Java tutorial
/* * 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.jena.hadoop.rdf.io.input.bnodes; import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Paths; import java.nio.file.StandardCopyOption; import java.nio.file.attribute.FileAttribute; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.LongWritable; import org.apache.hadoop.mapreduce.InputFormat; import org.apache.hadoop.mapreduce.InputSplit; import org.apache.hadoop.mapreduce.Job; import org.apache.hadoop.mapreduce.JobContext; import org.apache.hadoop.mapreduce.OutputFormat; import org.apache.hadoop.mapreduce.RecordReader; import org.apache.hadoop.mapreduce.RecordWriter; import org.apache.hadoop.mapreduce.TaskAttemptContext; import org.apache.hadoop.mapreduce.TaskAttemptID; import org.apache.hadoop.mapreduce.TaskType; import org.apache.hadoop.mapreduce.lib.input.FileInputFormat; import org.apache.hadoop.mapreduce.lib.input.NLineInputFormat; import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat; import org.apache.hadoop.mapreduce.task.JobContextImpl; import org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl; import org.apache.jena.graph.Node; import org.apache.jena.graph.NodeFactory; import org.apache.jena.hadoop.rdf.io.RdfIOConstants; import org.apache.jena.hadoop.rdf.types.AbstractNodeTupleWritable; import org.junit.Assert; import org.junit.Assume; import org.junit.BeforeClass; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; /** * Test case that embodies the scenario described in JENA-820 */ public abstract class AbstractBlankNodeTests<T, TValue extends AbstractNodeTupleWritable<T>> { private static final Logger LOGGER = LoggerFactory.getLogger(AbstractBlankNodeTests.class); @BeforeClass public static void setup() { // Enable if you need to diagnose test failures // Useful since it includes printing the file names of the temporary // files being used // BasicConfigurator.resetConfiguration(); // BasicConfigurator.configure(); } /** * Gets the extension for the initial input files */ protected abstract String getInitialInputExtension(); /** * Creates a tuple * * @param s * Subject * @param p * Predicate * @param o * Object * @return Tuple */ protected abstract T createTuple(Node s, Node p, Node o); /** * Writes out the given tuples to the given file * * @param f * File * @param tuples * Tuples * @throws FileNotFoundException */ protected abstract void writeTuples(File f, List<T> tuples) throws FileNotFoundException; /** * Creates the input format for reading the initial inputs * * @return Input format */ protected abstract InputFormat<LongWritable, TValue> createInitialInputFormat(); /** * Creates the output format for writing the intermediate output * * @return Output format */ protected abstract OutputFormat<LongWritable, TValue> createIntermediateOutputFormat(); /** * Creates the input format for reading the intermediate outputs back in * * @return Input format */ protected abstract InputFormat<LongWritable, TValue> createIntermediateInputFormat(); /** * Gets the subject of the tuple * * @param value * Tuple * @return Subject */ protected abstract Node getSubject(T value); /** * Gets whether the format being tested respects the RIOT * {@link ParserProfile} * * @return True if parser profile is respected, false otherwise */ protected boolean respectsParserProfile() { return true; } /** * Gets whether the format being tested preserves blank node identity * * @return True if identity is presereved, false otherwise */ protected boolean preservesBlankNodeIdentity() { return false; } /** * Test that starts with two blank nodes with the same identity in a single * file, splits them over two files and checks that we can workaround * JENA-820 successfully by setting the * {@link RdfIOConstants#GLOBAL_BNODE_IDENTITY} flag for our subsequent job * * @throws IOException * @throws InterruptedException */ @Test public final void blank_node_divergence_01() throws IOException, InterruptedException { Assume.assumeTrue("Requires ParserProfile be respected", this.respectsParserProfile()); Assume.assumeFalse("Requires that Blank Node identity not be preserved", this.preservesBlankNodeIdentity()); // Temporary files File a = File.createTempFile("bnode_divergence", getInitialInputExtension()); File intermediateOutputDir = Files.createTempDirectory("bnode_divergence", new FileAttribute[0]).toFile(); try { // Prepare the input data // Two mentions of the same blank node in the same file List<T> tuples = new ArrayList<>(); Node bnode = NodeFactory.createBlankNode(); Node pred = NodeFactory.createURI("http://example.org/predicate"); tuples.add(createTuple(bnode, pred, NodeFactory.createLiteral("first"))); tuples.add(createTuple(bnode, pred, NodeFactory.createLiteral("second"))); writeTuples(a, tuples); // Set up fake job which will process the file as a single split Configuration config = new Configuration(true); InputFormat<LongWritable, TValue> inputFormat = createInitialInputFormat(); Job job = Job.getInstance(config); job.setInputFormatClass(inputFormat.getClass()); NLineInputFormat.setNumLinesPerSplit(job, 100); FileInputFormat.setInputPaths(job, new Path(a.getAbsolutePath())); FileOutputFormat.setOutputPath(job, new Path(intermediateOutputDir.getAbsolutePath())); JobContext context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits List<InputSplit> splits = inputFormat.getSplits(context); Assert.assertEquals(1, splits.size()); for (InputSplit split : splits) { // Initialize the input reading TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, 1, 1)); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); // Copy the input to the output - each triple goes to a separate // output file // This is how we force multiple files to be produced int taskID = 1; while (reader.nextKeyValue()) { // Prepare the output writing OutputFormat<LongWritable, TValue> outputFormat = createIntermediateOutputFormat(); TaskAttemptContext outputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, ++taskID, 1)); RecordWriter<LongWritable, TValue> writer = outputFormat.getRecordWriter(outputTaskContext); writer.write(reader.getCurrentKey(), reader.getCurrentValue()); writer.close(outputTaskContext); } } // Promote outputs from temporary status promoteInputs(intermediateOutputDir); // Now we need to create a subsequent job that reads the // intermediate outputs // As described in JENA-820 at this point the blank nodes are // consistent, however when we read them from different files they // by default get treated as different nodes and so the blank nodes // diverge which is incorrect and undesirable behaviour in // multi-stage pipelines LOGGER.debug("Intermediate output directory is {}", intermediateOutputDir.getAbsolutePath()); job = Job.getInstance(config); inputFormat = createIntermediateInputFormat(); job.setInputFormatClass(inputFormat.getClass()); FileInputFormat.setInputPaths(job, new Path(intermediateOutputDir.getAbsolutePath())); // Enabling this flag works around the JENA-820 issue job.getConfiguration().setBoolean(RdfIOConstants.GLOBAL_BNODE_IDENTITY, true); context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits splits = inputFormat.getSplits(context); Assert.assertEquals(2, splits.size()); // Expect to end up with a single blank node Set<Node> nodes = new HashSet<Node>(); for (InputSplit split : splits) { TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), new TaskAttemptID()); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); while (reader.nextKeyValue()) { nodes.add(getSubject(reader.getCurrentValue().get())); } } // Nodes should not have diverged Assert.assertEquals(1, nodes.size()); } finally { a.delete(); deleteDirectory(intermediateOutputDir); } } /** * Test that starts with two blank nodes with the same identity in a single * file, splits them over two files and shows that they diverge in the * subsequent job when the JENA-820 workaround is not enabled * * @throws IOException * @throws InterruptedException */ @Test public void blank_node_divergence_02() throws IOException, InterruptedException { Assume.assumeTrue("Requires ParserProfile be respected", this.respectsParserProfile()); Assume.assumeFalse("Requires that Blank Node identity not be preserved", this.preservesBlankNodeIdentity()); // Temporary files File a = File.createTempFile("bnode_divergence", getInitialInputExtension()); File intermediateOutputDir = Files.createTempDirectory("bnode_divergence", new FileAttribute[0]).toFile(); try { // Prepare the input data // Two mentions of the same blank node in the same file List<T> tuples = new ArrayList<>(); Node bnode = NodeFactory.createBlankNode(); Node pred = NodeFactory.createURI("http://example.org/predicate"); tuples.add(createTuple(bnode, pred, NodeFactory.createLiteral("first"))); tuples.add(createTuple(bnode, pred, NodeFactory.createLiteral("second"))); writeTuples(a, tuples); // Set up fake job which will process the file as a single split Configuration config = new Configuration(true); InputFormat<LongWritable, TValue> inputFormat = createInitialInputFormat(); Job job = Job.getInstance(config); job.setInputFormatClass(inputFormat.getClass()); NLineInputFormat.setNumLinesPerSplit(job, 100); FileInputFormat.setInputPaths(job, new Path(a.getAbsolutePath())); FileOutputFormat.setOutputPath(job, new Path(intermediateOutputDir.getAbsolutePath())); JobContext context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits List<InputSplit> splits = inputFormat.getSplits(context); Assert.assertEquals(1, splits.size()); for (InputSplit split : splits) { // Initialize the input reading TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, 1, 1)); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); // Copy the input to the output - each triple goes to a separate // output file // This is how we force multiple files to be produced int taskID = 1; while (reader.nextKeyValue()) { // Prepare the output writing OutputFormat<LongWritable, TValue> outputFormat = createIntermediateOutputFormat(); TaskAttemptContext outputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, ++taskID, 1)); RecordWriter<LongWritable, TValue> writer = outputFormat.getRecordWriter(outputTaskContext); writer.write(reader.getCurrentKey(), reader.getCurrentValue()); writer.close(outputTaskContext); } } // Promote outputs from temporary status promoteInputs(intermediateOutputDir); // Now we need to create a subsequent job that reads the // intermediate outputs // As described in JENA-820 at this point the blank nodes are // consistent, however when we read them from different files they // by default get treated as different nodes and so the blank nodes // diverge which is incorrect and undesirable behaviour in // multi-stage pipelines. However it is the default behaviour // because when we start from external inputs we want them to be // file scoped. LOGGER.debug("Intermediate output directory is {}", intermediateOutputDir.getAbsolutePath()); job = Job.getInstance(config); inputFormat = createIntermediateInputFormat(); job.setInputFormatClass(inputFormat.getClass()); FileInputFormat.setInputPaths(job, new Path(intermediateOutputDir.getAbsolutePath())); // Make sure JENA-820 flag is disabled job.getConfiguration().setBoolean(RdfIOConstants.GLOBAL_BNODE_IDENTITY, false); context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits splits = inputFormat.getSplits(context); Assert.assertEquals(2, splits.size()); // Expect to end up with a single blank node Set<Node> nodes = new HashSet<Node>(); for (InputSplit split : splits) { TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), new TaskAttemptID()); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); while (reader.nextKeyValue()) { nodes.add(getSubject(reader.getCurrentValue().get())); } } // Nodes should have diverged Assert.assertEquals(2, nodes.size()); } finally { a.delete(); deleteDirectory(intermediateOutputDir); } } /** * Test that starts with two blank nodes in two different files and checks * that writing them to a single file does not conflate them * * @throws IOException * @throws InterruptedException */ @Test public void blank_node_identity_01() throws IOException, InterruptedException { Assume.assumeTrue("Requires ParserProfile be respected", this.respectsParserProfile()); Assume.assumeFalse("Requires that Blank Node identity not be preserved", this.preservesBlankNodeIdentity()); // Temporary files File a = File.createTempFile("bnode_identity", getInitialInputExtension()); File b = File.createTempFile("bnode_identity", getInitialInputExtension()); File intermediateOutputDir = Files.createTempDirectory("bnode_identity", new FileAttribute[0]).toFile(); try { // Prepare the input data // Different blank nodes in different files List<T> tuples = new ArrayList<>(); Node bnode1 = NodeFactory.createBlankNode(); Node bnode2 = NodeFactory.createBlankNode(); Node pred = NodeFactory.createURI("http://example.org/predicate"); tuples.add(createTuple(bnode1, pred, NodeFactory.createLiteral("first"))); writeTuples(a, tuples); tuples.clear(); tuples.add(createTuple(bnode2, pred, NodeFactory.createLiteral("second"))); writeTuples(b, tuples); // Set up fake job which will process the two files Configuration config = new Configuration(true); InputFormat<LongWritable, TValue> inputFormat = createInitialInputFormat(); Job job = Job.getInstance(config); job.setInputFormatClass(inputFormat.getClass()); NLineInputFormat.setNumLinesPerSplit(job, 100); FileInputFormat.setInputPaths(job, new Path(a.getAbsolutePath()), new Path(b.getAbsolutePath())); FileOutputFormat.setOutputPath(job, new Path(intermediateOutputDir.getAbsolutePath())); JobContext context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits List<InputSplit> splits = inputFormat.getSplits(context); Assert.assertEquals(2, splits.size()); // Prepare the output writing - putting all output to a single file OutputFormat<LongWritable, TValue> outputFormat = createIntermediateOutputFormat(); TaskAttemptContext outputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, 2, 1)); RecordWriter<LongWritable, TValue> writer = outputFormat.getRecordWriter(outputTaskContext); for (InputSplit split : splits) { // Initialize the input reading TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, 1, 1)); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); // Copy the input to the output - all triples go to a single // output while (reader.nextKeyValue()) { writer.write(reader.getCurrentKey(), reader.getCurrentValue()); } } writer.close(outputTaskContext); // Promote outputs from temporary status promoteInputs(intermediateOutputDir); // Now we need to create a subsequent job that reads the // intermediate outputs // The Blank nodes should have been given separate identities so we // should not be conflating them, this is the opposite problem to // that described in JENA-820 LOGGER.debug("Intermediate output directory is {}", intermediateOutputDir.getAbsolutePath()); job = Job.getInstance(config); inputFormat = createIntermediateInputFormat(); job.setInputFormatClass(inputFormat.getClass()); NLineInputFormat.setNumLinesPerSplit(job, 100); FileInputFormat.setInputPaths(job, new Path(intermediateOutputDir.getAbsolutePath())); context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits splits = inputFormat.getSplits(context); Assert.assertEquals(1, splits.size()); // Expect to end up with a single blank node Set<Node> nodes = new HashSet<Node>(); for (InputSplit split : splits) { TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), new TaskAttemptID()); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); while (reader.nextKeyValue()) { nodes.add(getSubject(reader.getCurrentValue().get())); } } // Nodes must not have converged Assert.assertEquals(2, nodes.size()); } finally { a.delete(); b.delete(); deleteDirectory(intermediateOutputDir); } } /** * Test that starts with two blank nodes in two different files and checks * that writing them to a single file does not conflate them * * @throws IOException * @throws InterruptedException */ @Test public void blank_node_identity_02() throws IOException, InterruptedException { Assume.assumeTrue("Requires ParserProfile be respected", this.respectsParserProfile()); Assume.assumeFalse("Requires that Blank Node identity not be preserved", this.preservesBlankNodeIdentity()); // Temporary files File a = File.createTempFile("bnode_identity", getInitialInputExtension()); File b = File.createTempFile("bnode_identity", getInitialInputExtension()); File intermediateOutputDir = Files.createTempDirectory("bnode_identity", new FileAttribute[0]).toFile(); try { // Prepare the input data // Same blank node but in different files so must be treated as // different blank nodes and not converge List<T> tuples = new ArrayList<>(); Node bnode = NodeFactory.createBlankNode(); Node pred = NodeFactory.createURI("http://example.org/predicate"); tuples.add(createTuple(bnode, pred, NodeFactory.createLiteral("first"))); writeTuples(a, tuples); tuples.clear(); tuples.add(createTuple(bnode, pred, NodeFactory.createLiteral("second"))); writeTuples(b, tuples); // Set up fake job which will process the two files Configuration config = new Configuration(true); InputFormat<LongWritable, TValue> inputFormat = createInitialInputFormat(); Job job = Job.getInstance(config); job.setInputFormatClass(inputFormat.getClass()); NLineInputFormat.setNumLinesPerSplit(job, 100); FileInputFormat.setInputPaths(job, new Path(a.getAbsolutePath()), new Path(b.getAbsolutePath())); FileOutputFormat.setOutputPath(job, new Path(intermediateOutputDir.getAbsolutePath())); JobContext context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits List<InputSplit> splits = inputFormat.getSplits(context); Assert.assertEquals(2, splits.size()); // Prepare the output writing - putting all output to a single file OutputFormat<LongWritable, TValue> outputFormat = createIntermediateOutputFormat(); TaskAttemptContext outputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, 2, 1)); RecordWriter<LongWritable, TValue> writer = outputFormat.getRecordWriter(outputTaskContext); for (InputSplit split : splits) { // Initialize the input reading TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), createAttemptID(1, 1, 1)); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); // Copy the input to the output - all triples go to a single // output while (reader.nextKeyValue()) { writer.write(reader.getCurrentKey(), reader.getCurrentValue()); } } writer.close(outputTaskContext); // Promote outputs from temporary status promoteInputs(intermediateOutputDir); // Now we need to create a subsequent job that reads the // intermediate outputs // The Blank nodes should have been given separate identities so we // should not be conflating them, this is the opposite problem to // that described in JENA-820 LOGGER.debug("Intermediate output directory is {}", intermediateOutputDir.getAbsolutePath()); job = Job.getInstance(config); inputFormat = createIntermediateInputFormat(); job.setInputFormatClass(inputFormat.getClass()); NLineInputFormat.setNumLinesPerSplit(job, 100); FileInputFormat.setInputPaths(job, new Path(intermediateOutputDir.getAbsolutePath())); context = new JobContextImpl(job.getConfiguration(), job.getJobID()); // Get the splits splits = inputFormat.getSplits(context); Assert.assertEquals(1, splits.size()); // Expect to end up with a single blank node Set<Node> nodes = new HashSet<Node>(); for (InputSplit split : splits) { TaskAttemptContext inputTaskContext = new TaskAttemptContextImpl(job.getConfiguration(), new TaskAttemptID()); RecordReader<LongWritable, TValue> reader = inputFormat.createRecordReader(split, inputTaskContext); reader.initialize(split, inputTaskContext); while (reader.nextKeyValue()) { nodes.add(getSubject(reader.getCurrentValue().get())); } } // Nodes must not diverge Assert.assertEquals(2, nodes.size()); } finally { a.delete(); b.delete(); deleteDirectory(intermediateOutputDir); } } private TaskAttemptID createAttemptID(int jobID, int taskID, int id) { return new TaskAttemptID("outputTest", jobID, TaskType.MAP, taskID, 1); } private void promoteInputs(File baseDir) throws IOException { for (File f : baseDir.listFiles()) { if (f.isDirectory()) { promoteInputs(baseDir, f); } } } private void promoteInputs(File targetDir, File dir) throws IOException { java.nio.file.Path target = Paths.get(targetDir.toURI()); for (File f : dir.listFiles()) { if (f.isDirectory()) { promoteInputs(targetDir, f); } else { LOGGER.debug("Moving {} to {}", f.getAbsolutePath(), target.resolve(f.getName())); Files.move(Paths.get(f.toURI()), target.resolve(f.getName()), StandardCopyOption.REPLACE_EXISTING); } } // Remove defunct sub-directory dir.delete(); } private void deleteDirectory(File dir) throws IOException { for (File f : dir.listFiles()) { if (f.isFile()) f.delete(); if (f.isDirectory()) deleteDirectory(f); } dir.delete(); } }