        CommandLineGATK instance = new CommandLineGATK();
        String[] command;

        // special case for ' and " so we can allow expressions
        if (args.indexOf('\'') != -1)
            command = escapeExpressions(args, "'");
        else if (args.indexOf('\"') != -1)
            command = escapeExpressions(args, "\"");
        else
            command = args.split(" ");

        if (outputFileLocation != null) {
            String[] cmd2 = Arrays.copyOf(command, command.length + 2);
            cmd2[command.length] = "-o";
            cmd2[command.length + 1] = this.outputFileLocation.getAbsolutePath();
            command = cmd2;
        }
        System.out.println(String.format("Executing test %s with GATK arguments: %s", name, Utils.join(" ",command)));
        CommandLineExecutable.start(instance, command);

        if (CommandLineExecutable.result != 0) {
            throw new RuntimeException("Error running the GATK with arguments: " + args);
        }

        return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, md5s));
    }

    private static String[] escapeExpressions(String args, String delimiter) {
        String[] command = {};
        String[] split = args.split(delimiter);
        for (int i = 0; i < split.length - 1; i += 2) {
            command = Utils.concatArrays(command, split[i].trim().split(" "));
            command = Utils.concatArrays(command, new String[]{split[i + 1]});
        }
        return Utils.concatArrays(command, split[split.length - 1].trim().split(" "));
    }

    @Test
    public void testWalkerTest() {
        //System.out.println("WalkerTest is just a framework");
    }
}