Examples with GraphPartitioner uk.gov.gchq.gaffer.parquetstore.partitioner.GraphPartitioner used on opensource projects

Example 1 with GraphPartitioner

use of uk.gov.gchq.gaffer.parquetstore.partitioner.GraphPartitioner in project Gaffer by gchq.

the class CalculatePartitionerTest method calculatePartitionerTest.

@Test
public void calculatePartitionerTest(@TempDir java.nio.file.Path tempDir) throws IOException {
    // Given
    final FileSystem fs = FileSystem.get(new Configuration());
    final Schema schema = getSchema();
    final SchemaUtils schemaUtils = new SchemaUtils(schema);
    final String topLevelFolder = tempDir.toString();
    writeData(topLevelFolder, schemaUtils);
    // When
    // - Calculate partitioner from files
    final GraphPartitioner actual = new CalculatePartitioner(new Path(topLevelFolder), schema, fs).call();
    // - Manually create the correct partitioner
    final GraphPartitioner expected = new GraphPartitioner();
    final List<PartitionKey> splitPointsEntity = new ArrayList<>();
    for (int i = 1; i < 10; i++) {
        splitPointsEntity.add(new PartitionKey(new Object[] { 10L * i }));
    }
    final GroupPartitioner groupPartitionerEntity = new GroupPartitioner(TestGroups.ENTITY, splitPointsEntity);
    expected.addGroupPartitioner(TestGroups.ENTITY, groupPartitionerEntity);
    final GroupPartitioner groupPartitionerEntity2 = new GroupPartitioner(TestGroups.ENTITY_2, splitPointsEntity);
    expected.addGroupPartitioner(TestGroups.ENTITY_2, groupPartitionerEntity2);
    final List<PartitionKey> splitPointsEdge = new ArrayList<>();
    for (int i = 1; i < 10; i++) {
        splitPointsEdge.add(new PartitionKey(new Object[] { 10L * i, 10L * i + 1, true }));
    }
    final GroupPartitioner groupPartitionerEdge = new GroupPartitioner(TestGroups.EDGE, splitPointsEdge);
    expected.addGroupPartitioner(TestGroups.EDGE, groupPartitionerEdge);
    final GroupPartitioner groupPartitionerEdge2 = new GroupPartitioner(TestGroups.EDGE_2, splitPointsEdge);
    expected.addGroupPartitioner(TestGroups.EDGE_2, groupPartitionerEdge2);
    final List<PartitionKey> splitPointsReversedEdge = new ArrayList<>();
    for (int i = 1; i < 10; i++) {
        splitPointsReversedEdge.add(new PartitionKey(new Object[] { 10L * i + 1, 10L * i, true }));
    }
    final GroupPartitioner reversedGroupPartitionerEdge = new GroupPartitioner(TestGroups.EDGE, splitPointsReversedEdge);
    expected.addGroupPartitionerForReversedEdges(TestGroups.EDGE, reversedGroupPartitionerEdge);
    final GroupPartitioner reversedGroupPartitionerEdge2 = new GroupPartitioner(TestGroups.EDGE_2, splitPointsReversedEdge);
    expected.addGroupPartitionerForReversedEdges(TestGroups.EDGE_2, reversedGroupPartitionerEdge2);
    // Then
    assertEquals(expected, actual);
}

Example 2 with GraphPartitioner

use of uk.gov.gchq.gaffer.parquetstore.partitioner.GraphPartitioner in project Gaffer by gchq.

the class WriteUnsortedDataTest method testNoSplitPointsCase.

@Test
public void testNoSplitPointsCase(@TempDir java.nio.file.Path tempDir) throws IOException, OperationException {
    // Given
    final String tempFilesDir = tempDir.toAbsolutePath().toString();
    final SchemaUtils schemaUtils = new SchemaUtils(TestUtils.gafferSchema("schemaUsingLongVertexType"));
    final GraphPartitioner graphPartitioner = new GraphPartitioner();
    graphPartitioner.addGroupPartitioner(TestGroups.ENTITY, new GroupPartitioner(TestGroups.ENTITY, new ArrayList<>()));
    graphPartitioner.addGroupPartitioner(TestGroups.ENTITY_2, new GroupPartitioner(TestGroups.ENTITY_2, new ArrayList<>()));
    graphPartitioner.addGroupPartitioner(TestGroups.EDGE, new GroupPartitioner(TestGroups.EDGE, new ArrayList<>()));
    graphPartitioner.addGroupPartitioner(TestGroups.EDGE_2, new GroupPartitioner(TestGroups.EDGE_2, new ArrayList<>()));
    graphPartitioner.addGroupPartitionerForReversedEdges(TestGroups.EDGE, new GroupPartitioner(TestGroups.EDGE, new ArrayList<>()));
    graphPartitioner.addGroupPartitionerForReversedEdges(TestGroups.EDGE_2, new GroupPartitioner(TestGroups.EDGE_2, new ArrayList<>()));
    final List<Element> elements = getData(3L);
    final BiFunction<String, Integer, String> fileNameForGroupAndPartitionId = (group, partitionId) -> tempFilesDir + "/GROUP=" + group + "/split-" + partitionId;
    final BiFunction<String, Integer, String> fileNameForGroupAndPartitionIdForReversedEdge = (group, partitionId) -> tempFilesDir + "/REVERSED-GROUP=" + group + "/split-" + partitionId;
    final WriteUnsortedData writeUnsortedData = new WriteUnsortedData(tempFilesDir, CompressionCodecName.GZIP, schemaUtils, graphPartitioner, fileNameForGroupAndPartitionId, fileNameForGroupAndPartitionIdForReversedEdge);
    // When
    writeUnsortedData.writeElements(elements);
    // Then
    // - Each directory should exist and contain one file
    testExistsAndContainsNFiles(tempFilesDir + "/GROUP=" + TestGroups.ENTITY + "/split-0", 1);
    testExistsAndContainsNFiles(tempFilesDir + "/GROUP=" + TestGroups.ENTITY_2 + "/split-0", 1);
    testExistsAndContainsNFiles(tempFilesDir + "/GROUP=" + TestGroups.EDGE + "/split-0", 1);
    testExistsAndContainsNFiles(tempFilesDir + "/GROUP=" + TestGroups.EDGE_2 + "/split-0", 1);
    testExistsAndContainsNFiles(tempFilesDir + "/REVERSED-GROUP=" + TestGroups.EDGE + "/split-0", 1);
    testExistsAndContainsNFiles(tempFilesDir + "/REVERSED-GROUP=" + TestGroups.EDGE_2 + "/split-0", 1);
    // - Each file should contain the data that was written to it, in the order it was in the iterable
    testContainsCorrectDataNoSplitPoints(TestGroups.ENTITY, tempFilesDir + "/GROUP=" + TestGroups.ENTITY + "/split-0", elements, schemaUtils);
    testContainsCorrectDataNoSplitPoints(TestGroups.ENTITY_2, tempFilesDir + "/GROUP=" + TestGroups.ENTITY_2 + "/split-0", elements, schemaUtils);
    testContainsCorrectDataNoSplitPoints(TestGroups.EDGE, tempFilesDir + "/GROUP=" + TestGroups.EDGE + "/split-0", elements, schemaUtils);
    testContainsCorrectDataNoSplitPoints(TestGroups.EDGE_2, tempFilesDir + "/GROUP=" + TestGroups.EDGE_2 + "/split-0", elements, schemaUtils);
    testContainsCorrectDataNoSplitPoints(TestGroups.EDGE, tempFilesDir + "/REVERSED-GROUP=" + TestGroups.EDGE + "/split-0", elements, schemaUtils);
    final List<Element> elementsWithSameSrcDstRemoved = elements.stream().filter(e -> e.getGroup().equals(TestGroups.EDGE_2)).map(e -> (Edge) e).filter(e -> !e.getSource().equals(e.getDestination())).collect(Collectors.toList());
    testContainsCorrectDataNoSplitPoints(TestGroups.EDGE_2, tempFilesDir + "/REVERSED-GROUP=" + TestGroups.EDGE_2 + "/split-0", elementsWithSameSrcDstRemoved, schemaUtils);
}

Example 3 with GraphPartitioner

use of uk.gov.gchq.gaffer.parquetstore.partitioner.GraphPartitioner in project Gaffer by gchq.

the class GraphPartitionerSerialiser method read.

public GraphPartitioner read(final DataInputStream stream) throws IOException {
    final GraphPartitioner graphPartitioner = new GraphPartitioner();
    int numGroups = stream.readInt();
    for (int i = 0; i < numGroups; i++) {
        final String group = stream.readUTF();
        graphPartitioner.addGroupPartitioner(group, groupPartitionerSerialiser.read(stream));
    }
    numGroups = stream.readInt();
    for (int i = 0; i < numGroups; i++) {
        final String group = stream.readUTF();
        graphPartitioner.addGroupPartitionerForReversedEdges(group, groupPartitionerSerialiser.read(stream));
    }
    return graphPartitioner;
}

Example 4 with GraphPartitioner

use of uk.gov.gchq.gaffer.parquetstore.partitioner.GraphPartitioner in project Gaffer by gchq.

the class ParquetStore method initialise.

private void initialise() throws IOException, StoreException {
    // If data directory is empty or does not exist then this is the first time the store has been created.
    final Path dataDirPath = new Path(getDataDir());
    if (!fs.exists(dataDirPath) || 0 == fs.listStatus(dataDirPath).length) {
        LOGGER.info("Data directory {} doesn't exist or is empty so initialising directory structure", dataDirPath);
        currentSnapshot = System.currentTimeMillis();
        LOGGER.info("Initialising snapshot id to {}", currentSnapshot);
        final Path snapshotPath = new Path(dataDirPath, getSnapshotPath(currentSnapshot));
        LOGGER.info("Creating snapshot directory {}", snapshotPath);
        fs.mkdirs(snapshotPath);
        LOGGER.info("Creating group directories under {}", snapshotPath);
        for (final String group : getSchema().getGroups()) {
            final Path groupDir = getGroupPath(group);
            fs.mkdirs(groupDir);
            LOGGER.info("Created directory {}", groupDir);
        }
        LOGGER.info("Creating group directories for reversed edges under {}", snapshotPath);
        for (final String group : getSchema().getEdgeGroups()) {
            final Path groupDir = getGroupPathForReversedEdges(group);
            fs.mkdirs(groupDir);
            LOGGER.info("Created directory {}", groupDir);
        }
        LOGGER.info("Creating GraphPartitioner with 0 split points for each group");
        graphPartitioner = new GraphPartitioner();
        for (final String group : getSchema().getGroups()) {
            graphPartitioner.addGroupPartitioner(group, new GroupPartitioner(group, new ArrayList<>()));
        }
        for (final String group : getSchema().getEdgeGroups()) {
            graphPartitioner.addGroupPartitionerForReversedEdges(group, new GroupPartitioner(group, new ArrayList<>()));
        }
        LOGGER.info("Writing GraphPartitioner to snapshot directory");
        final FSDataOutputStream dataOutputStream = fs.create(getGraphPartitionerPath());
        new GraphPartitionerSerialiser().write(graphPartitioner, dataOutputStream);
        dataOutputStream.close();
        LOGGER.info("Wrote GraphPartitioner to file {}", getGraphPartitionerPath().toString());
    } else {
        LOGGER.info("Data directory {} exists and is non-empty, validating a snapshot directory exists", dataDirPath);
        final FileStatus[] fileStatuses = fs.listStatus(dataDirPath, f -> f.getName().startsWith(SNAPSHOT + "="));
        final List<FileStatus> directories = Arrays.stream(fileStatuses).filter(f -> f.isDirectory()).collect(Collectors.toList());
        if (0 == directories.size()) {
            LOGGER.error("Data directory {} should contain a snapshot directory", dataDirPath);
            throw new StoreException("Data directory should contain a snapshot directory");
        }
        this.currentSnapshot = getLatestSnapshot();
        LOGGER.info("Latest snapshot directory in data directory {} is {}", dataDirPath, this.currentSnapshot);
        LOGGER.info("Verifying snapshot directory contains the correct directories");
        for (final String group : getSchema().getGroups()) {
            final Path groupDir = getGroupPath(group);
            if (!fs.exists(groupDir)) {
                LOGGER.error("Directory {} should exist", groupDir);
                throw new StoreException("Group directory " + groupDir + " should exist in snapshot directory " + getSnapshotPath(this.currentSnapshot));
            }
        }
        for (final String group : getSchema().getEdgeGroups()) {
            final Path groupDir = getGroupPathForReversedEdges(group);
            if (!fs.exists(groupDir)) {
                LOGGER.error("Directory {} should exist", groupDir);
                throw new StoreException("Group directory " + groupDir + " should exist in snapshot directory " + getSnapshotPath(this.currentSnapshot));
            }
        }
    }
}

Example 5 with GraphPartitioner

use of uk.gov.gchq.gaffer.parquetstore.partitioner.GraphPartitioner in project Gaffer by gchq.

the class AddElementsHandler method addElements.

private void addElements(final AddElements addElementsOperation, final Context context, final ParquetStore store) throws OperationException {
    // Set up
    final FileSystem fs = store.getFS();
    final Schema schema = store.getSchema();
    final SchemaUtils schemaUtils = store.getSchemaUtils();
    final SparkSession spark = SparkContextUtil.getSparkSession(context, store.getProperties());
    final ExecutorService threadPool = createThreadPool(spark, store.getProperties());
    final GraphPartitioner currentGraphPartitioner = store.getGraphPartitioner();
    SparkParquetUtils.configureSparkForAddElements(spark, store.getProperties());
    // Write data from addElementsOperation split by group and partition (NB this uses the existing partitioner -
    // adding elements using this operation does not effect the partitions).
    final String tmpDirectory = store.getTempFilesDir();
    final BiFunction<String, Integer, String> directoryForGroupAndPartitionId = (group, partitionId) -> tmpDirectory + "/unsorted_unaggregated_new" + "/group=" + group + "/partition=" + partitionId;
    final BiFunction<String, Integer, String> directoryForGroupAndPartitionIdForReversedEdges = (group, partitionId) -> tmpDirectory + "/unsorted_unaggregated_new" + "/reversed-group=" + group + "/partition=" + partitionId;
    LOGGER.info("Calling WriteUnsortedData to add elements");
    LOGGER.trace("currentGraphPartitioner is {}", currentGraphPartitioner);
    new WriteUnsortedData(store, currentGraphPartitioner, directoryForGroupAndPartitionId, directoryForGroupAndPartitionIdForReversedEdges).writeElements(addElementsOperation.getInput());
    // For every group and partition, aggregate the new data with the old data and then sort
    final BiFunction<String, Integer, String> directoryForSortedResultsForGroupAndPartitionId = (group, partitionId) -> tmpDirectory + "/sorted_new_old_merged" + "/group=" + group + "/partition=" + partitionId;
    final BiFunction<String, Integer, String> directoryForSortedResultsForGroupAndPartitionIdForReversedEdges = (group, partitionId) -> tmpDirectory + "/sorted_new_old_merged" + "/REVERSED-group=" + group + "/partition=" + partitionId;
    final List<Callable<CallableResult>> tasks = new ArrayList<>();
    for (final String group : schema.getGroups()) {
        final List<Partition> partitions = currentGraphPartitioner.getGroupPartitioner(group).getPartitions();
        for (final Partition partition : partitions) {
            final List<String> inputFiles = new ArrayList<>();
            // New data
            inputFiles.add(directoryForGroupAndPartitionId.apply(group, partition.getPartitionId()));
            // Old data
            inputFiles.add(store.getFile(group, partition));
            final String outputDir = directoryForSortedResultsForGroupAndPartitionId.apply(group, partition.getPartitionId());
            final AggregateAndSortData task = new AggregateAndSortData(schemaUtils, fs, inputFiles, outputDir, group, group + "-" + partition.getPartitionId(), false, store.getProperties().getCompressionCodecName(), spark);
            tasks.add(task);
            LOGGER.info("Created AggregateAndSortData task for group {}, partition {}", group, partition.getPartitionId());
        }
    }
    for (final String group : schema.getEdgeGroups()) {
        final List<Partition> partitions = currentGraphPartitioner.getGroupPartitionerForReversedEdges(group).getPartitions();
        for (final Partition partition : partitions) {
            final List<String> inputFiles = new ArrayList<>();
            // New data
            inputFiles.add(directoryForGroupAndPartitionIdForReversedEdges.apply(group, partition.getPartitionId()));
            // Old data
            inputFiles.add(store.getFileForReversedEdges(group, partition));
            final String outputDir = directoryForSortedResultsForGroupAndPartitionIdForReversedEdges.apply(group, partition.getPartitionId());
            final AggregateAndSortData task = new AggregateAndSortData(schemaUtils, fs, inputFiles, outputDir, group, "reversed-" + group + "-" + partition.getPartitionId(), true, store.getProperties().getCompressionCodecName(), spark);
            tasks.add(task);
            LOGGER.info("Created AggregateAndSortData task for reversed edge group {}, partition {}", group, partition.getPartitionId());
        }
    }
    try {
        LOGGER.info("Invoking {} AggregateAndSortData tasks", tasks.size());
        final List<Future<CallableResult>> futures = threadPool.invokeAll(tasks);
        for (final Future<CallableResult> future : futures) {
            final CallableResult result = future.get();
            LOGGER.info("Result {} from task", result);
        }
    } catch (final InterruptedException e) {
        throw new OperationException("InterruptedException running AggregateAndSortData tasks", e);
    } catch (final ExecutionException e) {
        throw new OperationException("ExecutionException running AggregateAndSortData tasks", e);
    }
    try {
        // Move results to a new snapshot directory (the -tmp at the end allows us to add data to the directory,
        // and then when this is all finished we rename the directory to remove the -tmp; this allows us to make
        // the replacement of the old data with the new data an atomic operation and ensures that a get operation
        // against the store will not read the directory when only some of the data has been moved there).
        final long snapshot = System.currentTimeMillis();
        final String newDataDir = store.getDataDir() + "/" + ParquetStore.getSnapshotPath(snapshot) + "-tmp";
        LOGGER.info("Moving aggregated and sorted data to new snapshot directory {}", newDataDir);
        fs.mkdirs(new Path(newDataDir));
        for (final String group : schema.getGroups()) {
            final Path groupDir = new Path(newDataDir, ParquetStore.getGroupSubDir(group, false));
            fs.mkdirs(groupDir);
            LOGGER.info("Created directory {}", groupDir);
        }
        for (final String group : schema.getEdgeGroups()) {
            final Path groupDir = new Path(newDataDir, ParquetStore.getGroupSubDir(group, true));
            fs.mkdirs(groupDir);
            LOGGER.info("Created directory {}", groupDir);
        }
        for (final String group : schema.getGroups()) {
            final String groupDir = newDataDir + "/" + ParquetStore.getGroupSubDir(group, false);
            final List<Partition> partitions = currentGraphPartitioner.getGroupPartitioner(group).getPartitions();
            for (final Partition partition : partitions) {
                final Path outputDir = new Path(directoryForSortedResultsForGroupAndPartitionId.apply(group, partition.getPartitionId()));
                if (!fs.exists(outputDir)) {
                    LOGGER.info("Not moving data for group {}, partition id {} as the outputDir {} does not exist", group, partition.getPartitionId(), outputDir);
                } else {
                    // One .parquet file and one .parquet.crc file
                    final FileStatus[] status = fs.listStatus(outputDir, path -> path.getName().endsWith(".parquet"));
                    if (1 != status.length) {
                        LOGGER.error("Didn't find one Parquet file in path {} (found {} files)", outputDir, status.length);
                        throw new OperationException("Expected to find one Parquet file in path " + outputDir + " (found " + status.length + " files)");
                    } else {
                        final Path destination = new Path(groupDir, ParquetStore.getFile(partition.getPartitionId()));
                        LOGGER.info("Renaming {} to {}", status[0].getPath(), destination);
                        fs.rename(status[0].getPath(), destination);
                    }
                }
            }
        }
        for (final String group : schema.getEdgeGroups()) {
            final String groupDir = newDataDir + "/" + ParquetStore.getGroupSubDir(group, true);
            final List<Partition> partitions = currentGraphPartitioner.getGroupPartitionerForReversedEdges(group).getPartitions();
            for (final Partition partition : partitions) {
                final Path outputDir = new Path(directoryForSortedResultsForGroupAndPartitionIdForReversedEdges.apply(group, partition.getPartitionId()));
                if (!fs.exists(outputDir)) {
                    LOGGER.info("Not moving data for reversed edge group {}, partition id {} as the outputDir {} does not exist", group, partition.getPartitionId(), outputDir);
                } else {
                    // One .parquet file and one .parquet.crc file
                    final FileStatus[] status = fs.listStatus(outputDir, path -> path.getName().endsWith(".parquet"));
                    if (1 != status.length) {
                        LOGGER.error("Didn't find one Parquet file in path {} (found {} files)", outputDir, status.length);
                        throw new OperationException("Expected to find one Parquet file in path " + outputDir + " (found " + status.length + " files)");
                    } else {
                        final Path destination = new Path(groupDir, ParquetStore.getFile(partition.getPartitionId()));
                        LOGGER.info("Renaming {} to {}", status[0].getPath(), destination);
                        fs.rename(status[0].getPath(), destination);
                    }
                }
            }
        }
        // Delete temporary data directory
        LOGGER.info("Deleting temporary directory {}", tmpDirectory);
        fs.delete(new Path(tmpDirectory), true);
        // Write out graph partitioner (unchanged from previous one)
        final Path newGraphPartitionerPath = new Path(newDataDir + "/graphPartitioner");
        final FSDataOutputStream stream = fs.create(newGraphPartitionerPath);
        LOGGER.info("Writing graph partitioner to {}", newGraphPartitionerPath);
        new GraphPartitionerSerialiser().write(currentGraphPartitioner, stream);
        stream.close();
        // Move snapshot-tmp directory to snapshot
        final String directoryWithoutTmp = newDataDir.substring(0, newDataDir.lastIndexOf("-tmp"));
        LOGGER.info("Renaming {} to {}", newDataDir, directoryWithoutTmp);
        fs.rename(new Path(newDataDir), new Path(directoryWithoutTmp));
        // Set snapshot on store to new value
        LOGGER.info("Updating latest snapshot on store to {}", snapshot);
        store.setLatestSnapshot(snapshot);
    } catch (final IOException | StoreException e) {
        throw new OperationException("IOException moving results files into new snapshot directory", e);
    }
}