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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 java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import hdf.hdf5lib.exceptions.HDF5JavaException;
import ch.systemsx.cisd.hdf5.cleanup.ICleanUpRegistry;
/**
* A class that byteifies Java value objects. The fields have to be specified by name. This class
* can handle all primitive types and Strings.
*
* @author Bernd Rinn
*/
class HDF5ValueObjectByteifyer<T>
{
private final HDF5MemberByteifyer[] byteifyers;
private final int recordSizeInMemory;
private final int recordSizeOnDisk;
private final int[] vlMemberIndices;
private Class<?> cachedRecordClass;
private Constructor<?> cachedDefaultConstructor;
@SuppressWarnings("unchecked")
private static <T> T newMap(int size)
{
return (T) new HDF5CompoundDataMap(size);
}
@SuppressWarnings("unchecked")
private static <T> T newList(int size)
{
return (T) new HDF5CompoundDataList(Collections.nCopies(size, null));
}
@SuppressWarnings("unchecked")
private static <T> T newArray(int size)
{
return (T) new Object[size];
}
/** A role that provides direct access to the HDF5 file to this byteifyer. */
interface IFileAccessProvider
{
public long getBooleanDataTypeId();
public long getStringDataTypeId(int maxLength);
public long getVariableLengthStringDataTypeId();
public long getArrayTypeId(long baseTypeId, int length);
public long getArrayTypeId(long baseTypeId, int[] dimensions);
public HDF5EnumerationType getEnumType(String[] options);
public CharacterEncoding getCharacterEncoding(long dataTypeId);
public byte[] createObjectReference(String referencedObjectPath);
}
HDF5ValueObjectByteifyer(Class<T> clazz, IFileAccessProvider fileInfoProvider,
CompoundTypeInformation compoundTypeInfoOrNull, HDF5CompoundMemberMapping... members)
{
byteifyers =
HDF5CompoundByteifyerFactory.createMemberByteifyers(clazz, fileInfoProvider,
compoundTypeInfoOrNull, members);
int numberOfVLMembers = 0;
if (compoundTypeInfoOrNull != null)
{
recordSizeOnDisk = compoundTypeInfoOrNull.recordSizeOnDisk;
recordSizeInMemory = compoundTypeInfoOrNull.recordSizeInMemory;
numberOfVLMembers = compoundTypeInfoOrNull.getNumberOfVLMembers();
} else if (byteifyers.length > 0)
{
recordSizeOnDisk = byteifyers[byteifyers.length - 1].getTotalSizeOnDisk();
recordSizeInMemory =
PaddingUtils.padOffset(
byteifyers[byteifyers.length - 1].getTotalSizeInMemory(),
PaddingUtils.findMaxElementSize(byteifyers));
for (HDF5MemberByteifyer byteifyer : byteifyers)
{
if (byteifyer.isVariableLengthType())
{
++numberOfVLMembers;
}
}
} else
{
recordSizeOnDisk = 0;
recordSizeInMemory = 0;
}
vlMemberIndices = new int[numberOfVLMembers];
int idx = 0;
for (HDF5MemberByteifyer byteifyer : byteifyers)
{
if (byteifyer.isVariableLengthType())
{
vlMemberIndices[idx++] = byteifyer.getOffsetInMemory();
}
}
}
public long insertMemberTypes(long dataTypeId)
{
for (HDF5MemberByteifyer byteifyer : byteifyers)
{
byteifyer.insertType(dataTypeId);
}
return dataTypeId;
}
public long insertNativeMemberTypes(long dataTypeId, HDF5 h5, ICleanUpRegistry registry)
{
for (HDF5MemberByteifyer byteifyer : byteifyers)
{
byteifyer.insertNativeType(dataTypeId, h5, registry);
}
return dataTypeId;
}
/**
* @throw {@link HDF5JavaException} if one of the elements in <var>arr</var> exceeding its
* pre-defined size.
*/
public byte[] byteify(long compoundDataTypeId, T[] arr) throws HDF5JavaException
{
final byte[] barray = new byte[arr.length * recordSizeInMemory];
int offset = 0;
int counter = 0;
for (Object obj : arr)
{
for (HDF5MemberByteifyer byteifyer : byteifyers)
{
try
{
final byte[] b = byteifyer.byteify(compoundDataTypeId, obj);
if (b.length > byteifyer.getSize() && byteifyer.mayBeCut() == false)
{
throw new HDF5JavaException("Compound " + byteifyer.describe()
+ " of array element " + counter + " must not exceed "
+ byteifyer.getSize() + " bytes, but is of size " + b.length
+ " bytes.");
}
System.arraycopy(b, 0, barray, offset + byteifyer.getOffsetInMemory(),
Math.min(b.length, byteifyer.getSize()));
} catch (IllegalAccessException ex)
{
throw new HDF5JavaException("Error accessing " + byteifyer.describe());
}
}
offset += recordSizeInMemory;
++counter;
}
return barray;
}
/**
* @throw {@link HDF5JavaException} if <var>obj</var> exceeding its pre-defined size.
*/
public byte[] byteify(long compoundDataTypeId, T obj) throws HDF5JavaException
{
final byte[] barray = new byte[recordSizeInMemory];
for (HDF5MemberByteifyer byteifyer : byteifyers)
{
try
{
final byte[] b = byteifyer.byteify(compoundDataTypeId, obj);
if (b.length > byteifyer.getSize() && byteifyer.mayBeCut() == false)
{
throw new HDF5JavaException("Compound " + byteifyer.describe()
+ " must not exceed " + byteifyer.getSize() + " bytes, but is of size "
+ b.length + " bytes.");
}
System.arraycopy(b, 0, barray, byteifyer.getOffsetInMemory(),
Math.min(b.length, byteifyer.getSize()));
} catch (IllegalAccessException ex)
{
throw new HDF5JavaException("Error accessing " + byteifyer.describe());
}
}
return barray;
}
public T[] arrayify(long compoundDataTypeId, byte[] byteArr, Class<T> recordClass)
{
final int length = byteArr.length / recordSizeInMemory;
if (length * recordSizeInMemory != byteArr.length)
{
throw new HDF5JavaException("Illegal byte array for compound type (length "
+ byteArr.length + " is not a multiple of record size " + recordSizeInMemory
+ ")");
}
final T[] result = HDF5Utils.createArray(recordClass, length);
int offset = 0;
for (int i = 0; i < length; ++i)
{
result[i] = primArrayifyScalar(compoundDataTypeId, byteArr, recordClass, offset);
offset += recordSizeInMemory;
}
return result;
}
public T arrayifyScalar(long compoundDataTypeId, byte[] byteArr, Class<T> recordClass)
{
if (byteArr.length < recordSizeInMemory)
{
throw new HDF5JavaException("Illegal byte array for scalar compound type (length "
+ byteArr.length + " is smaller than record size " + recordSizeInMemory + ")");
}
return primArrayifyScalar(compoundDataTypeId, byteArr, recordClass, 0);
}
private T primArrayifyScalar(long compoundDataTypeId, byte[] byteArr, Class<T> recordClass,
int offset)
{
T result = newInstance(recordClass);
for (HDF5MemberByteifyer byteifyer : byteifyers)
{
try
{
byteifyer.setFromByteArray(compoundDataTypeId, result, byteArr, offset);
} catch (IllegalAccessException ex)
{
throw new HDF5JavaException("Error accessing " + byteifyer.describe());
}
}
return result;
}
@SuppressWarnings("unchecked")
private T newInstance(Class<?> recordClass) throws HDF5JavaException
{
if (Map.class.isAssignableFrom(recordClass))
{
return newMap(byteifyers.length);
}
if (List.class.isAssignableFrom(recordClass))
{
return newList(byteifyers.length);
}
if (recordClass == Object[].class)
{
return newArray(byteifyers.length);
}
try
{
if (recordClass != cachedRecordClass)
{
cachedRecordClass = recordClass;
cachedDefaultConstructor = ReflectionUtils.getDefaultConstructor(recordClass);
}
return (T) cachedDefaultConstructor.newInstance();
} catch (Exception ex)
{
throw new HDF5JavaException("Creation of new object of class "
+ recordClass.getCanonicalName() + " by default constructor failed: "
+ ex.toString());
}
}
public int getRecordSizeOnDisk()
{
return recordSizeOnDisk;
}
public int getRecordSizeInMemory()
{
return recordSizeInMemory;
}
public HDF5MemberByteifyer[] getByteifyers()
{
return byteifyers;
}
/**
* Returns <code>true</code> if the value object byteifyer has any members that cannot be mapped
* to the in-memory representation.
*/
public boolean hasUnmappedMembers()
{
for (HDF5MemberByteifyer memberByteifyer : byteifyers)
{
if (memberByteifyer.isDummy())
{
return true;
}
}
return false;
}
/**
* Returns a list with the names of all members that cannot be mapped to the in-memory
* representation.
*/
public String[] getUnmappedMembers()
{
if (hasUnmappedMembers())
{
final List<String> unmappedMembers = new ArrayList<String>();
for (HDF5MemberByteifyer memberByteifyer : byteifyers)
{
if (memberByteifyer.isDummy())
{
unmappedMembers.add(memberByteifyer.getMemberName());
}
}
return unmappedMembers.toArray(new String[unmappedMembers.size()]);
} else
{
return new String[0];
}
}
boolean hasVLMembers()
{
return vlMemberIndices.length > 0;
}
int[] getVLMemberIndices()
{
return vlMemberIndices;
}
//
// Object
//
@Override
public String toString()
{
return "HDF5ValueObjectByteifyer [byteifyers=" + Arrays.toString(byteifyers) + "]";
}
}
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