ch.systemsx.cisd.hdf5.h5ar

Interface IHDF5ArchiveReader

All Superinterfaces:

IHDF5ArchiveInfoProvider

All Known Subinterfaces:

IHDF5Archiver

public interface IHDF5ArchiveReader
extends IHDF5ArchiveInfoProvider

An interface for an HDF5 archive reader.

Method Summary

Modifier and Type	Method and Description
void	close() Closes this object and the file referenced by this object.
IHDF5ArchiveReader	extractFile(java.lang.String path, java.io.OutputStream out) Extract the content of a file in the archive to an OutputStream.
byte[]	extractFileAsByteArray(java.lang.String path) Extract the content of a file in the archive to a byte array.
ch.systemsx.cisd.base.io.IInputStream	extractFileAsIInputStream(java.lang.String path) Extract the content of a file in the archive as an IInputStream.
java.io.InputStream	extractFileAsInputStream(java.lang.String path) Extract the content of a file in the archive as an InputStream.
IHDF5ArchiveReader	extractToFilesystem(java.io.File rootDirectory) Extracts the complete archive to the file system.
IHDF5ArchiveReader	extractToFilesystem(java.io.File rootDirectory, java.lang.String path) Extracts a path from the archive to the file system.
IHDF5ArchiveReader	extractToFilesystem(java.io.File rootDirectory, java.lang.String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) Extracts a path from the archive to the file system.
IHDF5ArchiveReader	extractToFilesystem(java.io.File rootDirectory, java.lang.String path, IArchiveEntryVisitor visitorOrNull) Extracts a path from the archive to the file system.
IHDF5ArchiveReader	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootInArchive) Extracts all paths below a given directory path from the archive to the file system.
IHDF5ArchiveReader	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootInArchive, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) Extracts all paths below a given directory path from the archive to the file system.
IHDF5ArchiveReader	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootInArchive, IArchiveEntryVisitor visitorOrNull) Extracts all paths below a given directory path from the archive to the file system.
IHDF5ArchiveReader	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootInArchive, java.lang.String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) Extracts a path from the archive below a given directory path to the file system.
boolean	isClosed() Returns true if this archive reader has been already closed.
java.util.List<ArchiveEntry>	verifyAgainstFilesystem(java.io.File rootDirectoryOnFS) Verifies the content of the complete archive against the filesystem.
java.util.List<ArchiveEntry>	verifyAgainstFilesystem(java.io.File rootDirectoryOnFS, VerifyParameters params) Verifies the content of the complete archive against the filesystem.
java.util.List<ArchiveEntry>	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS) Verifies the content of the archive against the filesystem.
IHDF5ArchiveReader	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, IArchiveEntryVisitor visitor) Verifies the content of the complete archive against the filesystem.
IHDF5ArchiveReader	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor) Verifies the content of the complete archive against the filesystem.
IHDF5ArchiveReader	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor, VerifyParameters params) Verifies the content of the complete archive against the filesystem.
IHDF5ArchiveReader	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, IArchiveEntryVisitor visitor, VerifyParameters params) Verifies the content of the complete archive against the filesystem.
java.util.List<ArchiveEntry>	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, java.lang.String rootDirectoryInArchive) Verifies the content of the archive against the filesystem.
IHDF5ArchiveReader	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, java.lang.String rootDirectoryInArchive, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor, VerifyParameters params) Verifies the content of the archive against the filesystem.
IHDF5ArchiveReader	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, java.lang.String rootDirectoryInArchive, IArchiveEntryVisitor visitor, VerifyParameters params) Verifies the content of the archive against the filesystem.
java.util.List<ArchiveEntry>	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, java.lang.String rootDirectoryInArchive, VerifyParameters params) Verifies the content of the archive against the filesystem.
java.util.List<ArchiveEntry>	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, VerifyParameters params) Verifies the content of the archive against the filesystem.

Methods inherited from interface ch.systemsx.cisd.hdf5.h5ar.IHDF5ArchiveInfoProvider

exists, isDirectory, isRegularFile, isSymLink, list, list, list, list, list, test, tryGetEntry, tryGetResolvedEntry, tryResolveLink

Method Detail

close

void close()

Closes this object and the file referenced by this object. This object must not be used after being closed. Calling this method for a second time is a no-op.

isClosed

boolean isClosed()

Returns true if this archive reader has been already closed.

verifyAgainstFilesystem

IHDF5ArchiveReader verifyAgainstFilesystem(java.lang.String fileOrDir,
                                           java.io.File rootDirectoryOnFS,
                                           java.lang.String rootDirectoryInArchive,
                                           IArchiveEntryVisitor visitor,
                                           IArchiveEntryVisitor missingArchiveEntryVisitor,
                                           VerifyParameters params)

Verifies the content of the archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

rootDirectoryInArchive - The root directory in the archive to start verify from. It will be stripped from each entry before rootDirectoryOnFS is added.

visitor - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful.

missingArchiveEntryVisitor - The entry visitor to call for each file that exists on the filesystem, but is missing in the archive.

params - The parameters to determine behavior of the verification process.

Returns:

This archive reader.

verifyAgainstFilesystem

IHDF5ArchiveReader verifyAgainstFilesystem(java.lang.String fileOrDir,
                                           java.io.File rootDirectoryOnFS,
                                           java.lang.String rootDirectoryInArchive,
                                           IArchiveEntryVisitor visitor,
                                           VerifyParameters params)

Verifies the content of the archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

rootDirectoryInArchive - The root directory in the archive to start verify from. It will be stripped from each entry before rootDirectoryOnFS is added.

visitor - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful.

params - The parameters to determine behavior of the verification process.

Returns:

This archive reader.

verifyAgainstFilesystem

IHDF5ArchiveReader verifyAgainstFilesystem(java.lang.String fileOrDir,
                                           java.io.File rootDirectoryOnFS,
                                           IArchiveEntryVisitor visitor,
                                           IArchiveEntryVisitor missingArchiveEntryVisitor,
                                           VerifyParameters params)

Verifies the content of the complete archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

visitor - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful.

missingArchiveEntryVisitor - The entry visitor to call for each file that exists on the filesystem, but is missing in the archive.

params - The parameters to determine behavior of the verification process.

Returns:

This archive reader.

verifyAgainstFilesystem

IHDF5ArchiveReader verifyAgainstFilesystem(java.lang.String fileOrDir,
                                           java.io.File rootDirectoryOnFS,
                                           IArchiveEntryVisitor visitor,
                                           VerifyParameters params)

Verifies the content of the complete archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

visitor - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful.

params - The parameters to determine behavior of the verification process.

Returns:

This archive reader.

verifyAgainstFilesystem

IHDF5ArchiveReader verifyAgainstFilesystem(java.lang.String fileOrDir,
                                           java.io.File rootDirectoryOnFS,
                                           IArchiveEntryVisitor visitor,
                                           IArchiveEntryVisitor missingArchiveEntryVisitor)

Verifies the content of the complete archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

visitor - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful.

missingArchiveEntryVisitor - The entry visitor to call for each file that exists on the filesystem, but is missing in the archive.

Returns:

This archive reader.

verifyAgainstFilesystem

IHDF5ArchiveReader verifyAgainstFilesystem(java.lang.String fileOrDir,
                                           java.io.File rootDirectoryOnFS,
                                           IArchiveEntryVisitor visitor)

Verifies the content of the complete archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

visitor - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful.

Returns:

This archive reader.

verifyAgainstFilesystem

java.util.List<ArchiveEntry> verifyAgainstFilesystem(java.lang.String fileOrDir,
                                                     java.io.File rootDirectoryOnFS,
                                                     java.lang.String rootDirectoryInArchive,
                                                     VerifyParameters params)

Verifies the content of the archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

rootDirectoryInArchive - The root directory in the archive to start verify from. It will be stripped from each entry before rootDirectoryOnFS is added.

params - The parameters to determine behavior of the verification process.

Returns:

The list of archive entries which failed verification.

verifyAgainstFilesystem

java.util.List<ArchiveEntry> verifyAgainstFilesystem(java.lang.String fileOrDir,
                                                     java.io.File rootDirectoryOnFS,
                                                     VerifyParameters params)

Verifies the content of the archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

params - The parameters to determine behavior of the verification process.

Returns:

The list of archive entries which failed verification.

verifyAgainstFilesystem

java.util.List<ArchiveEntry> verifyAgainstFilesystem(java.lang.String fileOrDir,
                                                     java.io.File rootDirectoryOnFS)

Verifies the content of the archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

Returns:

The list of archive entries which failed verification.

verifyAgainstFilesystem

java.util.List<ArchiveEntry> verifyAgainstFilesystem(java.io.File rootDirectoryOnFS)

Verifies the content of the complete archive against the filesystem.

Parameters:

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

Returns:

The list of archive entries which failed verification.

verifyAgainstFilesystem

java.util.List<ArchiveEntry> verifyAgainstFilesystem(java.io.File rootDirectoryOnFS,
                                                     VerifyParameters params)

Verifies the content of the complete archive against the filesystem.

Parameters:

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

params - The parameters to determine behavior of the verification process.

Returns:

The list of archive entries which failed verification.

verifyAgainstFilesystem

java.util.List<ArchiveEntry> verifyAgainstFilesystem(java.lang.String fileOrDir,
                                                     java.io.File rootDirectoryOnFS,
                                                     java.lang.String rootDirectoryInArchive)

Verifies the content of the archive against the filesystem.

Parameters:

fileOrDir - The file or directory entry in the archive to verify. May be empty, in which case all entries below rootDirectoryInArchive are verified.

rootDirectoryOnFS - The root directory on the file system that should be added to each entry in the archive when comparing.

rootDirectoryInArchive - The root directory in the archive to start verify from. It will be stripped from each entry before rootDirectoryOnFS is added.

extractFile

IHDF5ArchiveReader extractFile(java.lang.String path,
                               java.io.OutputStream out)

Extract the content of a file in the archive to an OutputStream.

Parameters:

path - The path of the file to extract the content of.

out - The output stream to extract the content to.

Returns:

This archive reader.

extractFileAsByteArray

byte[] extractFileAsByteArray(java.lang.String path)

Extract the content of a file in the archive to a byte array.

Parameters:

path - The path of the file to extract the content of.

Returns:

The byte array representing the content of the file.

extractFileAsIInputStream

ch.systemsx.cisd.base.io.IInputStream extractFileAsIInputStream(java.lang.String path)

Extract the content of a file in the archive as an IInputStream.

Parameters:

path - The path of the file to extract the content of.

Returns:

The input stream interface. If an error occurs and the IErrorStrategy of the archive reader does not re-throw the exception, the return value will be null on errors.

extractFileAsInputStream

java.io.InputStream extractFileAsInputStream(java.lang.String path)

Extract the content of a file in the archive as an InputStream.

Parameters:

path - The path of the file to extract the content of.

Returns:

The input stream. If an error occurs and the IErrorStrategy of the archive reader does not re-throw the exception, the return value will be null on errors.

extractToFilesystem

IHDF5ArchiveReader extractToFilesystem(java.io.File rootDirectory)

Extracts the complete archive to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

Returns:

This archive reader.

extractToFilesystem

IHDF5ArchiveReader extractToFilesystem(java.io.File rootDirectory,
                                       java.lang.String path)

Extracts a path from the archive to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

path - The path in the archive to extract. This path will be kept unchanged when extracted.

Returns:

This archive reader.

extractToFilesystem

IHDF5ArchiveReader extractToFilesystem(java.io.File rootDirectory,
                                       java.lang.String path,
                                       IArchiveEntryVisitor visitorOrNull)

Extracts a path from the archive to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

path - The path in the archive to extract. This path will be kept unchanged when extracted.

visitorOrNull - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful. May be null.

Returns:

This archive reader.

extractToFilesystem

IHDF5ArchiveReader extractToFilesystem(java.io.File rootDirectory,
                                       java.lang.String path,
                                       ArchivingStrategy strategy,
                                       IArchiveEntryVisitor visitorOrNull)

Extracts a path from the archive to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

path - The path in the archive to extract. This path will be kept unchanged when extracted.

strategy - The strategy to determine which files and directories to extract and which ones to suppress.

visitorOrNull - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful. May be null.

Returns:

This archive reader.

extractToFilesystemBelowDirectory

IHDF5ArchiveReader extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                                     java.lang.String rootInArchive)

Extracts all paths below a given directory path from the archive to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

rootInArchive - The root path in the archive to extract. This path will be stripped when extracted.

Returns:

This archive reader.

extractToFilesystemBelowDirectory

IHDF5ArchiveReader extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                                     java.lang.String rootInArchive,
                                                     IArchiveEntryVisitor visitorOrNull)

Extracts all paths below a given directory path from the archive to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

rootInArchive - The root path in the archive to extract. This path will be stripped when extracted.

visitorOrNull - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful. May be null.

Returns:

This archive reader.

extractToFilesystemBelowDirectory

IHDF5ArchiveReader extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                                     java.lang.String rootInArchive,
                                                     ArchivingStrategy strategy,
                                                     IArchiveEntryVisitor visitorOrNull)

Extracts all paths below a given directory path from the archive to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

rootInArchive - The root path in the archive to extract. This path will be stripped when extracted.

strategy - The strategy to determine which files and directories to extract and which ones to suppress.

visitorOrNull - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful. May be null.

Returns:

This archive reader.

extractToFilesystemBelowDirectory

IHDF5ArchiveReader extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                                     java.lang.String rootInArchive,
                                                     java.lang.String path,
                                                     ArchivingStrategy strategy,
                                                     IArchiveEntryVisitor visitorOrNull)

Extracts a path from the archive below a given directory path to the file system.

Parameters:

rootDirectory - The directory in the file system to use as root directory for the extracted archive path.

rootInArchive - The root path in the archive to extract. This path will be stripped when extracted.

path - The path in the archive to extract, relative to rootPathInArchive. This path will be kept unchanged when extracted.

strategy - The strategy to determine which files and directories to extract and which ones to suppress.

visitorOrNull - The entry visitor to call for each entry. Call ArchiveEntry.isOK() to check whether verification was successful. May be null.

Returns:

This archive reader.