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/*
* Copyright 2007 - 2018 ETH Zuerich, CISD and SIS.
*
* Licensed 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 ch.systemsx.cisd.hdf5;
import static hdf.hdf5lib.HDF5Constants.H5T_ARRAY;
import static hdf.hdf5lib.HDF5Constants.H5T_COMPOUND;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import ch.systemsx.cisd.hdf5.HDF5DataTypeInformation.DataTypeInfoOptions;
import ch.systemsx.cisd.hdf5.cleanup.ICallableWithCleanUp;
import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry;
import hdf.hdf5lib.exceptions.HDF5JavaException;
/**
* The implementation of {@link IHDF5CompoundInformationRetriever}.
*
* @author Bernd Rinn
*/
abstract class HDF5CompoundInformationRetriever implements IHDF5CompoundInformationRetriever
{
protected final HDF5BaseReader baseReader;
protected final IHDF5EnumTypeRetriever enumTypeRetriever;
HDF5CompoundInformationRetriever(HDF5BaseReader baseReader,
IHDF5EnumTypeRetriever enumTypeRetriever)
{
assert baseReader != null;
assert enumTypeRetriever != null;
this.baseReader = baseReader;
this.enumTypeRetriever = enumTypeRetriever;
}
@Override
public <T> HDF5CompoundMemberInformation[] getMemberInfo(final Class<T> compoundClass)
{
return getMemberInfo(compoundClass.getSimpleName());
}
@Override
public HDF5CompoundMemberInformation[] getMemberInfo(final String dataTypeName)
{
return getMemberInfo(dataTypeName, DataTypeInfoOptions.DEFAULT);
}
@Override
public HDF5CompoundMemberInformation[] getMemberInfo(final String dataTypeName,
final DataTypeInfoOptions dataTypeInfoOptions)
{
baseReader.checkOpen();
final ICallableWithCleanUp<HDF5CompoundMemberInformation[]> writeRunnable =
new ICallableWithCleanUp<HDF5CompoundMemberInformation[]>()
{
@Override
public HDF5CompoundMemberInformation[] call(final ICleanUpRegistry registry)
{
final String dataTypePath =
HDF5Utils.createDataTypePath(HDF5Utils.COMPOUND_PREFIX,
baseReader.houseKeepingNameSuffix, dataTypeName);
final long compoundDataTypeId =
baseReader.h5.openDataType(baseReader.fileId, dataTypePath,
registry);
final CompoundTypeInformation compoundInformation =
getCompoundTypeInformation(compoundDataTypeId, dataTypePath,
dataTypeInfoOptions, registry);
return compoundInformation.getCopyOfMembers();
}
};
return baseReader.runner.call(writeRunnable);
}
@Override
public HDF5CompoundMemberInformation[] getDataSetInfo(final String dataSetPath)
throws HDF5JavaException
{
return getDataSetInfo(dataSetPath, DataTypeInfoOptions.DEFAULT);
}
@Override
public HDF5CompoundMemberInformation[] getDataSetInfo(final String dataSetPath,
final DataTypeInfoOptions dataTypeInfoOptions) throws HDF5JavaException
{
final ICallableWithCleanUp<HDF5CompoundMemberInformation[]> infoRunnable =
new ICallableWithCleanUp<HDF5CompoundMemberInformation[]>()
{
@Override
public HDF5CompoundMemberInformation[] call(final ICleanUpRegistry registry)
{
return getFullCompoundDataSetInformation(dataSetPath,
dataTypeInfoOptions, registry).getCopyOfMembers();
}
};
final HDF5CompoundMemberInformation[] compoundInformation =
baseReader.runner.call(infoRunnable);
return compoundInformation;
}
private CompoundTypeInformation getFullCompoundAttributeInformation(final String objectPath,
final String attributeName, final DataTypeInfoOptions dataTypeInfoOptions,
final ICleanUpRegistry registry) throws HDF5JavaException
{
final long dataSetId = baseReader.h5.openObject(baseReader.fileId, objectPath, registry);
final long attributeId = baseReader.h5.openAttribute(dataSetId, attributeName, registry);
final long storageDataTypeId = baseReader.h5.getDataTypeForAttribute(attributeId, registry);
final long compoundDataTypeId;
int classType = baseReader.h5.getClassType(storageDataTypeId);
if (classType == H5T_ARRAY)
{
compoundDataTypeId = baseReader.h5.getBaseDataType(storageDataTypeId, registry);
classType = baseReader.h5.getClassType(compoundDataTypeId);
} else
{
compoundDataTypeId = storageDataTypeId;
}
if (classType != H5T_COMPOUND)
{
throw new HDF5JavaException("Attribute '" + attributeName + "' of object '"
+ objectPath + "' is not of compound type.");
}
final String dataTypePathOrNull = baseReader.tryGetDataTypePath(compoundDataTypeId);
final CompoundTypeInformation compoundInformation =
getCompoundTypeInformation(compoundDataTypeId, dataTypePathOrNull,
dataTypeInfoOptions, registry);
return compoundInformation;
}
private CompoundTypeInformation getFullCompoundDataSetInformation(final String dataSetPath,
final DataTypeInfoOptions dataTypeInfoOptions, final ICleanUpRegistry registry)
throws HDF5JavaException
{
final long dataSetId = baseReader.h5.openDataSet(baseReader.fileId, dataSetPath, registry);
final long compoundDataTypeId = baseReader.h5.getDataTypeForDataSet(dataSetId, registry);
if (baseReader.h5.getClassType(compoundDataTypeId) != H5T_COMPOUND)
{
throw new HDF5JavaException("Data set '" + dataSetPath + "' is not of compound type.");
}
// Note: the type variants for the compound members are stored at the compound type.
// So if we want to know the data set variant, we need to read the data type path as well.
final String dataTypePathOrNull =
(dataTypeInfoOptions.knowsDataTypePath() || dataTypeInfoOptions
.knowsDataTypeVariant()) ? baseReader
.tryGetDataTypePath(compoundDataTypeId) : null;
final CompoundTypeInformation compoundInformation =
getCompoundTypeInformation(compoundDataTypeId, dataTypePathOrNull,
dataTypeInfoOptions, registry);
return compoundInformation;
}
private CompoundTypeInformation getFullCompoundDataTypeInformation(final String dataTypePath,
final DataTypeInfoOptions dataTypeInfoOptions, final ICleanUpRegistry registry)
throws HDF5JavaException
{
final long compoundDataTypeId =
baseReader.h5.openDataType(baseReader.fileId, dataTypePath, registry);
if (baseReader.h5.getClassType(compoundDataTypeId) != H5T_COMPOUND)
{
throw new HDF5JavaException("Data type '" + dataTypePath + "' is not a compound type.");
}
final CompoundTypeInformation compoundInformation =
getCompoundTypeInformation(compoundDataTypeId, dataTypePath, dataTypeInfoOptions,
registry);
return compoundInformation;
}
CompoundTypeInformation getCompoundTypeInformation(final long compoundDataTypeId,
final String dataTypePathOrNull, final DataTypeInfoOptions dataTypeInfoOptions,
final ICleanUpRegistry registry)
{
final String typeName =
HDF5Utils.getDataTypeNameFromPath(dataTypePathOrNull,
baseReader.houseKeepingNameSuffix, HDF5DataClass.COMPOUND);
final String[] memberNames =
baseReader.h5.getNamesForEnumOrCompoundMembers(compoundDataTypeId);
final long nativeCompoundDataTypeId =
baseReader.h5.getNativeDataType(compoundDataTypeId, registry);
final int recordSizeOnDisk = baseReader.h5.getDataTypeSize(compoundDataTypeId);
final int recordSizeInMemory = baseReader.h5.getDataTypeSize(nativeCompoundDataTypeId);
final CompoundTypeInformation compoundInfo =
new CompoundTypeInformation(typeName, compoundDataTypeId, nativeCompoundDataTypeId,
memberNames.length, recordSizeOnDisk, recordSizeInMemory);
final HDF5DataTypeVariant[] memberTypeVariantsOrNull =
dataTypeInfoOptions.knowsDataTypeVariant() ? baseReader
.tryGetTypeVariantForCompoundMembers(dataTypePathOrNull, registry) : null;
if (memberTypeVariantsOrNull != null
&& memberTypeVariantsOrNull.length != memberNames.length)
{
throw new HDF5JavaException(
"Invalid member data type variant information on committed data type '"
+ dataTypePathOrNull + "'.");
}
int offsetOnDisk = 0;
int offsetInMemory = 0;
for (int i = 0; i < memberNames.length; ++i)
{
final long dataTypeId =
baseReader.h5.getDataTypeForIndex(compoundDataTypeId, i, registry);
// This should safe us from computing the offsets ourselves, but as it turns out, the
// offset for the native data type is wrong for bit fields,
// Test failing: HDF5RoundtripTest.testCompoundMap()
// Tested: 2014-07-28, HDF5 1.8.13
// offsetOnDisk = baseReader.h5.getOffsetForCompoundMemberIndex(compoundDataTypeId, i);
// offsetInMemory =
// baseReader.h5.getOffsetForCompoundMemberIndex(nativeCompoundDataTypeId, i);
compoundInfo.dataTypeIds[i] = dataTypeId;
final HDF5DataTypeInformation dataTypeInformation =
baseReader.getDataTypeInformation(dataTypeId, dataTypeInfoOptions, registry);
if (memberTypeVariantsOrNull != null && memberTypeVariantsOrNull[i].isTypeVariant())
{
dataTypeInformation.setTypeVariant(memberTypeVariantsOrNull[i]);
}
final HDF5EnumerationType enumTypeOrNull;
if (dataTypeInformation.getDataClass() == HDF5DataClass.ENUM)
{
if (dataTypeInformation.isArrayType())
{
final long baseDataSetType = baseReader.h5.getBaseDataType(dataTypeId, registry);
enumTypeOrNull =
baseReader.getEnumTypeForStorageDataType(null, baseDataSetType, false,
null, null, registry);
} else
{
enumTypeOrNull =
baseReader.getEnumTypeForStorageDataType(null, dataTypeId, false, null,
null, registry);
}
} else
{
enumTypeOrNull = null;
}
compoundInfo.enumTypes[i] = enumTypeOrNull;
if (enumTypeOrNull != null)
{
compoundInfo.setMember(i, new HDF5CompoundMemberInformation(memberNames[i],
dataTypeInformation, offsetOnDisk, offsetInMemory, enumTypeOrNull
.getEnumType().getValueArray()));
} else
{
compoundInfo.setMember(i, new HDF5CompoundMemberInformation(memberNames[i],
dataTypeInformation, offsetOnDisk, offsetInMemory));
}
final HDF5DataTypeInformation typeInfo = compoundInfo.getMember(i).getType();
final int size = typeInfo.getSize();
offsetOnDisk += size;
offsetInMemory =
PaddingUtils.padOffset(offsetInMemory + size,
typeInfo.getElementSizeForPadding());
}
return compoundInfo;
}
@Override
public <T> HDF5CompoundType<T> getType(final String name, final Class<T> pojoClass,
boolean requireTypesToBeEqual, final HDF5CompoundMemberMapping... members)
{
baseReader.checkOpen();
final HDF5ValueObjectByteifyer<T> objectArrayifyer =
baseReader.createCompoundByteifyers(pojoClass, members, null);
return getType(name, -1, pojoClass, requireTypesToBeEqual, objectArrayifyer);
}
@Override
public <T> HDF5CompoundType<T> getType(final String name, final Class<T> pojoClass,
final HDF5CompoundMemberMapping... members)
{
return getType(name, pojoClass, true, members);
}
<T> HDF5CompoundType<T> getType(final String name, long committedDataTypeId,
final Class<T> compoundType, final boolean requireEqualsType,
final HDF5ValueObjectByteifyer<T> objectArrayifyer)
{
final long storageDataTypeId =
(committedDataTypeId < 0) ? baseReader
.createStorageCompoundDataType(objectArrayifyer) : committedDataTypeId;
final long nativeDataTypeId = baseReader.createNativeCompoundDataType(objectArrayifyer);
return new HDF5CompoundType<T>(baseReader.fileId, storageDataTypeId, nativeDataTypeId,
name, compoundType, requireEqualsType, objectArrayifyer,
new HDF5CompoundType.IHDF5InternalCompoundMemberInformationRetriever()
{
@Override
public HDF5CompoundMemberInformation[] getCompoundMemberInformation(
final DataTypeInfoOptions dataTypeInfoOptions)
{
return HDF5CompoundInformationRetriever.this
.getCompoundMemberInformation(storageDataTypeId, name,
dataTypeInfoOptions);
}
}, baseReader);
}
HDF5CompoundMemberInformation[] getCompoundMemberInformation(final long storageDataTypeId,
final String dataTypeNameOrNull, final DataTypeInfoOptions dataTypeInfoOptions)
{
baseReader.checkOpen();
final ICallableWithCleanUp<HDF5CompoundMemberInformation[]> writeRunnable =
new ICallableWithCleanUp<HDF5CompoundMemberInformation[]>()
{
@Override
public HDF5CompoundMemberInformation[] call(final ICleanUpRegistry registry)
{
final String dataTypePath =
(dataTypeNameOrNull == null) ? null : HDF5Utils
.createDataTypePath(HDF5Utils.COMPOUND_PREFIX,
baseReader.houseKeepingNameSuffix,
dataTypeNameOrNull);
final CompoundTypeInformation compoundInformation =
getCompoundTypeInformation(storageDataTypeId, dataTypePath,
dataTypeInfoOptions, registry);
return compoundInformation.getCopyOfMembers();
}
};
return baseReader.runner.call(writeRunnable);
}
@Override
public <T> HDF5CompoundType<T> getType(final Class<T> pojoClass,
final HDF5CompoundMemberMapping... members)
{
return getType(null, pojoClass, members);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(String name, Class<T> pojoClass,
HDF5CompoundMappingHints hints)
{
return getInferredType(name, pojoClass, hints, true);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(String name, Class<T> pojoClass,
HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual)
{
return getType(
name,
pojoClass,
requireTypesToBeEqual,
addEnumTypes(HDF5CompoundMemberMapping.addHints(
HDF5CompoundMemberMapping.inferMapping(pojoClass), hints)));
}
@Override
public <T> HDF5CompoundType<T> getInferredType(Class<T> pojoClass,
HDF5CompoundMappingHints hints)
{
return getInferredType(null, pojoClass, hints);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(final String name, final Class<T> pojoClass)
{
return getInferredType(name, pojoClass, null);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(final Class<T> pojoClass)
{
return getInferredType(null, pojoClass);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(String name, T pojo,
HDF5CompoundMappingHints hints)
{
return getInferredType(name, pojo, hints, true);
}
@Override
@SuppressWarnings(
{ "unchecked", "rawtypes" })
public <T> HDF5CompoundType<T> getInferredType(String name, T pojo,
HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual)
{
if (Map.class.isInstance(pojo))
{
final String compoundTypeName =
(name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName(
((Map) pojo).keySet(), true) : name;
return (HDF5CompoundType<T>) getType(
compoundTypeName,
Map.class,
requireTypesToBeEqual,
addEnumTypes(HDF5CompoundMemberMapping.addHints(
HDF5CompoundMemberMapping.inferMapping((Map) pojo), hints)));
} else
{
final Class<T> pojoClass = (Class<T>) pojo.getClass();
return getType(name, pojoClass, requireTypesToBeEqual,
addEnumTypes(HDF5CompoundMemberMapping.addHints(HDF5CompoundMemberMapping
.inferMapping(pojo, HDF5CompoundMemberMapping.inferEnumerationTypeMap(
pojo, enumTypeRetriever), HDF5CompoundMappingHints
.isUseVariableLengthStrings(hints)), hints)));
}
}
@Override
public <T> HDF5CompoundType<T> getInferredType(final String name, final T[] pojo)
{
return getInferredType(name, pojo, null);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(final T[] pojo)
{
return getInferredType((String) null, pojo, null);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(String name, T[] pojo,
HDF5CompoundMappingHints hints)
{
return getInferredType(name, pojo, hints, true);
}
@Override
@SuppressWarnings(
{ "unchecked", "rawtypes" })
public <T> HDF5CompoundType<T> getInferredType(String name, T[] pojo,
HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual)
{
final Class<?> componentType = pojo.getClass().getComponentType();
if (pojo.length == 0)
{
return (HDF5CompoundType<T>) getInferredType(name, componentType, hints);
}
if (Map.class.isAssignableFrom(componentType))
{
final String compoundTypeName =
(name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName(
((Map) pojo[0]).keySet(), true) : name;
return (HDF5CompoundType<T>) getType(
compoundTypeName,
Map.class,
requireTypesToBeEqual,
addEnumTypes(HDF5CompoundMemberMapping.addHints(
HDF5CompoundMemberMapping.inferMapping((Map) pojo[0]), hints)));
} else
{
return (HDF5CompoundType<T>) getType(name, componentType, requireTypesToBeEqual,
addEnumTypes(HDF5CompoundMemberMapping.addHints(HDF5CompoundMemberMapping
.inferMapping(pojo, HDF5CompoundMemberMapping.inferEnumerationTypeMap(
pojo, enumTypeRetriever),
hints == null ? false : hints.isUseVariableLengthStrings()),
hints)));
}
}
HDF5CompoundMemberMapping[] addEnumTypes(HDF5CompoundMemberMapping[] mapping)
{
for (HDF5CompoundMemberMapping m : mapping)
{
final Class<?> memberClass = m.tryGetMemberClass();
if (memberClass != null)
{
if (memberClass.isEnum())
{
@SuppressWarnings("unchecked")
final Class<? extends Enum<?>> enumClass =
(Class<? extends Enum<?>>) memberClass;
final String typeName =
(StringUtils.isBlank(m.tryGetEnumTypeName())) ? memberClass
.getSimpleName() : m.tryGetEnumTypeName();
m.setEnumerationType(enumTypeRetriever.getType(typeName,
ReflectionUtils.getEnumOptions(enumClass)));
} else if (memberClass == HDF5EnumerationValue.class
|| memberClass == HDF5EnumerationValueArray.class
|| memberClass == HDF5EnumerationValueMDArray.class)
{
final HDF5CompoundMappingHints hintsOrNull = m.tryGetHints();
final HDF5EnumerationType typeOrNull =
(hintsOrNull != null) ? hintsOrNull.tryGetEnumType(m.getMemberName())
: null;
if (typeOrNull != null)
{
m.setEnumerationType(typeOrNull);
}
}
}
}
return mapping;
}
@Override
public <T> HDF5CompoundType<T> getInferredType(final String name, final T pojo)
{
return getInferredType(name, pojo, null);
}
@Override
public <T> HDF5CompoundType<T> getInferredType(final T pojo)
{
return getInferredType(null, pojo);
}
@Override
public HDF5CompoundType<List<?>> getInferredType(String name, List<String> memberNames,
List<?> data, HDF5CompoundMappingHints hints)
{
return getInferredType(name, memberNames, data, hints, true);
}
@Override
@SuppressWarnings("unchecked")
public HDF5CompoundType<List<?>> getInferredType(String name, List<String> memberNames,
List<?> data, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual)
{
final String compoundTypeName =
(name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName(memberNames,
false) : name;
final HDF5CompoundType<?> type =
getType(compoundTypeName,
List.class,
requireTypesToBeEqual,
HDF5CompoundMemberMapping.addHints(
HDF5CompoundMemberMapping.inferMapping(memberNames, data), hints));
return (HDF5CompoundType<List<?>>) type;
}
@Override
public HDF5CompoundType<List<?>> getInferredType(String name, List<String> memberNames,
List<?> data)
{
return getInferredType(name, memberNames, data, null);
}
@Override
public HDF5CompoundType<List<?>> getInferredType(List<String> memberNames, List<?> data)
{
return getInferredType(null, memberNames, data);
}
@Override
public HDF5CompoundType<List<?>> getInferredType(List<String> memberNames, List<?> data,
HDF5CompoundMappingHints hints)
{
return getInferredType(null, memberNames, data, hints);
}
@Override
public HDF5CompoundType<Object[]> getInferredType(String[] memberNames, Object[] data)
{
return getInferredType(null, memberNames, data);
}
@Override
public HDF5CompoundType<Object[]> getInferredType(String name, String[] memberNames,
Object[] data)
{
final String compoundTypeName =
(name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName(
Arrays.asList(memberNames), false) : name;
return getType(compoundTypeName, Object[].class,
HDF5CompoundMemberMapping.inferMapping(memberNames, data));
}
@Override
public HDF5CompoundType<Object[]> getInferredType(String name, String[] memberNames,
Object[] data, HDF5CompoundMappingHints hints)
{
return getInferredType(name, memberNames, data, hints, true);
}
@Override
public HDF5CompoundType<Object[]> getInferredType(String name, String[] memberNames,
Object[] data, HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual)
{
final String compoundTypeName =
(name == null) ? HDF5CompoundMemberMapping.constructCompoundTypeName(
Arrays.asList(memberNames), false) : name;
return getType(compoundTypeName, Object[].class, requireTypesToBeEqual,
HDF5CompoundMemberMapping.inferMapping(memberNames, data, hints));
}
@Override
public HDF5CompoundType<Object[]> getInferredType(String[] memberNames, Object[] data,
HDF5CompoundMappingHints hints)
{
return getInferredType(null, memberNames, data, hints);
}
@Override
public <T> HDF5CompoundType<T> getDataSetType(String objectPath, Class<T> pojoClass,
HDF5CompoundMemberMapping... members)
{
return getDataSetType(objectPath, pojoClass, true, members);
}
@Override
public <T> HDF5CompoundType<T> getDataSetType(String objectPath, Class<T> pojoClass,
boolean requireTypesToBeEqual, HDF5CompoundMemberMapping... members)
{
baseReader.checkOpen();
final CompoundTypeInformation cpdTypeInfo =
getFullCompoundDataSetInformation(objectPath, DataTypeInfoOptions.MINIMAL,
baseReader.fileRegistry);
final HDF5CompoundType<T> typeForClass =
getType(cpdTypeInfo.name, cpdTypeInfo.compoundDataTypeId, pojoClass,
requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, members));
return typeForClass;
}
@Override
public <T> HDF5CompoundType<T> getDataSetType(String objectPath, Class<T> pojoClass,
HDF5CompoundMappingHints hints)
{
return getDataSetType(objectPath, pojoClass, hints, true);
}
@Override
public <T> HDF5CompoundType<T> getDataSetType(String objectPath, Class<T> pojoClass,
HDF5CompoundMappingHints hints, boolean requireTypesToBeEqual)
{
baseReader.checkOpen();
// We need to get ALL information for the type as otherwise the mapping might be wrong (due
// to a missing data type variant).
final CompoundTypeInformation cpdTypeInfo =
getFullCompoundDataSetInformation(objectPath, DataTypeInfoOptions.ALL,
baseReader.fileRegistry);
final HDF5CompoundType<T> typeForClass =
getType(cpdTypeInfo.name, cpdTypeInfo.compoundDataTypeId, pojoClass,
requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, hints));
return typeForClass;
}
@Override
public <T> HDF5CompoundType<T> getDataSetType(String objectPath, Class<T> pojoClass)
{
return getDataSetType(objectPath, pojoClass, (HDF5CompoundMappingHints) null);
}
@Override
public <T> HDF5CompoundType<T> getAttributeType(String objectPath, String attributeName,
Class<T> pojoClass)
{
return getAttributeType(objectPath, attributeName, pojoClass, null);
}
@Override
public <T> HDF5CompoundType<T> getAttributeType(String objectPath, String attributeName,
Class<T> pojoClass, HDF5CompoundMappingHints hints)
{
return getAttributeType(objectPath, attributeName, pojoClass, hints,
DataTypeInfoOptions.DEFAULT);
}
@Override
public <T> HDF5CompoundType<T> getAttributeType(String objectPath, String attributeName,
Class<T> pojoClass, HDF5CompoundMappingHints hints,
DataTypeInfoOptions dataTypeInfoOptions)
{
return getAttributeType(objectPath, attributeName, pojoClass, hints, dataTypeInfoOptions,
true);
}
@Override
public <T> HDF5CompoundType<T> getAttributeType(String objectPath, String attributeName,
Class<T> pojoClass, HDF5CompoundMappingHints hints,
DataTypeInfoOptions dataTypeInfoOptions, boolean requireTypesToBeEqual)
{
final CompoundTypeInformation cpdTypeInfo =
getFullCompoundAttributeInformation(objectPath, attributeName, dataTypeInfoOptions,
baseReader.fileRegistry);
final HDF5CompoundType<T> typeForClass =
getType(cpdTypeInfo.name, cpdTypeInfo.compoundDataTypeId, pojoClass,
requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, hints));
return typeForClass;
}
@Override
public <T> HDF5CompoundType<T> getNamedType(Class<T> pojoClass)
{
return getNamedType(pojoClass.getSimpleName(), pojoClass);
}
@Override
public <T> HDF5CompoundType<T> getNamedType(String dataTypeName, Class<T> pojoClass)
{
return getNamedType(dataTypeName, pojoClass, null, DataTypeInfoOptions.DEFAULT);
}
@Override
public <T> HDF5CompoundType<T> getNamedType(String dataTypeName, Class<T> pojoClass,
HDF5CompoundMappingHints hints)
{
return getNamedType(dataTypeName, pojoClass, hints, DataTypeInfoOptions.DEFAULT);
}
@Override
public <T> HDF5CompoundType<T> getNamedType(String dataTypeName, Class<T> pojoClass,
DataTypeInfoOptions dataTypeInfoOptions)
{
return getNamedType(dataTypeName, pojoClass, null, dataTypeInfoOptions);
}
@Override
public <T> HDF5CompoundType<T> getNamedType(String dataTypeName, Class<T> pojoClass,
HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions)
{
return getNamedType(dataTypeName, pojoClass, hints, dataTypeInfoOptions, true);
}
@Override
public <T> HDF5CompoundType<T> getNamedType(String dataTypeName, Class<T> pojoClass,
HDF5CompoundMappingHints hints, DataTypeInfoOptions dataTypeInfoOptions,
boolean requireTypesToBeEqual)
{
final String dataTypePath =
HDF5Utils.createDataTypePath(HDF5Utils.COMPOUND_PREFIX,
baseReader.houseKeepingNameSuffix, dataTypeName);
final CompoundTypeInformation cpdTypeInfo =
getFullCompoundDataTypeInformation(dataTypePath, dataTypeInfoOptions,
baseReader.fileRegistry);
final HDF5CompoundType<T> typeForClass =
getType(dataTypeName, cpdTypeInfo.compoundDataTypeId, pojoClass,
requireTypesToBeEqual, createByteifyers(pojoClass, cpdTypeInfo, hints));
return typeForClass;
}
private <T> HDF5ValueObjectByteifyer<T> createByteifyers(final Class<T> compoundClazz,
final CompoundTypeInformation compoundTypeInfo,
final HDF5CompoundMemberMapping[] mapping)
{
return baseReader.createCompoundByteifyers(compoundClazz, mapping, compoundTypeInfo);
}
private <T> HDF5ValueObjectByteifyer<T> createByteifyers(final Class<T> compoundClazz,
final CompoundTypeInformation compoundTypeInfo,
final HDF5CompoundMappingHints hintsOrNull)
{
return baseReader.createCompoundByteifyers(compoundClazz,
inferMemberMapping(compoundClazz, compoundTypeInfo, hintsOrNull), compoundTypeInfo);
}
private HDF5CompoundMemberMapping[] inferMemberMapping(final Class<?> compoundClazz,
final CompoundTypeInformation compoundTypeInfo,
final HDF5CompoundMappingHints hintsOrNull)
{
final List<HDF5CompoundMemberMapping> mapping =
new ArrayList<HDF5CompoundMemberMapping>(compoundTypeInfo.getNumberOfMembers());
final Map<String, Field> fields = ReflectionUtils.getFieldMap(compoundClazz);
for (int i = 0; i < compoundTypeInfo.getNumberOfMembers(); ++i)
{
final HDF5CompoundMemberInformation compoundMember = compoundTypeInfo.getMember(i);
final long compoundMemberTypeId = compoundTypeInfo.dataTypeIds[i];
final Field fieldOrNull = fields.get(compoundMember.getName());
final String memberName = compoundMember.getName();
final String fieldName = (fieldOrNull != null) ? fieldOrNull.getName() : memberName;
final HDF5DataTypeInformation typeInfo = compoundMember.getType();
final int[] dimensions = typeInfo.getDimensions();
if (typeInfo.getDataClass() == HDF5DataClass.ENUM)
{
if (dimensions.length == 0 || (dimensions.length == 1 && dimensions[0] == 1))
{
mapping.add(HDF5CompoundMemberMapping.mapping(memberName).fieldName(fieldName)
.enumType(compoundTypeInfo.enumTypes[i])
.typeVariant(typeInfo.tryGetTypeVariant()));
} else if (dimensions.length == 1)
{
mapping.add(HDF5CompoundMemberMapping.mappingWithStorageTypeId(
fieldName,
memberName,
new HDF5EnumerationType(baseReader.fileId, -1, baseReader.h5
.getNativeDataType(compoundMemberTypeId,
baseReader.fileRegistry), baseReader
.getEnumDataTypeName(compoundMember.getType().tryGetName(),
compoundMemberTypeId), compoundMember
.tryGetEnumValues(), baseReader), dimensions,
compoundMemberTypeId, typeInfo.tryGetTypeVariant()));
}
} else if (typeInfo.getDataClass() == HDF5DataClass.STRING)
{
if (fieldOrNull != null && (fieldOrNull.getType() != String.class)
&& (fieldOrNull.getType() != char[].class))
{
throw new HDF5JavaException(
"Field of string type does not correspond to string or char[] value");
}
mapping.add(HDF5CompoundMemberMapping.mappingArrayWithStorageId(fieldName,
memberName, String.class, new int[]
{ typeInfo.getElementSize() }, compoundMemberTypeId, false,
typeInfo.isVariableLengthString(), false, typeInfo.tryGetTypeVariant()));
} else if (typeInfo.getDataClass() == HDF5DataClass.REFERENCE)
{
if (fieldOrNull != null && (fieldOrNull.getType() != String.class)
&& (fieldOrNull.getType() != char[].class))
{
throw new HDF5JavaException(
"Field of rererence type does not correspond to string or char[] value");
}
mapping.add(HDF5CompoundMemberMapping.mappingArrayWithStorageId(fieldName,
memberName, String.class, new int[]
{ typeInfo.getElementSize() }, compoundMemberTypeId, false,
false, true, typeInfo.tryGetTypeVariant()));
} else
{
final Class<?> memberClazz;
if (fieldOrNull != null)
{
memberClazz = fieldOrNull.getType();
} else
{
memberClazz = typeInfo.tryGetJavaType();
}
mapping.add(HDF5CompoundMemberMapping.mappingArrayWithStorageId(fieldName,
memberName, memberClazz, dimensions, compoundMemberTypeId,
false == compoundMember.getType().isSigned(), false, false,
typeInfo.tryGetTypeVariant()));
}
}
return HDF5CompoundMemberMapping.addHints(
mapping.toArray(new HDF5CompoundMemberMapping[mapping.size()]), hintsOrNull);
}
}
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