/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF 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
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License 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 org.apache.sysds.test;

import static java.lang.Thread.sleep;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;

import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.PrintStream;
import java.net.ServerSocket;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Properties;

import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.util.GenericOptionsParser;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.SparkSession.Builder;
import org.apache.sysds.api.DMLScript;
import org.apache.sysds.common.Types.DataType;
import org.apache.sysds.common.Types.ExecMode;
import org.apache.sysds.common.Types.FileFormat;
import org.apache.sysds.common.Types.ValueType;
import org.apache.sysds.conf.ConfigurationManager;
import org.apache.sysds.conf.DMLConfig;
import org.apache.sysds.hops.OptimizerUtils;
import org.apache.sysds.lops.Lop;
import org.apache.sysds.lops.LopProperties.ExecType;
import org.apache.sysds.parser.DataExpression;
import org.apache.sysds.parser.ParseException;
import org.apache.sysds.runtime.DMLRuntimeException;
import org.apache.sysds.runtime.DMLScriptException;
import org.apache.sysds.runtime.controlprogram.caching.MatrixObject;
import org.apache.sysds.runtime.controlprogram.context.SparkExecutionContext;
import org.apache.sysds.runtime.controlprogram.federated.FederationMap;
import org.apache.sysds.runtime.io.FileFormatPropertiesCSV;
import org.apache.sysds.runtime.io.FrameReader;
import org.apache.sysds.runtime.io.FrameReaderFactory;
import org.apache.sysds.runtime.io.ReaderWriterFederated;
import org.apache.sysds.runtime.matrix.data.FrameBlock;
import org.apache.sysds.runtime.matrix.data.MatrixBlock;
import org.apache.sysds.runtime.matrix.data.MatrixValue.CellIndex;
import org.apache.sysds.runtime.meta.MatrixCharacteristics;
import org.apache.sysds.runtime.privacy.CheckedConstraintsLog;
import org.apache.sysds.runtime.privacy.PrivacyConstraint;
import org.apache.sysds.runtime.privacy.PrivacyConstraint.PrivacyLevel;
import org.apache.sysds.runtime.privacy.PrivacyUtils;
import org.apache.sysds.runtime.util.DataConverter;
import org.apache.sysds.runtime.util.HDFSTool;
import org.apache.sysds.utils.ParameterBuilder;
import org.apache.sysds.utils.Statistics;
import org.apache.wink.json4j.JSONException;
import org.apache.wink.json4j.JSONObject;
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;

/**
 * <p>
 * Extend this class to easily
 * </p>
 * <ul>
 * <li>set up an environment for DML script execution</li>
 * <li>use multiple test cases</li>
 * <li>generate test data></li>
 * <li>check results</li>
 * <li>clean up after test run</li>
 * </ul>
 *
 */
@SuppressWarnings("deprecation")
public abstract class AutomatedTestBase {

	private static final Log LOG = LogFactory.getLog(AutomatedTestBase.class.getName());

	public static final boolean EXCEPTION_EXPECTED = true;
	public static final boolean EXCEPTION_NOT_EXPECTED = false;

	// By default: TEST_GPU is set to false to allow developers without Nvidia GPU to run integration test suite
	public static boolean TEST_GPU = false;
	public static final double GPU_TOLERANCE = 1e-9;

	public static final int FED_WORKER_WAIT = 1000; // in ms

	// With OpenJDK 8u242 on Windows, the new changes in JDK are not allowing
	// to set the native library paths internally thus breaking the code.
	// That is why, these static assignments to java.library.path and hadoop.home.dir
	// (for native winutils) have been removed.

	/**
	 * Script source directory for .dml and .r files only (TEST_DATA_DIR for generated test data artifacts).
	 */
	protected static final String SCRIPT_DIR = "./src/test/scripts/";
	protected static final String INPUT_DIR = "in/";
	protected static final String OUTPUT_DIR = "out/";
	protected static final String EXPECTED_DIR = "expected/";

	/** Location where this class writes files for inspection if DEBUG is set to true. */
	private static final String DEBUG_TEMP_DIR = "./tmp/";

	/** Directory under which config files shared across tests are located. */
	private static final String CONFIG_DIR = "./src/test/config/";

	/**
	 * Location of the SystemDS config file that we use as a template when generating the configs for each test case.
	 */
	private static final File CONFIG_TEMPLATE_FILE = new File(CONFIG_DIR, "SystemDS-config.xml");

	protected enum CodegenTestType {
		DEFAULT, FUSE_ALL, FUSE_NO_REDUNDANCY;

		public String getCodgenConfig() {
			switch(this) {
				case DEFAULT:
					return "SystemDS-config-codegen.xml";
				case FUSE_ALL:
					return "SystemDS-config-codegen-fuse-all.xml";
				case FUSE_NO_REDUNDANCY:
					return "SystemDS-config-codegen-fuse-no-redundancy.xml";
				default:
					throw new RuntimeException("Unsupported codegen test config: " + this.name());
			}
		}
	}

	/**
	 * Location under which we create local temporary directories for test cases. To adjust where testTemp is located,
	 * use -Dsystemds.testTemp.root.dir=<new location>. This is necessary if any parent directories are
	 * public-protected.
	 */
	private static final String LOCAL_TEMP_ROOT_DIR = System.getProperty("systemds.testTemp.root.dir",
		"target/testTemp");
	private static final File LOCAL_TEMP_ROOT = new File(LOCAL_TEMP_ROOT_DIR);

	/** Base directory for generated IN, OUT, EXPECTED test data artifacts instead of SCRIPT_DIR. */
	protected static final String TEST_DATA_DIR = LOCAL_TEMP_ROOT_DIR + "/";
	protected static final boolean TEST_CACHE_ENABLED = true;
	/** Optional sub-directory under EXPECTED_DIR for reusing R script test results */
	private String cacheDir = "";

	/**
	 * Runtime backend to use for all integration tests. Some individual tests override this value, but the rest will
	 * use whatever is the default here.
	 * <p>
	 * Also set DMLScript.USE_LOCAL_SPARK_CONFIG to true for running the test suite in spark mode
	 */
	protected static ExecMode rtplatform = ExecMode.HYBRID;

	protected static final boolean DEBUG = false;

	public static boolean VERBOSE_STATS = false;

	protected String fullDMLScriptName; // utilize for both DML and PyDML, should probably be renamed.
	// protected String fullPYDMLScriptName;
	protected String fullRScriptName;

	protected static String baseDirectory;
	protected static String sourceDirectory;
	protected HashMap<String, TestConfiguration> availableTestConfigurations;

	/* For testing in the old way */
	protected HashMap<String, String> testVariables; /* variables and their values */

	/* For testing in the new way */
	// protected String[] dmlArgs; /* program-independent arguments to SystemDS (e.g., debug, execution mode) */
	protected String[] programArgs; /* program-specific arguments, which are passed to SystemDS via -args option */
	protected String rCmd; /* Rscript foo.R arg1, arg2 ... */

	protected String selectedTest;
	protected String[] outputDirectories;
	protected String[] comparisonFiles;
	protected ArrayList<String> inputDirectories;
	protected ArrayList<String> inputRFiles;
	protected ArrayList<String> expectedFiles;

	private File curLocalTempDir = null;

	private boolean isOutAndExpectedDeletionDisabled = false;

	private static boolean outputBuffering = false;

	static {
		java.io.InputStream inputStream = Thread.currentThread().getContextClassLoader()
			.getResourceAsStream("my.properties");
		java.util.Properties properties = new Properties();
		try {
			properties.load(inputStream);
		}
		catch(IOException e) {
			e.printStackTrace();
		}
		outputBuffering = Boolean.parseBoolean(properties.getProperty("automatedtestbase.outputbuffering"));
		boolean gpu = Boolean.parseBoolean(properties.getProperty("enableGPU"));
		TEST_GPU = TEST_GPU || gpu;
		boolean stats = Boolean.parseBoolean(properties.getProperty("enableStats"));
		VERBOSE_STATS = VERBOSE_STATS || stats;
	}

	// Timestamp before test start.
	private long lTimeBeforeTest;

	@Before
	public abstract void setUp();

	/**
	 * <p>
	 * Adds a test configuration to the list of available test configurations.
	 * </p>
	 *
	 * @param testName test name
	 * @param config   test configuration
	 */
	protected void addTestConfiguration(String testName, TestConfiguration config) {
		availableTestConfigurations.put(testName, config);
	}

	protected void addTestConfiguration(TestConfiguration config) {
		availableTestConfigurations.put(config.getTestScript(), config);
	}

	/**
	 * <p>
	 * Adds a test configuration to the list of available test configurations based on the test directory and the test
	 * name.
	 * </p>
	 *
	 * @param testDirectory test directory
	 * @param testName      test name
	 */
	protected void addTestConfiguration(String testDirectory, String testName) {
		TestConfiguration config = new TestConfiguration(testDirectory, testName);
		availableTestConfigurations.put(testName, config);
	}

	@Before
	public final void setUpBase() {
		availableTestConfigurations = new HashMap<>();
		testVariables = new HashMap<>();
		inputDirectories = new ArrayList<>();
		inputRFiles = new ArrayList<>();
		expectedFiles = new ArrayList<>();
		outputDirectories = new String[0];
		setOutAndExpectedDeletionDisabled(false);
		lTimeBeforeTest = System.currentTimeMillis();

		TestUtils.clearAssertionInformation();
	}

	protected void setOutputBuffering(boolean value) {
		outputBuffering = value;
	}

	/**
	 * <p>
	 * Returns a test configuration from the list of available configurations. If no configuration is added for the
	 * specified name, the test will fail.
	 * </p>
	 *
	 * @param testName test name
	 * @return test configuration
	 */
	protected TestConfiguration getTestConfiguration(String testName) {
		if(!availableTestConfigurations.containsKey(testName))
			fail("unable to load test configuration");

		return availableTestConfigurations.get(testName);
	}

	/**
	 * <p>
	 * Gets a test configuration from the list of available configurations and loads it if it's available. It is then
	 * returned. If no configuration exists for the specified name, the test will fail.
	 *
	 * </p>
	 *
	 * @param testName test name
	 * @return test configuration
	 */
	protected TestConfiguration getAndLoadTestConfiguration(String testName) {
		TestConfiguration testConfiguration = getTestConfiguration(testName);
		loadTestConfiguration(testConfiguration);
		return testConfiguration;
	}

	/**
	 * Subclasses must call {@link #loadTestConfiguration(TestConfiguration)} before calling this method.
	 *
	 * @return the directory where the current test case should write temp files. This directory also contains the
	 *         current test's customized SystemDS config file.
	 */
	protected File getCurLocalTempDir() {
		if(null == curLocalTempDir) {
			throw new RuntimeException("Called getCurLocalTempDir() before calling loadTestConfiguration()");
		}
		return curLocalTempDir;
	}

	/**
	 * Subclasses must call {@link #loadTestConfiguration(TestConfiguration)} before calling this method.
	 *
	 * @return the location of the current test case's SystemDS config file
	 */
	protected File getCurConfigFile() {
		return new File(getCurLocalTempDir(), "SystemDS-config.xml");
	}

	/**
	 * <p>
	 * Tests that use custom SystemDS configuration should override to ensure scratch space and local temporary
	 * directory locations are also updated.
	 * </p>
	 */
	protected File getConfigTemplateFile() {
		return CONFIG_TEMPLATE_FILE;
	}

	protected File getCodegenConfigFile(String parent, CodegenTestType type) {
		// Instrumentation in this test's output log to show custom configuration file used for template.
		File tmp = new File(parent, type.getCodgenConfig());
		if(LOG.isInfoEnabled())
			LOG.info("This test case overrides default configuration with " + tmp.getPath());
		return tmp;
	}

	protected ExecMode setExecMode(ExecType instType) {
		switch(instType) {
			case SPARK:
				return setExecMode(ExecMode.SPARK);
			default:
				return setExecMode(ExecMode.HYBRID);
		}
	}

	protected ExecMode setExecMode(ExecMode execMode) {
		ExecMode platformOld = rtplatform;
		rtplatform = execMode;
		if(rtplatform != ExecMode.SINGLE_NODE)
			DMLScript.USE_LOCAL_SPARK_CONFIG = true;
		return platformOld;
	}

	protected void resetExecMode(ExecMode execModeOld) {
		rtplatform = execModeOld;
		DMLScript.USE_LOCAL_SPARK_CONFIG = false;
	}

	/**
	 * <p>
	 * Generates a random matrix with the specified characteristics and returns it as a two dimensional array.
	 * </p>
	 *
	 * @param rows     number of rows
	 * @param cols     number of columns
	 * @param min      minimum value
	 * @param max      maximum value
	 * @param sparsity sparsity
	 * @param seed     seed
	 * @return two dimensional array containing random matrix
	 */
	protected double[][] getRandomMatrix(int rows, int cols, double min, double max, double sparsity, long seed) {
		return TestUtils.generateTestMatrix(rows, cols, min, max, sparsity, seed);
	}

	/**
	 * <p>
	 * Generates a random matrix with the specified characteristics and returns it as a two dimensional array.
	 * </p>
	 *
	 * @param rows     number of rows
	 * @param cols     number of columns
	 * @param min      minimum value
	 * @param max      maximum value
	 * @param sparsity sparsity
	 * @param seed     seed
	 * @param delta    The minimum value in between values.
	 * @return two dimensional array containing random matrix
	 */
	protected double[][] getRandomMatrix(int rows, int cols, double min, double max, double sparsity, long seed,
		double delta) {
		return TestUtils.generateTestMatrix(rows, cols, min, max, sparsity, seed, delta);
	}

	/**
	 * <p>
	 * Generates a random matrix with the specified characteristics which does not contain any zero values and returns
	 * it as a two dimensional array.
	 * </p>
	 *
	 * @param rows number of rows
	 * @param cols number of columns
	 * @param min  minimum value
	 * @param max  maximum value
	 * @param seed seed
	 * @return two dimensional array containing random matrix
	 */
	protected double[][] getNonZeroRandomMatrix(int rows, int cols, double min, double max, long seed) {
		return TestUtils.generateNonZeroTestMatrix(rows, cols, min, max, seed);
	}

	/**
	 * <p>
	 * Generates a random matrix with the specified characteristics and writes it to a file.
	 * </p>
	 *
	 * @param name     directory name
	 * @param rows     number of rows
	 * @param cols     number of columns
	 * @param min      minimum value
	 * @param max      maximum value
	 * @param sparsity sparsity
	 * @param seed     seed
	 */
	protected double[][] createRandomMatrix(String name, int rows, int cols, double min, double max, double sparsity,
		long seed) {
		return createRandomMatrix(name, rows, cols, min, max, sparsity, seed, false);
	}

	/**
	 * <p>
	 * Generates a random matrix with the specified characteristics and writes it to a file.
	 * </p>
	 *
	 * @param name      directory name
	 * @param rows      number of rows
	 * @param cols      number of columns
	 * @param min       minimum value
	 * @param max       maximum value
	 * @param sparsity  sparsity
	 * @param seed      seed
	 * @param bIncludeR If true, writes also a R matrix to disk
	 */
	protected double[][] createRandomMatrix(String name, int rows, int cols, double min, double max, double sparsity,
		long seed, boolean bIncludeR) {
		double[][] matrix = TestUtils.generateTestMatrix(rows, cols, min, max, sparsity, seed);
		String completePath = baseDirectory + INPUT_DIR + name + "/in";

		TestUtils.writeTestMatrix(completePath, matrix, bIncludeR);
		if(DEBUG)
			TestUtils.writeTestMatrix(DEBUG_TEMP_DIR + completePath, matrix);
		inputDirectories.add(baseDirectory + INPUT_DIR + name);
		return matrix;
	}

	private static void cleanupExistingData(String fname, boolean cleanupRData) throws IOException {
		HDFSTool.deleteFileIfExistOnHDFS(fname);
		HDFSTool.deleteFileIfExistOnHDFS(fname + ".mtd");
		if(cleanupRData)
			HDFSTool.deleteFileIfExistOnHDFS(fname + ".mtx");
	}

	/**
	 * <p>
	 * Adds a matrix to the input path and writes it to a file.
	 * </p>
	 *
	 * @param name      directory name
	 * @param matrix    two dimensional matrix
	 * @param bIncludeR generates also the corresponding R matrix
	 */
	protected double[][] writeInputMatrix(String name, double[][] matrix, boolean bIncludeR) {
		String completePath = baseDirectory + INPUT_DIR + name + "/in";
		String completeRPath = baseDirectory + INPUT_DIR + name + ".mtx";

		try {
			cleanupExistingData(baseDirectory + INPUT_DIR + name, bIncludeR);
		}
		catch(IOException e) {
			e.printStackTrace();
			throw new RuntimeException(e);
		}

		TestUtils.writeTestMatrix(completePath, matrix);
		if(bIncludeR) {
			TestUtils.writeTestMatrix(completeRPath, matrix, true);
			inputRFiles.add(completeRPath);
		}
		if(DEBUG)
			TestUtils.writeTestMatrix(DEBUG_TEMP_DIR + completePath, matrix);
		inputDirectories.add(baseDirectory + INPUT_DIR + name);

		return matrix;
	}

	protected double[][] writeInputMatrixWithMTD(String name, MatrixBlock matrix, boolean bIncludeR) {
		double[][] data = DataConverter.convertToDoubleMatrix(matrix);
		return writeInputMatrixWithMTD(name, data, bIncludeR);
	}

	protected double[][] writeInputMatrixWithMTD(String name, double[][] matrix, boolean bIncludeR) {
		MatrixCharacteristics mc = new MatrixCharacteristics(matrix.length, matrix[0].length,
			OptimizerUtils.DEFAULT_BLOCKSIZE, -1);
		return writeInputMatrixWithMTD(name, matrix, bIncludeR, mc);
	}

	protected double[][] writeInputMatrixWithMTD(String name, double[][] matrix, long nnz, boolean bIncludeR) {
		MatrixCharacteristics mc = new MatrixCharacteristics(matrix.length, matrix[0].length,
			OptimizerUtils.DEFAULT_BLOCKSIZE, nnz);
		return writeInputMatrixWithMTD(name, matrix, bIncludeR, mc, null);
	}

	protected double[][] writeInputMatrixWithMTD(String name, double[][] matrix, boolean bIncludeR,
		MatrixCharacteristics mc) {
		return writeInputMatrixWithMTD(name, matrix, bIncludeR, mc, null);
	}

	protected double[][] writeInputMatrixWithMTD(String name, double[][] matrix, PrivacyConstraint privacyConstraint) {
		return writeInputMatrixWithMTD(name, matrix, false, null, privacyConstraint);
	}

	protected double[][] writeInputMatrixWithMTD(String name, double[][] matrix, boolean bIncludeR,
		PrivacyConstraint privacyConstraint) {
		MatrixCharacteristics mc = new MatrixCharacteristics(matrix.length, matrix[0].length,
			OptimizerUtils.DEFAULT_BLOCKSIZE, -1);
		return writeInputMatrixWithMTD(name, matrix, bIncludeR, mc, privacyConstraint);
	}

	protected double[][] writeInputMatrixWithMTD(String name, double[][] matrix, boolean bIncludeR,
		MatrixCharacteristics mc, PrivacyConstraint privacyConstraint) {
		writeInputMatrix(name, matrix, bIncludeR);

		// write metadata file
		try {
			String completeMTDPath = baseDirectory + INPUT_DIR + name + ".mtd";
			HDFSTool.writeMetaDataFile(completeMTDPath, ValueType.FP64, mc, FileFormat.TEXT, privacyConstraint);
		}
		catch(IOException e) {
			e.printStackTrace();
			throw new RuntimeException(e);
		}

		return matrix;
	}

	protected void writeInputFederatedWithMTD(String name, MatrixObject fm, PrivacyConstraint privacyConstraint){
		writeFederatedInputMatrix(name, fm.getFedMapping());
		MatrixCharacteristics mc = (MatrixCharacteristics)fm.getDataCharacteristics();
		try {
			String completeMTDPath = baseDirectory + INPUT_DIR + name + ".mtd";
			HDFSTool.writeMetaDataFile(completeMTDPath, ValueType.FP64, mc, FileFormat.FEDERATED, privacyConstraint);
		}
		catch(IOException e) {
			e.printStackTrace();
			throw new RuntimeException(e);
		}

	}

	protected void writeFederatedInputMatrix(String name, FederationMap fedMap){
		String completePath = baseDirectory + INPUT_DIR + name;
		try {
			cleanupExistingData(baseDirectory + INPUT_DIR + name, false);
		}
		catch(IOException e) {
			e.printStackTrace();
			throw new RuntimeException(e);
		}

		ReaderWriterFederated.write(completePath, fedMap);
		inputDirectories.add(baseDirectory + INPUT_DIR + name);
	}

	/**
	 * <p>
	 * Adds a matrix to the input path and writes it to a file.
	 * </p>
	 *
	 * @param name   directory name
	 * @param matrix two dimensional matrix
	 */
	protected double[][] writeInputMatrix(String name, double[][] matrix) {
		return writeInputMatrix(name, matrix, false);
	}

	/**
	 * <p>
	 * Adds a matrix to the input path and writes it to a file in binary format.
	 * </p>
	 *
	 * @param name         directory name
	 * @param matrix       two dimensional matrix
	 * @param rowsInBlock  rows in block
	 * @param colsInBlock  columns in block
	 * @param sparseFormat sparse format
	 */
	protected void writeInputBinaryMatrix(String name, double[][] matrix, int rowsInBlock, int colsInBlock,
		boolean sparseFormat) {
		String completePath = baseDirectory + INPUT_DIR + name + "/in";

		try {
			cleanupExistingData(baseDirectory + INPUT_DIR + name, false);
		}
		catch(IOException e) {
			e.printStackTrace();
			throw new RuntimeException(e);
		}

		if(rowsInBlock == 1 && colsInBlock == 1) {
			TestUtils.writeBinaryTestMatrixCells(completePath, matrix);
			if(DEBUG)
				TestUtils.writeBinaryTestMatrixCells(DEBUG_TEMP_DIR + completePath, matrix);
		}
		else {
			TestUtils.writeBinaryTestMatrixBlocks(completePath, matrix, rowsInBlock, colsInBlock, sparseFormat);
			if(DEBUG)
				TestUtils.writeBinaryTestMatrixBlocks(DEBUG_TEMP_DIR +
					completePath, matrix, rowsInBlock, colsInBlock, sparseFormat);
		}
		inputDirectories.add(baseDirectory + INPUT_DIR + name);
	}

	/**
	 * Writes the given matrix to input path, and writes the associated metadata file.
	 *
	 * @param name
	 * @param matrix
	 * @param rowsInBlock
	 * @param colsInBlock
	 * @param sparseFormat
	 * @param mc
	 * @throws IOException
	 */
	protected void writeInputBinaryMatrixWithMTD(String name, double[][] matrix, int rowsInBlock, int colsInBlock,
		boolean sparseFormat, MatrixCharacteristics mc) throws IOException {
		writeInputBinaryMatrix(name, matrix, rowsInBlock, colsInBlock, sparseFormat);
		// write metadata file
		String completeMTDPath = baseDirectory + INPUT_DIR + name + ".mtd";
		HDFSTool.writeMetaDataFile(completeMTDPath, ValueType.FP64, mc, FileFormat.BINARY);
	}

	/**
	 * <p>
	 * Adds a matrix to the expectation path and writes it to a file.
	 * </p>
	 *
	 * @param name   directory name
	 * @param matrix two dimensional matrix
	 */
	protected void writeExpectedMatrix(String name, double[][] matrix) {
		TestUtils.writeTestMatrix(baseDirectory + EXPECTED_DIR + cacheDir + name, matrix);
		expectedFiles.add(baseDirectory + EXPECTED_DIR + cacheDir + name);
	}

	/**
	 * <p>
	 * Adds a matrix to the expectation path and writes it to a file.
	 * </p>
	 *
	 * @param name   directory name
	 * @param matrix two dimensional matrix
	 */
	protected void writeExpectedMatrixMarket(String name, double[][] matrix) {
		File path = new File(baseDirectory, EXPECTED_DIR + cacheDir);
		path.mkdirs();

		TestUtils.writeTestMatrix(baseDirectory + EXPECTED_DIR + cacheDir + name, matrix, true);
		expectedFiles.add(baseDirectory + EXPECTED_DIR + cacheDir + name);
	}

	/**
	 * <p>
	 * Adds a matrix to the expectation path and writes it to a file in binary format.
	 * </p>
	 *
	 * @param name         directory name
	 * @param matrix       two dimensional matrix
	 * @param rowsInBlock  rows in block
	 * @param colsInBlock  columns in block
	 * @param sparseFormat sparse format
	 */
	protected void writeExpectedBinaryMatrix(String name, double[][] matrix, int rowsInBlock, int colsInBlock,
		boolean sparseFormat) {
		if(rowsInBlock == 1 && colsInBlock == 1) {
			TestUtils.writeBinaryTestMatrixCells(baseDirectory + EXPECTED_DIR + name + "/in", matrix);
		}
		else {
			TestUtils.writeBinaryTestMatrixBlocks(baseDirectory + EXPECTED_DIR + name
				+ "/in", matrix, rowsInBlock, colsInBlock, sparseFormat);
		}
		inputDirectories.add(baseDirectory + EXPECTED_DIR + name);
	}

	/**
	 * <p>
	 * Creates a helper matrix which can be used for writing scalars to a file.
	 * </p>
	 */
	protected void createHelperMatrix() {
		TestUtils.writeTestMatrix(baseDirectory + INPUT_DIR + "helper/in", new double[][] {{1, 1}});
		inputDirectories.add(baseDirectory + INPUT_DIR + "helper");
	}

	/**
	 * <p>
	 * Creates a expectation helper matrix which can be used to compare scalars.
	 * </p>
	 *
	 * @param name  file name
	 * @param value scalar value
	 */
	protected void writeExpectedHelperMatrix(String name, double value) {
		TestUtils.writeTestMatrix(baseDirectory + EXPECTED_DIR + cacheDir + name, new double[][] {{value, value}});
		expectedFiles.add(baseDirectory + EXPECTED_DIR + cacheDir + name);
	}

	protected void writeExpectedScalar(String name, double value) {
		File path = new File(baseDirectory, EXPECTED_DIR + cacheDir);
		path.mkdirs();

		TestUtils.writeTestScalar(baseDirectory + EXPECTED_DIR + cacheDir + name, value);
		expectedFiles.add(baseDirectory + EXPECTED_DIR + cacheDir + name);
	}

	protected void writeExpectedScalar(String name, long value) {
		File path = new File(baseDirectory, EXPECTED_DIR + cacheDir);
		path.mkdirs();

		TestUtils.writeTestScalar(baseDirectory + EXPECTED_DIR + cacheDir + name, value);
		expectedFiles.add(baseDirectory + EXPECTED_DIR + cacheDir + name);
	}

	protected static HashMap<CellIndex, Double> readDMLMatrixFromHDFS(String fileName) {
		return TestUtils.readDMLMatrixFromHDFS(baseDirectory + OUTPUT_DIR + fileName);
	}

	public HashMap<CellIndex, Double> readRMatrixFromFS(String fileName) {
		if(LOG.isInfoEnabled())
			LOG.info("R script out: " + baseDirectory + EXPECTED_DIR + cacheDir + fileName);
		return TestUtils.readRMatrixFromFS(baseDirectory + EXPECTED_DIR + cacheDir + fileName);
	}

	protected static HashMap<CellIndex, Double> readDMLScalarFromHDFS(String fileName) {
		return TestUtils.readDMLScalarFromHDFS(baseDirectory + OUTPUT_DIR + fileName);
	}

	protected static String readDMLLineageFromHDFS(String fileName) {
		return TestUtils.readDMLString(baseDirectory + OUTPUT_DIR + fileName + ".lineage");
	}

	protected static String readDMLLineageDedupFromHDFS(String fileName) {
		return TestUtils.readDMLString(baseDirectory + OUTPUT_DIR + fileName + ".lineage.dedup");
	}

	protected static FrameBlock readDMLFrameFromHDFS(String fileName, FileFormat fmt) throws IOException {
		// read frame data from hdfs
		String strFrameFileName = baseDirectory + OUTPUT_DIR + fileName;
		FrameReader reader = FrameReaderFactory.createFrameReader(fmt);

		MatrixCharacteristics md = readDMLMetaDataFile(fileName);
		return reader.readFrameFromHDFS(strFrameFileName, md.getRows(), md.getCols());
	}

	protected static FrameBlock readDMLFrameFromHDFS(String fileName, FileFormat fmt, MatrixCharacteristics md)
		throws IOException {
		// read frame data from hdfs
		String strFrameFileName = baseDirectory + OUTPUT_DIR + fileName;
		FrameReader reader = FrameReaderFactory.createFrameReader(fmt);

		return reader.readFrameFromHDFS(strFrameFileName, md.getRows(), md.getCols());
	}

	protected static FrameBlock readRFrameFromHDFS(String fileName, FileFormat fmt, MatrixCharacteristics md)
		throws IOException {
		// read frame data from hdfs
		String strFrameFileName = baseDirectory + EXPECTED_DIR + fileName;

		FileFormatPropertiesCSV fprop = new FileFormatPropertiesCSV();
		fprop.setHeader(true);
		FrameReader reader = FrameReaderFactory.createFrameReader(fmt, fprop);

		return reader.readFrameFromHDFS(strFrameFileName, md.getRows(), md.getCols());
	}

	public HashMap<CellIndex, Double> readRScalarFromFS(String fileName) {
		if(LOG.isInfoEnabled())
			LOG.info("R script out: " + baseDirectory + EXPECTED_DIR + cacheDir + fileName);
		return TestUtils.readRScalarFromFS(baseDirectory + EXPECTED_DIR + cacheDir + fileName);
	}

	public static void checkDMLMetaDataFile(String fileName, MatrixCharacteristics mc) {
		MatrixCharacteristics rmc = readDMLMetaDataFile(fileName);
		Assert.assertEquals(mc.getRows(), rmc.getRows());
		Assert.assertEquals(mc.getCols(), rmc.getCols());
	}

	public static MatrixCharacteristics readDMLMetaDataFile(String fileName) {
		try {
			JSONObject meta = getMetaDataJSON(fileName);
			long rlen = Long.parseLong(meta.get(DataExpression.READROWPARAM).toString());
			long clen = Long.parseLong(meta.get(DataExpression.READCOLPARAM).toString());
			return new MatrixCharacteristics(rlen, clen, -1, -1);
		}
		catch(Exception ex) {
			throw new RuntimeException(ex);
		}
	}

	public static JSONObject getMetaDataJSON(String fileName) {
		return getMetaDataJSON(fileName, OUTPUT_DIR);
	}

	public static JSONObject getMetaDataJSON(String fileName, String outputDir) {
		String fname = baseDirectory + outputDir + fileName + ".mtd";
		return new DataExpression().readMetadataFile(fname, false);
	}

	/**
	 * Returns the privacy constraint as read from metadata file.
	 * @param fileName name of file
	 * @return loaded privacy constraint
	 * @throws DMLRuntimeException in case of problems with reading the metadata file
	 */
	public static PrivacyConstraint getPrivacyConstraintFromMetaData(String fileName, String dir) throws DMLRuntimeException {
		PrivacyConstraint outputPrivacyConstraint = new PrivacyConstraint();
		try {
			JSONObject metadata = getMetaDataJSON(fileName, dir);
			if ( metadata != null ){
				if ( metadata.containsKey(DataExpression.PRIVACY) ){
					PrivacyLevel readPrivacyLevel = PrivacyLevel.valueOf(metadata.get(DataExpression.PRIVACY).toString());
					outputPrivacyConstraint.setPrivacyLevel(readPrivacyLevel);
				} else {
					outputPrivacyConstraint.setPrivacyLevel(PrivacyLevel.None);
				}
				if ( metadata.containsKey(DataExpression.FINE_GRAINED_PRIVACY)){
					JSONObject fineGrainedJSON = (JSONObject) metadata.get(DataExpression.FINE_GRAINED_PRIVACY);
					PrivacyUtils.putFineGrainedConstraintsFromString(outputPrivacyConstraint.getFineGrainedPrivacy(), fineGrainedJSON.toString());
				}
			}
		} catch (JSONException e){
			throw new DMLRuntimeException("Exception when reading from meta data file", e);
		}
		return outputPrivacyConstraint;
	}

	public static PrivacyConstraint getPrivacyConstraintFromMetaData(String fileName) throws DMLRuntimeException {
		return getPrivacyConstraintFromMetaData(fileName, OUTPUT_DIR);
	}

	public static String readDMLMetaDataValue(String fileName, String outputDir, String key) throws JSONException {
		JSONObject meta = getMetaDataJSON(fileName, outputDir);
		return meta.get(key).toString();
	}

	/**
	 * Call readDMLMetaDataValue but fail test in case of JSONException or NullPointerException.
	 * 
	 * @param fileName  of metadata file
	 * @param outputDir directory of metadata file
	 * @param key       key to find in metadata
	 * @return value retrieved from metadata for the given key
	 */
	public static String readDMLMetaDataValueCatchException(String fileName, String outputDir, String key) {
		try {
			return readDMLMetaDataValue(fileName, outputDir, key);
		}
		catch(JSONException | NullPointerException e) {
			fail("Privacy constraint not written to output metadata file:\n" + e);
			return null;
		}
	}

	public static ValueType readDMLMetaDataValueType(String fileName) {
		try {
			JSONObject meta = getMetaDataJSON(fileName);
			return ValueType.fromExternalString(meta.get(DataExpression.VALUETYPEPARAM).toString());
		}
		catch(Exception ex) {
			throw new RuntimeException(ex);
		}
	}

	/**
	 * <p>
	 * Loads a test configuration with its parameters. Adds the output directories to the output list as well as to the
	 * list of possible comparison files.
	 * </p>
	 *
	 * @param config test configuration name
	 *
	 */
	protected void loadTestConfiguration(TestConfiguration config) {
		loadTestConfiguration(config, null);
	}

	/**
	 * <p>
	 * Loads a test configuration with its parameters. Adds the output directories to the output list as well as to the
	 * list of possible comparison files.
	 * </p>
	 *
	 * @param config         test configuration name
	 * @param cacheDirectory subdirectory for reusing R script expected results if null, defaults to empty string (i.e.,
	 *                       no cache)
	 */
	protected void loadTestConfiguration(TestConfiguration config, String cacheDirectory) {
		if(!availableTestConfigurations.containsValue(config))
			fail("test configuration not available: " + config.getTestScript());
		String testDirectory = config.getTestDirectory();
		if(testDirectory != null) {
			if(isTargetTestDirectory(testDirectory)) {
				baseDirectory = TEST_DATA_DIR + testDirectory;
				sourceDirectory = SCRIPT_DIR + getSourceDirectory(testDirectory);
			}
			else {
				baseDirectory = SCRIPT_DIR + testDirectory;
				sourceDirectory = baseDirectory;
			}
		}

		setCacheDirectory(cacheDirectory);

		selectedTest = config.getTestScript();

		String[] outputFiles = config.getOutputFiles();
		if(outputFiles != null) {
			outputDirectories = new String[outputFiles.length];
			comparisonFiles = new String[outputFiles.length];
			for(int i = 0; i < outputFiles.length; i++) {
				outputDirectories[i] = baseDirectory + OUTPUT_DIR + outputFiles[i];
				comparisonFiles[i] = baseDirectory + EXPECTED_DIR + cacheDir + outputFiles[i];
			}
		}

		testVariables = config.getVariables();
		testVariables.put("basedir", baseDirectory);
		testVariables.put("indir", baseDirectory + INPUT_DIR);
		testVariables.put("outdir", baseDirectory + OUTPUT_DIR);
		testVariables.put("readhelper",
			"Helper = read(\"" + baseDirectory + INPUT_DIR + "helper/in\", " + "rows=1, cols=2, format=\"text\");");
		testVariables.put("Routdir", baseDirectory + EXPECTED_DIR + cacheDir);

		// Create a temporary directory for this test case.
		// Eventually all files written by the tests should go under here, but making
		// that change will take quite a bit of effort.
		try {
			if(null == testDirectory) {
				System.err.printf("Warning: Test configuration did not specify a test directory.\n");
				curLocalTempDir = new File(LOCAL_TEMP_ROOT, String.format("unknownTest/%s", selectedTest));
			}
			else {
				curLocalTempDir = new File(LOCAL_TEMP_ROOT, String.format("%s/%s", testDirectory, selectedTest));
			}

			curLocalTempDir.mkdirs();
			TestUtils.clearDirectory(curLocalTempDir.getPath());

			// Create a SystemDS config file for this test case based on default template
			// from src/test/config or derive from custom configuration provided by test.
			String configTemplate = FileUtils.readFileToString(getConfigTemplateFile(), "UTF-8");
			String localTemp = curLocalTempDir.getPath();
			String configContents = configTemplate
				.replace(createXMLElement(DMLConfig.SCRATCH_SPACE, "scratch_space"),
					createXMLElement(DMLConfig.SCRATCH_SPACE, localTemp + "/scratch_space"))
				.replace(createXMLElement(DMLConfig.LOCAL_TMP_DIR, "/tmp/systemds"),
					createXMLElement(DMLConfig.LOCAL_TMP_DIR, localTemp + "/localtmp"));

			FileUtils.write(getCurConfigFile(), configContents, "UTF-8");

			if(LOG.isDebugEnabled())
				LOG.debug("This test case will use SystemDS config file %s\n" + getCurConfigFile());
		}
		catch(IOException e) {
			throw new RuntimeException(e);
		}

		if(DEBUG)
			TestUtils.clearDirectory(DEBUG_TEMP_DIR + baseDirectory + INPUT_DIR);
	}

	public String createXMLElement(String tagName, String value) {
		return String.format("<%s>%s</%s>", tagName, value, tagName);
	}

	/**
	 * <p>
	 * Loads a test configuration with its parameters. Adds the output directories to the output list as well as to the
	 * list of possible comparison files.
	 * </p>
	 *
	 * @param configurationName test configuration name
	 *
	 */
	@Deprecated
	protected void loadTestConfiguration(String configurationName) {
		if(!availableTestConfigurations.containsKey(configurationName))
			fail("test configuration not available: " + configurationName);

		TestConfiguration config = availableTestConfigurations.get(configurationName);

		loadTestConfiguration(config);
	}

	/**
	 * Runs an R script, default to the old way
	 */
	protected void runRScript() {
		runRScript(false);

	}

	/**
	 * Runs an R script in the old or the new way
	 */
	protected void runRScript(boolean newWay) {

		String executionFile = sourceDirectory + selectedTest + ".R";
		;
		if(fullRScriptName != null)
			executionFile = fullRScriptName;

		// *** HACK ALERT *** HACK ALERT *** HACK ALERT ***
		// Some of the R scripts will fail if the "expected" directory doesn't exist.
		// Make sure the directory exists.
		File expectedDir = new File(baseDirectory, "expected" + "/" + cacheDir);
		expectedDir.mkdirs();
		// *** END HACK ***

		String cmd;
		if(!newWay) {
			executionFile = executionFile + "t";
			cmd = "R -f " + executionFile;
		}
		else {
			// *** HACK ALERT *** HACK ALERT *** HACK ALERT ***
			// Rscript does *not* load the "methods" package by default
			// to save on start time. The "Matrix" package used in the
			// tests requires the "methods" package and should still
			// load and attach it, but in R 3.2 with the latest version
			// of the "Matrix" package, "methods" is loaded *but not
			// attached* when run with Rscript. Therefore, we need to
			// explicitly load it with Rscript.
			cmd = rCmd.replaceFirst("Rscript",
				"Rscript --default-packages=methods,datasets,graphics,grDevices,stats,utils");
			// *** END HACK ***
		}

		if(System.getProperty("os.name").contains("Windows")) {
			cmd = cmd.replace('/', '\\');
			executionFile = executionFile.replace('/', '\\');
		}
		if(DEBUG) {
			if(!newWay) { // not sure why have this condition
				TestUtils.printRScript(executionFile);
			}
		}
		if(!newWay) {
			ParameterBuilder.setVariablesInScript(sourceDirectory, selectedTest + ".R", testVariables);
		}

		if(cacheDir.length() > 0) {
			File expectedFile = null;
			String[] outputFiles = null;
			TestConfiguration testConfig = getTestConfiguration(selectedTest);
			if(testConfig != null) {
				outputFiles = testConfig.getOutputFiles();
			}

			if(outputFiles != null && outputFiles.length > 0) {
				expectedFile = new File(expectedDir.getPath() + "/" + outputFiles[0]);
				if(expectedFile.canRead()) {
					if(LOG.isInfoEnabled())
						LOG.info("Skipping R script cmd: " + cmd);
					return;
				}
			}
		}

		String outputR;
		String errorString;
		try {
			long t0 = System.nanoTime();
			if(LOG.isInfoEnabled()) {
				LOG.info("starting R script");
				LOG.debug("R cmd: " + cmd);
			}
			Process child = Runtime.getRuntime().exec(cmd);

			outputR = IOUtils.toString(child.getInputStream());
			errorString = IOUtils.toString(child.getErrorStream());
			if(LOG.isTraceEnabled()) {
				LOG.trace("Standard Output from R:" + outputR);
				LOG.trace("Standard Error from R:" + errorString);
			}

			//
			// To give any stream enough time to print all data, otherwise there
			// are situations where the test case fails, even before everything
			// has been printed
			//
			child.waitFor();

			try {
				if(child.exitValue() != 0) {
					throw new Exception(
						"ERROR: R has ended irregularly\n" + outputR + "\nscript file: " + executionFile);
				}
			}
			catch(IllegalThreadStateException ie) {
				// In UNIX JVM does not seem to be able to close threads
				// correctly. However, give it a try, since R processed the
				// script, therefore we can terminate the process.
				child.destroy();
			}

			long t1 = System.nanoTime();

			LOG.info("R is finished (in " + ((double) t1 - t0) / 1000000000 + " sec)");
		}
		catch(Exception e) {
			if(e.getMessage().contains("ERROR: R has ended irregularly")) {
				StringBuilder errorMessage = new StringBuilder();
				errorMessage.append(e.getMessage());
				fail(errorMessage.toString());
			}
			else {
				e.printStackTrace();
				StringBuilder errorMessage = new StringBuilder();
				errorMessage.append("failed to run script " + executionFile);
				errorMessage.append("\nexception: " + e.toString());
				errorMessage.append("\nmessage: " + e.getMessage());
				errorMessage.append("\nstack trace:");
				for(StackTraceElement ste : e.getStackTrace()) {
					errorMessage.append("\n>" + ste);
				}
				fail(errorMessage.toString());
			}
		}
	}

	/**
	 * <p>
	 * Runs a test for which no exception is expected.
	 * </p>
	 */
	protected ByteArrayOutputStream runTest() {
		return runTest(false, null);
	}

	/**
	 * <p>
	 * Runs a test for which no exception is expected. If SystemDS executes more MR jobs than specified in maxMRJobs
	 * this test will fail.
	 * </p>
	 *
	 * @param maxMRJobs specifies a maximum limit for the number of MR jobs. If set to -1 there is no limit.
	 */
	protected ByteArrayOutputStream runTest(int maxMRJobs) {
		return runTest(false, null, maxMRJobs);
	}

	/**
	 * <p>
	 * Runs a test for which the exception expectation can be specified.
	 * </p>
	 *
	 * @param exceptionExpected exception expected
	 */
	protected ByteArrayOutputStream runTest(boolean exceptionExpected) {
		return runTest(exceptionExpected, null);
	}

	/**
	 * <p>
	 * Runs a test for which the exception expectation can be specified as well as the specific expectation which is
	 * expected.
	 * </p>
	 *
	 * @param exceptionExpected exception expected
	 * @param expectedException expected exception
	 */
	protected ByteArrayOutputStream runTest(boolean exceptionExpected, Class<?> expectedException) {
		return runTest(exceptionExpected, expectedException, -1);
	}

	/**
	 * <p>
	 * Runs a test for which the exception expectation can be specified as well as the specific expectation which is
	 * expected. If SystemDS executes more MR jobs than specified in maxMRJobs this test will fail.
	 * </p>
	 *
	 * @param exceptionExpected exception expected
	 * @param expectedException expected exception
	 * @param maxMRJobs         specifies a maximum limit for the number of MR jobs. If set to -1 there is no limit.
	 */
	protected ByteArrayOutputStream runTest(boolean exceptionExpected, Class<?> expectedException, int maxMRJobs) {
		return runTest(false, exceptionExpected, expectedException, null, maxMRJobs);
	}

	/**
	 * <p>
	 * Runs a test for which the exception expectation can be specified as well as the specific expectation which is
	 * expected. If SystemDS executes more MR jobs than specified in maxMRJobs this test will fail.
	 * </p>
	 * 
	 * @param newWay            in the new way if it is set to true
	 * @param exceptionExpected exception expected
	 * @param expectedException expected exception
	 * @param maxMRJobs         specifies a maximum limit for the number of MR jobs. If set to -1 there is no limit.
	 */
	protected ByteArrayOutputStream runTest(boolean newWay, boolean exceptionExpected, Class<?> expectedException,
		int maxMRJobs) {
		return runTest(newWay, exceptionExpected, expectedException, null, maxMRJobs);
	}

	/**
	 * Run a test for which an exception is expected if not set to null.
	 * 
	 * Note this test execute in the "new" way.
	 * 
	 * @param expectedException The expected exception
	 * @return The Std output from the test.
	 */
	protected ByteArrayOutputStream runTest(Class<?> expectedException) {
		return runTest(expectedException, -1);
	}

	protected ByteArrayOutputStream runTest(Class<?> expectedException, int maxSparkInst) {
		return runTest(expectedException, null, maxSparkInst);
	}

	protected ByteArrayOutputStream runTest(Class<?> expectedException, String errMessage, int maxSparkInst) {
		return runTest(true, expectedException != null, expectedException, errMessage, maxSparkInst);
	}

	/**
	 * <p>
	 * Runs a test for which the exception expectation and the error message can be specified as well as the specific
	 * expectation which is expected. If SystemDS executes more MR jobs than specified in maxMRJobs this test will fail.
	 * </p>
	 * 
	 * @param newWay            in the new way if it is set to true
	 * @param exceptionExpected exception expected
	 * @param expectedException expected exception
	 * @param errMessage        expected error message
	 * @param maxSparkInst      specifies a maximum limit for the number of MR jobs. If set to -1 there is no limit.
	 */
	protected ByteArrayOutputStream runTest(boolean newWay, boolean exceptionExpected, Class<?> expectedException,
		String errMessage, int maxSparkInst) {

		String name = "";
		final StackTraceElement[] ste = Thread.currentThread().getStackTrace();
		for(int i = 0; i < ste.length; i++) {
			if(ste[i].getMethodName().equalsIgnoreCase("invoke0"))
				name = ste[i - 1].getClassName() + "." + ste[i - 1].getMethodName();
		}
		LOG.info("Test method name: " + name);

		String executionFile = sourceDirectory + selectedTest + ".dml";

		if(!newWay) {
			executionFile = executionFile + "t";
			ParameterBuilder.setVariablesInScript(sourceDirectory, selectedTest + ".dml", testVariables);
		}

		// cleanup scratch folder (prevent side effect between tests)
		cleanupScratchSpace();

		ArrayList<String> args = new ArrayList<>();
		// setup arguments to SystemDS
		if(DEBUG) {
			args.add("-Dsystemds.logging=trace");
		}

		if(newWay) {
			// Need a null pointer check because some tests read DML from a string.
			if(null != fullDMLScriptName) {
				args.add("-f");
				args.add(fullDMLScriptName);
			}
		}
		else {
			args.add("-f");
			args.add(executionFile);
		}

		addProgramIndependentArguments(args);

		// program-specific parameters
		if(newWay) {
			for(int i = 0; i < programArgs.length; i++)
				args.add(programArgs[i]);
		}

		if(DEBUG) {
			if(!newWay)
				TestUtils.printDMLScript(executionFile);
			else {
				TestUtils.printDMLScript(fullDMLScriptName);
			}
		}

		ByteArrayOutputStream buff = outputBuffering ? new ByteArrayOutputStream() : null;
		PrintStream old = System.out;
		if(outputBuffering)
			System.setOut(new PrintStream(buff));

		try {
			String[] dmlScriptArgs = args.toArray(new String[args.size()]);
			if(LOG.isTraceEnabled())
				LOG.trace("arguments to DMLScript: " + Arrays.toString(dmlScriptArgs));
			main(dmlScriptArgs);

			if(maxSparkInst > -1 && maxSparkInst < Statistics.getNoOfCompiledSPInst())
				fail("Limit of Spark jobs is exceeded: expected: " + maxSparkInst + ", occurred: "
					+ Statistics.getNoOfCompiledSPInst());

			if(exceptionExpected)
				fail("expected exception which has not been raised: " + expectedException);
		}
		catch(Exception | Error e) {
			if(!outputBuffering)
				e.printStackTrace();
			if(errMessage != null && !errMessage.equals("")) {
				boolean result = rCompareException(exceptionExpected, errMessage, e, false);
				if(exceptionExpected && !result) {
					fail(String.format("expected exception message '%s' has not been raised.", errMessage));
				}
			}
			if(!exceptionExpected || (expectedException != null && !(e.getClass().equals(expectedException)))) {
				StringBuilder errorMessage = new StringBuilder();
				errorMessage.append("\nfailed to run script: " + executionFile);
				errorMessage.append("\nStandard Out:");
				if(outputBuffering)
					errorMessage.append("\n" + buff);
				errorMessage.append("\nStackTrace:");
				errorMessage.append(getStackTraceString(e, 0));
				fail(errorMessage.toString());
			}
		}
		if(outputBuffering) {
			System.out.flush();
			System.setOut(old);
		}
		return buff;
	}

	/**
	 *
	 * @param args command-line arguments
	 * @throws IOException if an IOException occurs in the hadoop GenericOptionsParser
	 */
	public static void main(String[] args) throws IOException, ParseException, DMLScriptException {
		Configuration conf = new Configuration(ConfigurationManager.getCachedJobConf());
		String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs();
		DMLScript.executeScript(conf, otherArgs);
	}

	private void addProgramIndependentArguments(ArrayList<String> args) {

		// program-independent parameters
		args.add("-exec");
		if(rtplatform == ExecMode.HYBRID) {
			DMLScript.USE_LOCAL_SPARK_CONFIG = true;
			args.add("hybrid");
		}
		else if(rtplatform == ExecMode.SINGLE_NODE)
			args.add("singlenode");
		else if(rtplatform == ExecMode.SPARK)
			args.add("spark");
		else {
			throw new RuntimeException("Unknown runtime platform: " + rtplatform);
		}
		// use optional config file since default under SystemDS/DML
		args.add("-config");
		args.add(getCurConfigFile().getPath());

		if(TEST_GPU)
			args.add("-gpu");
		if(VERBOSE_STATS)
			args.add("-stats");
	}

	public static int getRandomAvailablePort() {
		try(ServerSocket availableSocket = new ServerSocket(0)) {
			return availableSocket.getLocalPort();
		}
		catch(IOException e) {
			// If no port was found just use 9999
			return 9990;
		}
	}

	/**
	 * Start new JVM for a federated worker at the port.
	 * 
	 * 
	 * @param port Port to use for the JVM
	 * @return the process associated with the worker.
	 */
	protected Process startLocalFedWorker(int port) {
		Process process = null;
		String separator = System.getProperty("file.separator");
		String classpath = System.getProperty("java.class.path");
		String path = System.getProperty("java.home") + separator + "bin" + separator + "java";
		ProcessBuilder processBuilder = new ProcessBuilder(path, "-cp", classpath, DMLScript.class.getName(), "-w",
			Integer.toString(port), "-stats");

		try {
			process = processBuilder.start();
			// Give some time to startup the worker.
			sleep(FED_WORKER_WAIT);
		}
		catch(IOException | InterruptedException e) {
			e.printStackTrace();
		}
		return process;
	}

	/**
	 * Start a thread for a worker. This will share the same JVM, so all static variables will be shared.!
	 * 
	 * Also when using the local Fed Worker thread the statistics printing, and clearing from the worker is disabled.
	 * 
	 * @param port Port to use
	 * @return the thread associated with the worker.
	 */
	protected Thread startLocalFedWorkerThread(int port) {
		Thread t = null;
		String[] fedWorkArgs = {"-w", Integer.toString(port)};
		ArrayList<String> args = new ArrayList<>();

		addProgramIndependentArguments(args);

		for(int i = 0; i < fedWorkArgs.length; i++)
			args.add(fedWorkArgs[i]);

		String[] finalArguments = args.toArray(new String[args.size()]);

		Statistics.allowWorkerStatistics = false;

		try {
			t = new Thread(() -> {
				try {
					main(finalArguments);
				}
				catch(IOException e) {
				}
			});
			t.start();
			java.util.concurrent.TimeUnit.MILLISECONDS.sleep(FED_WORKER_WAIT);
		}
		catch(InterruptedException e) {
			e.printStackTrace();
		}
		return t;
	}

	/**
	 * Start java worker in same JVM.
	 * 
	 * @param args the command line arguments
	 * @return the thread associated with the process.s
	 */
	public static Thread startLocalFedWorkerWithArgs(String[] args) {
		Thread t = null;

		try {
			t = new Thread(() -> {
				try {
					main(args);
				}
				catch(IOException e) {
				}
			});
			t.start();
			java.util.concurrent.TimeUnit.MILLISECONDS.sleep(FED_WORKER_WAIT);
		}
		catch(InterruptedException e) {
			// Should happen at closing of the worker so don't print
		}
		return t;
	}

	private boolean rCompareException(boolean exceptionExpected, String errMessage, Throwable e, boolean result) {
		if(e.getCause() != null) {
			result |= rCompareException(exceptionExpected, errMessage, e.getCause(), result);
		}
		if(exceptionExpected && errMessage != null && e.getMessage().contains(errMessage)) {
			result = true;
		}
		return result;
	}

	public static String getStackTraceString(Throwable e, int level) {
		StringBuilder sb = new StringBuilder();
		sb.append("\nLEVEL : " + level);
		sb.append("\nException : " + e.getClass());
		sb.append("\nMessage   : " + e.getMessage());
		for(StackTraceElement ste : e.getStackTrace()) {
			if(ste.toString().contains("org.junit")) {
				sb.append("\n   >  ... Stopping Stack Trace at JUnit");
				break;
			}
			else {
				sb.append("\n" + level + "  >  " + ste);
			}
		}
		if(e.getCause() == null) {
			return sb.toString();
		}
		sb.append(getStackTraceString(e.getCause(), level + 1));
		return sb.toString();
	}

	public void cleanupScratchSpace() {
		try {
			// parse config file
			DMLConfig conf = new DMLConfig(getCurConfigFile().getPath());

			// delete the scratch_space and all contents
			// (prevent side effect between tests)
			String dir = conf.getTextValue(DMLConfig.SCRATCH_SPACE);
			HDFSTool.deleteFileIfExistOnHDFS(dir);
		}
		catch(Exception ex) {
			// ex.printStackTrace();
			return; // no effect on tests
		}
	}

	/**
	 * <p>
	 * Checks if a process-local temporary directory exists in the current working directory.
	 * </p>
	 *
	 * @return true if a process-local temp directory is present.
	 */
	public boolean checkForProcessLocalTemporaryDir() {
		try {
			DMLConfig conf = new DMLConfig(getCurConfigFile().getPath());

			StringBuilder sb = new StringBuilder();
			sb.append(conf.getTextValue(DMLConfig.SCRATCH_SPACE));
			sb.append(Lop.FILE_SEPARATOR);
			sb.append(Lop.PROCESS_PREFIX);
			sb.append(DMLScript.getUUID());
			String pLocalDir = sb.toString();

			return HDFSTool.existsFileOnHDFS(pLocalDir);
		}
		catch(Exception ex) {
			ex.printStackTrace();
			return true;
		}
	}

	/**
	 * <p>
	 * Compares the results of the computation with the expected ones.
	 * </p>
	 */
	protected void compareResults() {
		compareResults(0);
	}

	/**
	 * <p>
	 * Compares the results of the computation with the expected ones with a specified tolerance.
	 * </p>
	 *
	 * @param epsilon tolerance
	 */
	protected void compareResultsWithR(double epsilon) {
		for(int i = 0; i < comparisonFiles.length; i++) {
			TestUtils.compareDMLHDFSFileWithRFile(comparisonFiles[i], outputDirectories[i], epsilon);
		}
	}

	/**
	 * <p>
	 * Compares the results of the computation with the Result calculated by R
	 * </p>
	 */
	protected void compareResultsWithR() {
		compareResultsWithR(0);
	}

	protected void compareResultsWithMM() {
		TestUtils.compareMMMatrixWithJavaMatrix(comparisonFiles[0], outputDirectories[0], 0);
	}

	/**
	 * <p>
	 * Compares the results of the computation with the expected ones with a specified tolerance.
	 * </p>
	 *
	 * @param epsilon tolerance
	 */
	protected void compareResults(double epsilon) {
		for(int i = 0; i < comparisonFiles.length; i++) {
			/* Note that DML scripts may generate a file with only scalar value */
			if(outputDirectories[i].endsWith(".scalar")) {
				String javaFile = comparisonFiles[i].replace(".scalar", "");
				String dmlFile = outputDirectories[i].replace(".scalar", "");
				TestUtils.compareDMLScalarWithJavaScalar(javaFile, dmlFile, epsilon);
			}
			else {
				TestUtils.compareDMLMatrixWithJavaMatrix(comparisonFiles[i], outputDirectories[i], epsilon);
			}
		}
	}

	/**
	 * <p>
	 * Compares the results of the computation of the frame with the expected ones.
	 * </p>
	 *
	 * @param schema the frame schema
	 */
	protected void compareResults(ValueType[] schema) {
		for(int i = 0; i < comparisonFiles.length; i++) {
			TestUtils.compareDMLFrameWithJavaFrame(schema, comparisonFiles[i], outputDirectories[i]);
		}
	}

	/**
	 * Compare results of the computation with the expected results where rows may be permuted.
	 * 
	 * @param epsilon
	 */
	protected void compareResultsRowsOutOfOrder(double epsilon) {
		for(int i = 0; i < comparisonFiles.length; i++) {
			/* Note that DML scripts may generate a file with only scalar value */
			if(outputDirectories[i].endsWith(".scalar")) {
				String javaFile = comparisonFiles[i].replace(".scalar", "");
				String dmlFile = outputDirectories[i].replace(".scalar", "");
				TestUtils.compareDMLScalarWithJavaScalar(javaFile, dmlFile, epsilon);
			}
			else {
				TestUtils
					.compareDMLMatrixWithJavaMatrixRowsOutOfOrder(comparisonFiles[i], outputDirectories[i], epsilon);
			}
		}
	}

	/**
	 * Checks that the number of Spark instructions that the current test case has compiled is equal to the expected
	 * number. Generates a JUnit error message if the number is out of line.
	 *
	 * @param expectedNumCompiled number of Spark instructions that the current test case is expected to compile
	 */
	protected void checkNumCompiledSparkInst(int expectedNumCompiled) {
		assertEquals("Unexpected number of compiled Spark instructions.",
			expectedNumCompiled,
			Statistics.getNoOfCompiledSPInst());
	}

	/**
	 * Checks that the number of Spark instructions that the current test case has executed (as opposed to compiling
	 * into the execution plan) is equal to the expected number. Generates a JUnit error message if the number is out of
	 * line.
	 *
	 * @param expectedNumExecuted number of Spark instructions that the current test case is expected to run
	 */
	protected void checkNumExecutedSparkInst(int expectedNumExecuted) {
		assertEquals("Unexpected number of executed Spark instructions.",
			expectedNumExecuted,
			Statistics.getNoOfExecutedSPInst());
	}

	/**
	 * <p>
	 * Checks the results of a computation against a number of characteristics.
	 * </p>
	 *
	 * @param rows number of rows
	 * @param cols number of columns
	 * @param min  minimum value
	 * @param max  maximum value
	 */
	protected void checkResults(long rows, long cols, double min, double max) {
		for(int i = 0; i < outputDirectories.length; i++) {
			TestUtils.checkMatrix(outputDirectories[i], rows, cols, min, max);
		}
	}

	/**
	 * <p>
	 * Checks for the existence for all of the outputs.
	 * </p>
	 */
	protected void checkForResultExistence() {
		for(int i = 0; i < outputDirectories.length; i++) {
			TestUtils.checkForOutputExistence(outputDirectories[i]);
		}
	}

	@After
	public void tearDown() {
		LOG.trace("Duration: " + (System.currentTimeMillis() - lTimeBeforeTest) + "ms");

		// assertTrue("expected String did not occur: " + expectedStdOut,
		// iExpectedStdOutState == 0 || iExpectedStdOutState == 2);
		// assertTrue("expected String did not occur (stderr): " + expectedStdErr,
		// iExpectedStdErrState == 0 || iExpectedStdErrState == 2);
		// assertFalse("unexpected String occurred: " + unexpectedStdOut, iUnexpectedStdOutState == 1);
		TestUtils.displayAssertionBuffer();

		if(!isOutAndExpectedDeletionDisabled()) {

			TestUtils.removeHDFSDirectories(inputDirectories.toArray(new String[inputDirectories.size()]));
			TestUtils.removeFiles(inputRFiles.toArray(new String[inputRFiles.size()]));

			// The following cleanup code is disabled (see [SYSTEMML-256]) until we can figure out
			// what test cases are creating temporary directories at the root of the project.
			// TestUtils.removeTemporaryFiles();

			TestUtils.clearDirectory(baseDirectory + OUTPUT_DIR);
			TestUtils.removeHDFSFiles(expectedFiles.toArray(new String[expectedFiles.size()]));
			TestUtils.clearDirectory(baseDirectory + EXPECTED_DIR);
			TestUtils.removeFiles(new String[] {sourceDirectory + selectedTest + ".dmlt"});
			TestUtils.removeFiles(new String[] {sourceDirectory + selectedTest + ".Rt"});
		}

		TestUtils.clearAssertionInformation();
	}

	public boolean bufferContainsString(ByteArrayOutputStream buffer, String str) {
		return Arrays.stream(buffer.toString().split("\n")).anyMatch(x -> x.contains(str));
	}

	/**
	 * Disables the deletion of files and directories in the output and expected folder for this test.
	 */
	public void disableOutAndExpectedDeletion() {
		setOutAndExpectedDeletionDisabled(true);
	}

	/**
	 * <p>
	 * Generates a matrix containing easy to debug values in its cells.
	 * </p>
	 *
	 * @param rows
	 * @param cols
	 * @param bContainsZeros If true, the matrix contains zeros. If false, the matrix contains only positive values.
	 * @return
	 */
	protected double[][] createNonRandomMatrixValues(int rows, int cols, boolean bContainsZeros) {
		return TestUtils.createNonRandomMatrixValues(rows, cols, bContainsZeros);
	}

	/**
	 * <p>
	 * Generates a matrix containing easy to debug values in its cells. The generated matrix contains zero values
	 * </p>
	 *
	 * @param rows
	 * @param cols
	 * @return
	 */
	protected double[][] createNonRandomMatrixValues(int rows, int cols) {
		return TestUtils.createNonRandomMatrixValues(rows, cols, true);
	}

	/**
	 * @return TRUE if the test harness is not deleting temporary files
	 */
	protected boolean isOutAndExpectedDeletionDisabled() {
		return isOutAndExpectedDeletionDisabled;
	}

	/**
	 * Call this method from a subclass's setUp() method.
	 * 
	 * @param isOutAndExpectedDeletionDisabled TRUE to disable code that deletes temporary files for this test case
	 */
	protected void setOutAndExpectedDeletionDisabled(boolean isOutAndExpectedDeletionDisabled) {
		this.isOutAndExpectedDeletionDisabled = isOutAndExpectedDeletionDisabled;
	}

	protected String input(String input) {
		return baseDirectory + INPUT_DIR + input;
	}

	protected String inputDir() {
		return baseDirectory + INPUT_DIR;
	}

	protected String output(String output) {
		return baseDirectory + OUTPUT_DIR + output;
	}

	protected String outputDir() {
		return baseDirectory + OUTPUT_DIR;
	}

	protected String expected(String expected) {
		return baseDirectory + EXPECTED_DIR + cacheDir + expected;
	}

	protected String expectedDir() {
		return baseDirectory + EXPECTED_DIR + cacheDir;
	}

	protected String getScript() {
		return sourceDirectory + selectedTest + ".dml";
	}

	protected String getRScript() {
		if(fullRScriptName != null)
			return fullRScriptName;
		return sourceDirectory + selectedTest + ".R";
	}

	protected String getRCmd(String... args) {
		StringBuilder sb = new StringBuilder();
		sb.append("Rscript ");
		sb.append(getRScript());
		for(String arg : args) {
			sb.append(" ");
			sb.append(arg);
		}
		return sb.toString();
	}

	private boolean isTargetTestDirectory(String path) {
		return(path != null && path.contains(getClass().getSimpleName()));
	}

	private void setCacheDirectory(String directory) {
		cacheDir = (directory != null) ? directory : "";
		if(cacheDir.length() > 0 && !cacheDir.endsWith("/")) {
			cacheDir += "/";
		}
	}

	private static String getSourceDirectory(String testDirectory) {
		String sourceDirectory = "";
		if(null != testDirectory) {
			if(testDirectory.endsWith("/"))
				testDirectory = testDirectory.substring(0, testDirectory.length() - "/".length());
			sourceDirectory = testDirectory.substring(0, testDirectory.lastIndexOf("/") + "/".length());
		}
		return sourceDirectory;
	}

	/**
	 * <p>
	 * Adds a frame to the input path and writes it to a file.
	 * </p>
	 *
	 * @param name      directory name
	 * @param data      two dimensional frame data
	 * @param bIncludeR generates also the corresponding R frame data
	 * @throws IOException
	 */
	protected double[][] writeInputFrame(String name, double[][] data, boolean bIncludeR, ValueType[] schema,
		FileFormat fmt) throws IOException {
		String completePath = baseDirectory + INPUT_DIR + name;
		String completeRPath = baseDirectory + INPUT_DIR + name + ".csv";

		try {
			cleanupExistingData(baseDirectory + INPUT_DIR + name, bIncludeR);
		}
		catch(IOException e) {
			e.printStackTrace();
			throw new RuntimeException(e);
		}

		TestUtils.writeTestFrame(completePath, data, schema, fmt);
		if(bIncludeR) {
			TestUtils.writeTestFrame(completeRPath, data, schema, FileFormat.CSV, true);
			inputRFiles.add(completeRPath);
		}
		if(DEBUG)
			TestUtils.writeTestFrame(DEBUG_TEMP_DIR + completePath, data, schema, fmt);
		inputDirectories.add(baseDirectory + INPUT_DIR + name);

		return data;
	}

	protected double[][] writeInputFrameWithMTD(String name, double[][] data, boolean bIncludeR, ValueType[] schema,
		FileFormat fmt) throws IOException {
		MatrixCharacteristics mc = new MatrixCharacteristics(data.length, data[0].length,
			OptimizerUtils.DEFAULT_BLOCKSIZE, -1);
		return writeInputFrameWithMTD(name, data, bIncludeR, mc, schema, fmt);
	}

	protected double[][] writeInputFrameWithMTD(String name, double[][] data, boolean bIncludeR,
		MatrixCharacteristics mc, ValueType[] schema, FileFormat fmt) throws IOException {
		writeInputFrame(name, data, bIncludeR, schema, fmt);

		// write metadata file
		try {
			String completeMTDPath = baseDirectory + INPUT_DIR + name + ".mtd";
			HDFSTool.writeMetaDataFile(completeMTDPath, null, schema, DataType.FRAME, mc, fmt);
		}
		catch(IOException e) {
			e.printStackTrace();
			throw new RuntimeException(e);
		}

		return data;
	}

	/**
	 * <p>
	 * Adds a frame to the input path and writes it to a file.
	 * </p>
	 *
	 * @param name   directory name
	 * @param data   two dimensional frame data
	 * @param schema The schema of the frame
	 * @param fmt    The format of the frame
	 * @throws IOException
	 */
	protected double[][] writeInputFrame(String name, double[][] data, ValueType[] schema, FileFormat fmt)
		throws IOException {
		return writeInputFrame(name, data, false, schema, fmt);
	}

	protected boolean heavyHittersContainsString(String... str) {
		for(String opcode : Statistics.getCPHeavyHitterOpCodes())
			for(String s : str)
				if(opcode.equals(s))
					return true;
		return false;
	}

	protected boolean heavyHittersContainsString(String str, int minCount) {
		int count = 0;
		for(String opcode : Statistics.getCPHeavyHitterOpCodes())
			count += opcode.equals(str) ? 1 : 0;
		return(count >= minCount);
	}

	protected boolean heavyHittersContainsSubString(String... str) {
		for(String opcode : Statistics.getCPHeavyHitterOpCodes())
			for(String s : str)
				if(opcode.contains(s))
					return true;
		return false;
	}

	protected boolean heavyHittersContainsSubString(String str, int minCount) {
		int count = 0;
		for(String opcode : Statistics.getCPHeavyHitterOpCodes())
			count += opcode.contains(str) ? 1 : 0;
		return(count >= minCount);
	}

	protected boolean checkedPrivacyConstraintsContains(PrivacyLevel... levels) {
		for(PrivacyLevel level : levels)
			if(!(CheckedConstraintsLog.getCheckedConstraints().containsKey(level)))
				return false;
		return true;
	}

	protected boolean checkedPrivacyConstraintsAbove(Map<PrivacyLevel, Long> levelCounts) {
		for(Map.Entry<PrivacyLevel, Long> levelCount : levelCounts.entrySet()) {
			if(!(CheckedConstraintsLog.getCheckedConstraints().get(levelCount.getKey()).longValue() >= levelCount
				.getValue()))
				return false;
		}
		return true;
	}

	/**
	 * Create a SystemDS-preferred Spark Session.
	 *
	 * @param appName the application name
	 * @param master  the master value (ie, "local", etc)
	 * @return Spark Session
	 */
	public static SparkSession createSystemDSSparkSession(String appName, String master) {
		Builder builder = SparkSession.builder();
		if(appName != null) {
			builder.appName(appName);
		}
		if(master != null) {
			builder.master(master);
		}
		builder.config("spark.driver.maxResultSize", "0");
		if(SparkExecutionContext.FAIR_SCHEDULER_MODE) {
			builder.config("spark.scheduler.mode", "FAIR");
		}
		builder.config("spark.locality.wait", "5s");
		SparkSession spark = builder.getOrCreate();
		return spark;
	}

	public static String getMatrixAsString(double[][] matrix) {
		try {
			return DataConverter.toString(DataConverter.convertToMatrixBlock(matrix));
		}
		catch(DMLRuntimeException e) {
			return "N/A";
		}
	}

	public static void appendToJavaLibraryPath(String additional_path) {
		String current_path = System.getProperty("java.library.path");
		System.setProperty("java.library.path", current_path + File.pathSeparator + additional_path);
	}
}