[GitHub] [drill] cgivre commented on a change in pull request #1778: Drill-7233: [WIP] Format Plugin for HDF5

[GitBox <gi...@apache.org>]

cgivre commented on a change in pull request #1778: Drill-7233: [WIP] Format Plugin for HDF5
URL: https://github.com/apache/drill/pull/1778#discussion_r342361368
 
 

 ##########
 File path: contrib/format-hdf5/src/main/java/org/apache/drill/exec/store/hdf5/HDF5Utils.java
 ##########
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+/*
+ * 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.drill.common.types.TypeProtos.MinorType;
+import java.io.IOException;
+import java.util.BitSet;
+import java.util.List;
+import java.util.Map;
+
+public class HDF5Utils {
+  private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(HDF5Utils.class);
+
+  private static final boolean caseSensitive = false;
+
+  protected static void reorder(final long[] array) {
+    long a;
+    final int max = array.length - 1;
+    for (int i = (max - 1) / 2; i >= 0; --i) {
+      final int j = max - i;
+      a = array[i];
+      array[i] = array[j];
+      array[j] = a;
+    }
+  }
+
+  protected static void reorder(final int[] array) {
+    int a;
+    final int max = array.length - 1;
+    for (int i = (max - 1) / 2; i >= 0; --i) {
+      final int j = max - i;
+      a = array[i];
+      array[i] = array[j];
+      array[j] = a;
+    }
+  }
+
+  public static boolean exists(String pathName, IHDF5Reader reader) {
+    if (pathName.equals("")) {
+      pathName = "/";
+    }
+
+    return reader.exists(pathName);
+  }
+
+  /**
+   * This function returns and HDF5Attribute object for use when Drill maps the attributes.
+   *
+   * @param pathName
+   * @param key
+   * @param reader
+   * @return
+   * @throws IOException
+   */
+  public static HDF5Attribute getAttribute(String pathName, final String key, IHDF5Reader reader) throws IOException {
+    if (pathName.equals("")) {
+      pathName = "/";
+    }
+
+    if (!reader.exists(pathName)) {
+      return null;
+    }
+
+    if (key.equals("dimensions")) {
+      final HDF5DataSetInformation datasetInfo = reader.object().getDataSetInformation(pathName);
+      final long[] dimensions = datasetInfo.getDimensions();
+      reorder(dimensions);
+      return new HDF5Attribute(MinorType.LIST, "dimensions", dimensions);
+    }
+
+    if (key.equals("dataType")) {
+      final 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.enums().getAttr(pathName, key));
+    } else if (type.isAssignableFrom(BitSet.class)) {
+      return new HDF5Attribute(MinorType.BIT, key, reader.bool().getAttr(pathName, key));
+    }
+
+    logger.info("Reading attributes of type " + attributeInfo + " not yet implemented.");
+    return null;
+  }
+
+  public static MinorType getDataType(final HDF5DataSetInformation datasetInfo) {
+
+    HDF5DataTypeInformation typeInfo = datasetInfo.getTypeInformation();
+    Class<?> type = typeInfo.tryGetJavaType();
+    if (type == null) {
+      logger.info("Datasets of type " + typeInfo + " not implemented.");
+      //Fall back to string
+      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(byte.class) || 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;
 
 Review comment:
   How would you suggest resolving this?

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