cgivre commented on a change in pull request #1778: Drill-7233: Format Plugin for HDF5 URL: https://github.com/apache/drill/pull/1778#discussion_r363600477
########## File path: contrib/format-hdf5/src/main/java/org/apache/drill/exec/store/hdf5/HDF5Utils.java ########## @@ -0,0 +1,269 @@ +/* + * 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.HDF5DataClass; +import ch.systemsx.cisd.hdf5.HDF5EnumerationValue; +import ch.systemsx.cisd.hdf5.IHDF5Reader; +import ch.systemsx.cisd.hdf5.HDF5DataSetInformation; +import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation; +import org.apache.commons.lang3.ArrayUtils; +import org.apache.drill.common.types.TypeProtos.MinorType; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.BitSet; +import java.util.List; +import java.util.Map; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + +public class HDF5Utils { + private static final Logger logger = LoggerFactory.getLogger(HDF5Utils.class); + + private static final boolean caseSensitive = false; + + /* + * This regex is used to extract the final part of an HDF5 path, which is the name of the data field or column. + * While these look like file paths, they are fully contained within HDF5. This regex would extract part3 from: + * /part1/part2/part3 + */ + private static final Pattern PATH_PATTERN = Pattern.compile("/*.*/(.+?)$"); + + /** + * This function returns and HDF5Attribute object for use when Drill maps the attributes. + * + * @param pathName The path to retrieve attributes from + * @param key The key for the specific attribute you are retrieving + * @param reader The IHDF5 reader object for the file you are querying + * @return HDF5Attribute The attribute from the path with the key that was requested. + */ + public static HDF5Attribute getAttribute(String pathName, String key, IHDF5Reader reader) { + if (pathName.equals("")) { + pathName = "/"; + } + + if (!reader.exists(pathName)) { + return null; + } + + if (key.equals("dimensions")) { + HDF5DataSetInformation datasetInfo = reader.object().getDataSetInformation(pathName); + long[] dimensions = datasetInfo.getDimensions(); + ArrayUtils.reverse(dimensions); + return new HDF5Attribute(MinorType.LIST, "dimensions", dimensions); + } + + if (key.equals("dataType")) { + HDF5DataSetInformation datasetInfo = reader.object().getDataSetInformation(pathName); + return new HDF5Attribute(getDataType(datasetInfo), "DataType", datasetInfo.getTypeInformation().getDataClass()); + } + + if (!reader.object().hasAttribute(pathName, key)) { + return null; + } + + HDF5DataTypeInformation attributeInfo = reader.object().getAttributeInformation(pathName, key); + Class<?> type = attributeInfo.tryGetJavaType(); + if (type.isAssignableFrom(long[].class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.BIGINT, key, reader.int64().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.BIGINT, key, reader.uint64().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(int[].class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.INT, key, reader.int32().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.INT, key, reader.uint32().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(short[].class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.INT, key, reader.int16().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.INT, key, reader.uint16().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(byte[].class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.INT, key, reader.int8().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.INT, key, reader.uint8().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(double[].class)) { + return new HDF5Attribute(MinorType.FLOAT8, key, reader.float64().getAttr(pathName, key)); + } else if (type.isAssignableFrom(float[].class)) { + return new HDF5Attribute(MinorType.FLOAT8, key, reader.float32().getAttr(pathName, key)); + } else if (type.isAssignableFrom(String[].class)) { + return new HDF5Attribute(MinorType.VARCHAR, key, reader.string().getAttr(pathName, key)); + } else if (type.isAssignableFrom(long.class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.BIGINT, key, reader.int64().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.BIGINT, key, reader.uint64().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(int.class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.INT, key, reader.int32().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.INT, key, reader.uint32().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(short.class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.INT, key, reader.int16().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.INT, key, reader.uint16().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(byte.class)) { + if (attributeInfo.isSigned()) { + return new HDF5Attribute(MinorType.INT, key, reader.int8().getAttr(pathName, key)); + } else { + return new HDF5Attribute(MinorType.INT, key, reader.uint8().getAttr(pathName, key)); + } + } else if (type.isAssignableFrom(double.class)) { + return new HDF5Attribute(MinorType.FLOAT8, key, reader.float64().getAttr(pathName, key)); + } else if (type.isAssignableFrom(float.class)) { + return new HDF5Attribute(MinorType.FLOAT4, key, reader.float32().getAttr(pathName, key)); + } else if (type.isAssignableFrom(String.class)) { + return new HDF5Attribute(MinorType.VARCHAR, key, reader.string().getAttr(pathName, key)); + } else if (type.isAssignableFrom(boolean.class)) { + return new HDF5Attribute(MinorType.BIT, key, reader.bool().getAttr(pathName, key)); + } else if (type.isAssignableFrom(HDF5EnumerationValue.class)) { + // Convert HDF5 Enum to String + return new HDF5Attribute(MinorType.GENERIC_OBJECT, key, reader.enumeration().getAttr(pathName, key)); + } else if (type.isAssignableFrom(BitSet.class)) { + return new HDF5Attribute(MinorType.BIT, key, reader.bool().getAttr(pathName, key)); + } + + logger.warn("Reading attributes of type {} not yet implemented.", attributeInfo); + return null; + } + + /** + * This function returns the Drill data type of a given HDF5 dataset. + * @param datasetInfo The input data set. + * @return MinorType The Drill data type of the dataset in question + */ + public static MinorType getDataType(HDF5DataSetInformation datasetInfo) { + + HDF5DataTypeInformation typeInfo = datasetInfo.getTypeInformation(); + Class<?> type = typeInfo.tryGetJavaType(); + String name = typeInfo.getDataClass().name(); + if (type == null) { + logger.warn("Datasets of type {} not implemented.", typeInfo); + //Fall back to string + if(name.equalsIgnoreCase("OTHER")) { + return MinorType.GENERIC_OBJECT; + } else { + return MinorType.VARCHAR; + } + } else if (type.isAssignableFrom(long.class)) { + return MinorType.BIGINT; + } else if (type.isAssignableFrom(short.class)) { + return MinorType.SMALLINT; + } else if (type.isAssignableFrom(byte.class)) { + return MinorType.TINYINT; + } else if (type.isAssignableFrom(int.class)) { + return MinorType.INT; + } else if (type.isAssignableFrom(double.class) || type.isAssignableFrom(float.class)) { + return MinorType.FLOAT8; + } else if (type.isAssignableFrom(String.class)) { + return MinorType.VARCHAR; + } else if (type.isAssignableFrom(java.util.Date.class)) { + return MinorType.TIMESTAMP; + } else if (type.isAssignableFrom(boolean.class) || type.isAssignableFrom(BitSet.class)) { + return MinorType.BIT; + } else if (type.isAssignableFrom(Map.class)) { + return MinorType.MAP; + } else if (type.isAssignableFrom(Enum.class)) { + return MinorType.GENERIC_OBJECT; + } + return MinorType.GENERIC_OBJECT; + } + + /** + * This function gets the type of dataset + * @param path The path of the dataset + * @param reader The HDF5 reader + * @return The data type + */ + public static Class<?> getDatasetClass(String path, IHDF5Reader reader) { + HDF5DataSetInformation info = reader.getDataSetInformation(resolvePath(path, reader)); + return info.getTypeInformation().tryGetJavaType(); + } + Review comment: Fixed ---------------------------------------------------------------- This is an automated message from the Apache Git Service. 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