cgivre commented on a change in pull request #1778: Drill-7233: Format Plugin for HDF5 URL: https://github.com/apache/drill/pull/1778#discussion_r362264460
########## File path: contrib/format-hdf5/src/main/java/org/apache/drill/exec/store/hdf5/HDF5BatchReader.java ########## @@ -0,0 +1,1164 @@ +/* + * 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.drill.exec.store.hdf5; + +import ch.systemsx.cisd.hdf5.HDF5CompoundMemberInformation; +import ch.systemsx.cisd.hdf5.HDF5DataSetInformation; +import ch.systemsx.cisd.hdf5.HDF5FactoryProvider; +import ch.systemsx.cisd.hdf5.HDF5LinkInformation; +import ch.systemsx.cisd.hdf5.IHDF5Factory; +import ch.systemsx.cisd.hdf5.IHDF5Reader; +import org.apache.commons.io.IOUtils; +import org.apache.drill.common.config.DrillConfig; +import org.apache.drill.common.exceptions.UserException; +import org.apache.drill.common.types.TypeProtos; +import org.apache.drill.exec.ExecConstants; +import org.apache.drill.exec.physical.impl.scan.file.FileScanFramework.FileSchemaNegotiator; +import org.apache.drill.exec.physical.impl.scan.framework.ManagedReader; +import org.apache.drill.exec.physical.resultSet.ResultSetLoader; +import org.apache.drill.exec.physical.resultSet.RowSetLoader; +import org.apache.drill.exec.record.metadata.ColumnMetadata; +import org.apache.drill.exec.record.metadata.MapBuilder; +import org.apache.drill.exec.record.metadata.MetadataUtils; +import org.apache.drill.exec.record.metadata.SchemaBuilder; +import org.apache.drill.exec.record.metadata.TupleMetadata; +import org.apache.drill.exec.store.hdf5.writers.HDF5DataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5DoubleDataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5EnumDataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5FloatDataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5IntDataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5LongDataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5MapDataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5StringDataWriter; +import org.apache.drill.exec.store.hdf5.writers.HDF5TimestampDataWriter; +import org.apache.drill.exec.vector.accessor.ArrayWriter; +import org.apache.drill.exec.vector.accessor.ScalarWriter; +import org.apache.drill.exec.vector.accessor.TupleWriter; + +import org.apache.drill.shaded.guava.com.google.common.io.Files; +import org.apache.hadoop.mapred.FileSplit; +import org.joda.time.Instant; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.BufferedReader; +import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.nio.file.StandardCopyOption; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.BitSet; +import java.util.Iterator; +import java.util.List; +import java.util.Map; + +public class HDF5BatchReader implements ManagedReader<FileSchemaNegotiator> { + private static final Logger logger = LoggerFactory.getLogger(HDF5BatchReader.class); + + private static final String PATH_COLUMN_NAME = "path"; + + private static final String DATA_TYPE_COLUMN_NAME = "data_type"; + + private static final String FILE_NAME_COLUMN_NAME = "file_name"; + + private static final String INT_COLUMN_PREFIX = "int_col_"; + + private static final String LONG_COLUMN_PREFIX = "long_col_"; + + private static final String FLOAT_COLUMN_PREFIX = "float_col_"; + + private static final String DOUBLE_COLUMN_PREFIX = "double_col_"; + + private static final String INT_COLUMN_NAME = "int_data"; + + private static final String FLOAT_COLUMN_NAME = "float_data"; + + private static final String DOUBLE_COLUMN_NAME = "double_data"; + + private static final String LONG_COLUMN_NAME = "long_data"; + + private FileSplit split; + + private IHDF5Reader hdf5Reader; + + private File infile; + + private BufferedReader reader; + + private RowSetLoader rowWriter; + + private Iterator<HDF5DrillMetadata> metadataIterator; + + private final HDF5ReaderConfig readerConfig; + + private boolean deleteTmpDir; + + private ScalarWriter pathWriter; + + private ScalarWriter dataTypeWriter; + + private ScalarWriter fileNameWriter; + + private List<HDF5DataWriter> dataWriters; + + private long[] dimensions; + + public static class HDF5ReaderConfig { + final HDF5FormatPlugin plugin; + + final String defaultPath; + + final HDF5FormatConfig formatConfig; + + public HDF5ReaderConfig(HDF5FormatPlugin plugin, HDF5FormatConfig formatConfig) { + this.plugin = plugin; + this.formatConfig = formatConfig; + defaultPath = formatConfig.getDefaultPath(); + } + } + + public HDF5BatchReader(HDF5ReaderConfig readerConfig) { + this.readerConfig = readerConfig; + dataWriters = new ArrayList<>(); + } + + @Override + public boolean open(FileSchemaNegotiator negotiator) { + split = negotiator.split(); + try { + openFile(negotiator); + } catch (IOException e) { + throw UserException + .dataReadError(e) + .message("Failed to close input file: {}", split.getPath()) + .message(e.getMessage()) + .build(logger); + } + + ResultSetLoader loader; + if (readerConfig.defaultPath == null) { + // Get file metadata + List<HDF5DrillMetadata> metadata = getFileMetadata(hdf5Reader.object().getGroupMemberInformation("/", true), new ArrayList<>()); + metadataIterator = metadata.iterator(); + + // Schema for Metadata query + SchemaBuilder builder = new SchemaBuilder().addNullable(PATH_COLUMN_NAME, TypeProtos.MinorType.VARCHAR).addNullable(DATA_TYPE_COLUMN_NAME, TypeProtos.MinorType.VARCHAR).addNullable(FILE_NAME_COLUMN_NAME, TypeProtos.MinorType.VARCHAR); + negotiator.setTableSchema(builder.buildSchema(), false); + + loader = negotiator.build(); + dimensions = new long[0]; + rowWriter = loader.writer(); + + } else { + // This is the case when the default path is specified. Since the user is explicitly asking for a dataset + // Drill can obtain the schema by getting the datatypes below and ultimately mapping that schema to columns + HDF5DataSetInformation dsInfo = hdf5Reader.object().getDataSetInformation(readerConfig.defaultPath); + dimensions = dsInfo.getDimensions(); + + loader = negotiator.build(); + rowWriter = loader.writer(); + if (dimensions.length <= 1) { + buildSchemaFor1DimensionalDataset(dsInfo); + } else if (dimensions.length == 2) { + buildSchemaFor2DimensionalDataset(dsInfo); + } else { + // Case for datasets of greater than 2D + // These are automatically flattened + buildSchemaFor2DimensionalDataset(dsInfo); + } + } + if (readerConfig.defaultPath == null) { + pathWriter = rowWriter.scalar(PATH_COLUMN_NAME); + dataTypeWriter = rowWriter.scalar(DATA_TYPE_COLUMN_NAME); + fileNameWriter = rowWriter.scalar(FILE_NAME_COLUMN_NAME); + } + return true; + } + + /** + * This function is called when the default path is set and the data set is a single dimension. This function will create an array of one dataWriter of the + * correct datatype + * @param dsInfo The HDF5 dataset information + */ + private void buildSchemaFor1DimensionalDataset(HDF5DataSetInformation dsInfo) { + TypeProtos.MinorType currentDataType = HDF5Utils.getDataType(dsInfo); + + // Case for null or unknown data types: + if (currentDataType == null) { + logger.warn("Couldn't add " + dsInfo.getTypeInformation().tryGetJavaType().toGenericString()); + return; + } + + switch (currentDataType) { + case GENERIC_OBJECT: + dataWriters.add(new HDF5EnumDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + case VARCHAR: + dataWriters.add(new HDF5StringDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + case TIMESTAMP: + dataWriters.add(new HDF5TimestampDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + case INT: + dataWriters.add(new HDF5IntDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + case BIGINT: + dataWriters.add(new HDF5LongDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + case FLOAT8: + dataWriters.add(new HDF5DoubleDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + case FLOAT4: + dataWriters.add(new HDF5FloatDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + case MAP: + dataWriters.add(new HDF5MapDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath)); + break; + } + } + + /** + * This function builds a Drill schema from a dataset with 2 or more dimensions. HDF5 only supports INT, LONG, DOUBLE and FLOAT for >2 data types so this function is + * not as inclusinve as the 1D function. This function will build the schema by adding DataWriters to the dataWriters array. + * @param dsInfo The dataset which Drill will use to build a schema + */ + + private void buildSchemaFor2DimensionalDataset(HDF5DataSetInformation dsInfo) { + TypeProtos.MinorType currentDataType = HDF5Utils.getDataType(dsInfo); + // Case for null or unknown data types: + if (currentDataType == null) { + logger.warn("Couldn't add {}", dsInfo.getTypeInformation().tryGetJavaType().toGenericString()); + return; + } + long cols = dimensions[1]; + + String tempFieldName; + for (int i = 0; i < cols; i++) { + switch (currentDataType) { + case INT: + tempFieldName = INT_COLUMN_PREFIX + i; + dataWriters.add(new HDF5IntDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath, tempFieldName, i)); + break; + case BIGINT: + tempFieldName = LONG_COLUMN_PREFIX + i; + dataWriters.add(new HDF5LongDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath, tempFieldName, i)); + break; + case FLOAT8: + tempFieldName = DOUBLE_COLUMN_PREFIX + i; + dataWriters.add(new HDF5DoubleDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath, tempFieldName, i)); + break; + case FLOAT4: + tempFieldName = FLOAT_COLUMN_PREFIX + i; + dataWriters.add(new HDF5FloatDataWriter(hdf5Reader, rowWriter, readerConfig.defaultPath, tempFieldName, i)); + break; + } + } + } + /** + * This function contains the logic to open an HDF5 file. + * @param negotiator The negotiator represents Drill's interface with the file system + */ + private void openFile(FileSchemaNegotiator negotiator) throws IOException { + InputStream in = null; + try { + in = negotiator.fileSystem().openPossiblyCompressedStream(split.getPath()); + IHDF5Factory factory = HDF5FactoryProvider.get(); + infile = convertInputStreamToFile(in); + hdf5Reader = factory.openForReading(infile); + } catch (Exception e) { + if (in != null) { + in.close(); + } + throw UserException + .dataReadError(e) + .message("Failed to open open input file: {}", split.getPath()) + .build(logger); + } + assert in != null; + reader = new BufferedReader(new InputStreamReader(in)); + } + + /** + * This function converts the Drill InputStream into a File object for the HDF5 library. This function + * exists due to a known limitation in the HDF5 library which cannot parse HDF5 directly from an input stream. A future + * release of the library will support this. + * + * @param stream The input stream to be converted to a File + * @return File The file which was converted from an InputStream + * @throws IOException Throws IOException if the InputStream cannot be opened or read. + */ + private File convertInputStreamToFile(InputStream stream) throws IOException { + File tmpDir = getTmpDir(); + String tempFileName = tmpDir.getPath() + "/~" + split.getPath().getName(); + File targetFile = new File(tempFileName); + + try { + java.nio.file.Files.copy(stream, targetFile.toPath(), StandardCopyOption.REPLACE_EXISTING); + } catch (Exception e) { + if (targetFile.exists()) { + targetFile.delete(); + } + + throw UserException + .dataWriteError(e) + .message("Failed to create temp HDF5 file: {}", split.getPath()) Review comment: Fixed ---------------------------------------------------------------- This is an automated message from the Apache Git Service. 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