ch.systemsx.cisd.hdf5.h5ar

Interface IHDF5Archiver

All Superinterfaces:

IHDF5ArchiveInfoProvider, IHDF5ArchiveReader

public interface IHDF5Archiver
extends IHDF5ArchiveReader

An interface for the HDF5 archiver.

Method Summary

Methods

Modifier and Type	Method and Description
IHDF5Archiver	archiveDirectory(NewArchiveEntry.NewDirectoryArchiveEntry entry) Add a new directory to the archive.
IHDF5Archiver	archiveDirectory(java.lang.String path) Add a new directory to the archive.
IHDF5Archiver	archiveFile(NewArchiveEntry.NewFileArchiveEntry entry, byte[] data) Archive the data as file in the archive.
IHDF5Archiver	archiveFile(NewArchiveEntry.NewFileArchiveEntry entry, java.io.InputStream input) Archive the input as file in the archive.
IHDF5Archiver	archiveFile(java.lang.String path, byte[] data) Archive the data as file in the archive.
IHDF5Archiver	archiveFile(java.lang.String path, java.io.InputStream input) Archive the input as file in the archive.
ch.systemsx.cisd.base.io.IOutputStream	archiveFileAsIOutputStream(NewArchiveEntry.NewFileArchiveEntry entry) Return an IOutputStream that can be used to write the content of a file into the archive.
java.io.OutputStream	archiveFileAsOutputStream(NewArchiveEntry.NewFileArchiveEntry entry) Return an OutputStream that can be used to write the content of a file into the archive.
IHDF5Archiver	archiveFromFilesystem(java.io.File path) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.io.File path, ArchivingStrategy strategy) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.io.File path, ArchivingStrategy strategy, boolean keepNameFromPath, IArchiveEntryVisitor visitor) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.io.File parentDirToStrip, java.io.File path) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.io.File parentDirToStrip, java.io.File path, ArchivingStrategy strategy) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.io.File parentDirToStrip, java.io.File path, ArchivingStrategy strategy, IArchiveEntryVisitor visitor) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.io.File path, IArchiveEntryVisitor visitor) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.lang.String rootInArchive, java.io.File path) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.lang.String rootInArchive, java.io.File path, ArchivingStrategy strategy) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystem(java.lang.String rootInArchive, java.io.File path, ArchivingStrategy strategy, IArchiveEntryVisitor visitor) Archive the path from the filesystem.
IHDF5Archiver	archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive, java.io.File directory) Archive the content below directory from the filesystem.
IHDF5Archiver	archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive, java.io.File directory, ArchivingStrategy strategy) Archive the content below directory from the filesystem.
IHDF5Archiver	archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive, java.io.File directory, ArchivingStrategy strategy, IArchiveEntryVisitor visitor) Archive the content below directory from the filesystem.
IHDF5Archiver	archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive, java.io.File directory, IArchiveEntryVisitor visitor) Archive the content below directory from the filesystem.
IHDF5Archiver	archiveSymlink(NewArchiveEntry.NewSymLinkArchiveEntry entry) Add a new symbolic link to the archive.
IHDF5Archiver	archiveSymlink(java.lang.String path, java.lang.String linkTarget) Add a new symbolic link to the archive.
IHDF5Archiver	delete(java.util.List<java.lang.String> paths) Deletes a list of paths from the archive.
IHDF5Archiver	delete(java.util.List<java.lang.String> paths, IArchiveEntryVisitor entryVisitorOrNull) Deletes a list of paths from the archive.
IHDF5Archiver	delete(java.lang.String path) Deletes a path from the archive.
IHDF5Archiver	extractFile(java.lang.String path, java.io.OutputStream out) Extract the content of a file in the archive to an OutputStream.
IHDF5Archiver	extractToFilesystem(java.io.File rootDirectory) Extracts the complete archive to the file system.
IHDF5Archiver	extractToFilesystem(java.io.File rootDirectory, java.lang.String path) Extracts a path from the archive to the file system.
IHDF5Archiver	extractToFilesystem(java.io.File rootDirectory, java.lang.String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitor) Extracts a path from the archive to the file system.
IHDF5Archiver	extractToFilesystem(java.io.File rootDirectory, java.lang.String path, IArchiveEntryVisitor visitor) Extracts a path from the archive to the file system.
IHDF5Archiver	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootPathInArchive) Extracts all paths below a given directory path from the archive to the file system.
IHDF5Archiver	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootPathInArchive, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) Extracts all paths below a given directory path from the archive to the file system.
IHDF5Archiver	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootPathInArchive, IArchiveEntryVisitor visitorOrNull) Extracts all paths below a given directory path from the archive to the file system.
IHDF5Archiver	extractToFilesystemBelowDirectory(java.io.File rootDirectory, java.lang.String rootPathInArchive, java.lang.String path, ArchivingStrategy strategy, IArchiveEntryVisitor visitorOrNull) Extracts a path from the archive below a given directory path to the file system.
void	flush() Flush the underlying HDF5 writer.
IHDF5Archiver	list(java.lang.String fileOrDir, IArchiveEntryVisitor visitor) Returns the list of all entries below fileOrDir in the archive recursively.
IHDF5Archiver	list(java.lang.String fileOrDir, IArchiveEntryVisitor visitor, ListParameters params) Returns the list of entries below fileOrDir in the archive.
IHDF5Archiver	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, IArchiveEntryVisitor visitor) Verifies the content of the complete archive against the filesystem.
IHDF5Archiver	verifyAgainstFilesystem(java.lang.String fileOrDir, java.io.File rootDirectoryOnFS, IArchiveEntryVisitor visitor, IArchiveEntryVisitor missingArchiveEntryVisitor) Verifies the content of the complete archive against the filesystem.
IHDF5Archiver	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.
IHDF5Archiver	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.
IHDF5Archiver	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.
IHDF5Archiver	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.

Methods inherited from interface ch.systemsx.cisd.hdf5.h5ar.IHDF5ArchiveReader

close, extractFileAsByteArray, extractFileAsIInputStream, extractFileAsInputStream, isClosed, verifyAgainstFilesystem, verifyAgainstFilesystem, verifyAgainstFilesystem

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

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

Method Detail

flush

void flush()
           throws java.io.IOException

Flush the underlying HDF5 writer.

Throws:

java.io.IOException

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.io.File path)
                                    throws java.lang.IllegalStateException

Archive the path from the filesystem.

Parameters:

path - The file or directory to archive. Everything below this path is archived.

Throws:

java.lang.IllegalStateException

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.io.File path,
                                  ArchivingStrategy strategy)

Archive the path from the filesystem.

Parameters:

path - The file or directory to archive. Everything below this path is archived.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.io.File path,
                                  IArchiveEntryVisitor visitor)

Archive the path from the filesystem.

Parameters:

path - The file or directory to archive. Everything below this path is archived.

visitor - The IArchiveEntryVisitor to use. Can be null.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.io.File path,
                                  ArchivingStrategy strategy,
                                  boolean keepNameFromPath,
                                  IArchiveEntryVisitor visitor)

Archive the path from the filesystem.

Parameters:

path - The file or directory to archive. Everything below this path is archived. The name part of path may be kept, depending on the value of keepNameFromPath.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

keepNameFromPath - If true, the name part of path is kept in the archive. Otherwise, path will represent "/" in the archive.

visitor - The IArchiveEntryVisitor to use. Can be null.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.io.File parentDirToStrip,
                                  java.io.File path)

Archive the path from the filesystem.

Parameters:

parentDirToStrip - The parent directory of path on the filesystem which should be stripped in the archive. It is an error, if parentDirToStrip is not a parent directory of path. Example: If path=/home/joe/work/a/b/c and parentDirToStrip=/home/joe/work, then c will end up in the archive at the path a/b.

path - The file or directory to archive.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.io.File parentDirToStrip,
                                  java.io.File path,
                                  ArchivingStrategy strategy)

Archive the path from the filesystem.

Parameters:

parentDirToStrip - The parent directory of path on the filesystem which should be stripped in the archive. It is an error, if parentDirToStrip is not a parent directory of path. Example: If path=/home/joe/work/a/b/c and parentDirToStrip=/home/joe/work, then c will end up in the archive at the path a/b.

path - The file or directory to archive.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.io.File parentDirToStrip,
                                  java.io.File path,
                                  ArchivingStrategy strategy,
                                  IArchiveEntryVisitor visitor)

Archive the path from the filesystem.

Parameters:

parentDirToStrip - The parent directory of path on the filesystem which should be stripped in the archive. It is an error, if parentDirToStrip is not a parent directory of path. Example: If path=/home/joe/work/a/b/c and parentDirToStrip=/home/joe/work, then c will end up in the archive at the path /a/b/c.

path - The file or directory to archive.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

visitor - The IArchiveEntryVisitor to use. Can be null.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.lang.String rootInArchive,
                                  java.io.File path)

Archive the path from the filesystem.

Parameters:

rootInArchive - The root directory of path in the archive. Example: If path=/home/joe/work/a/b/c and rootInArchive=/t, then c will end up in the archive at the path /t/c. If rootInArchive is the last part of the parent directory of path on the filesystem, then its metadata will be taken from the filesystem.

path - The file or directory to archive.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.lang.String rootInArchive,
                                  java.io.File path,
                                  ArchivingStrategy strategy)

Archive the path from the filesystem.

Parameters:

rootInArchive - The root directory of path in the archive. Example: If path=/home/joe/work/a/b/c and rootInArchive=/t, then c will end up in the archive at the path /t/c. If rootInArchive is the last part of the parent directory of path on the filesystem, then its metadata will be taken from the filesystem.

path - The file or directory to archive.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

archiveFromFilesystem

IHDF5Archiver archiveFromFilesystem(java.lang.String rootInArchive,
                                  java.io.File path,
                                  ArchivingStrategy strategy,
                                  IArchiveEntryVisitor visitor)

Archive the path from the filesystem.

Parameters:

rootInArchive - The root directory of path in the archive. Example: If path=/home/joe/work/a/b/c and rootInArchive=/t, then c will end up in the archive at the path /t/c. If rootInArchive is the last part of the parent directory of path on the filesystem, then its metadata will be taken from the filesystem.

path - The file or directory to archive.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

visitor - The IArchiveEntryVisitor to use. Can be null.

archiveFromFilesystemBelowDirectory

IHDF5Archiver archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive,
                                                java.io.File directory)

Archive the content below directory from the filesystem.

Parameters:

rootInArchive - The root directory of path in the archive. Example: If directory=/home/joe/work/a/b, directory b has two files c and d, and rootInArchive=/t, then the archive will have c at path /t/c and d at path /t/d.

directory - The directory to archive the content of. It is an error if this is not a directory on the filesystem.

archiveFromFilesystemBelowDirectory

IHDF5Archiver archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive,
                                                java.io.File directory,
                                                ArchivingStrategy strategy)

Archive the content below directory from the filesystem.

Parameters:

rootInArchive - The root directory of path in the archive. Example: If path=/home/joe/work/a/b/c and rootInArchive=/t, then c will end up in the archive at the path /t/c. If rootInArchive is the last part of the parent directory of path on the filesystem, then its metadata will be taken from the filesystem.

directory - The directory to archive the content of. It is an error if this is not an existing directory.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

archiveFromFilesystemBelowDirectory

IHDF5Archiver archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive,
                                                java.io.File directory,
                                                IArchiveEntryVisitor visitor)

Archive the content below directory from the filesystem.

Parameters:

rootInArchive - The root directory of path in the archive. Example: If path=/home/joe/work/a/b/c and rootInArchive=/t, then c will end up in the archive at the path /t/c. If rootInArchive is the last part of the parent directory of path on the filesystem, then its metadata will be taken from the filesystem.

directory - The directory to archive the content of. It is an error if this is not an existing directory.

visitor - The IArchiveEntryVisitor to use. Can be null.

archiveFromFilesystemBelowDirectory

IHDF5Archiver archiveFromFilesystemBelowDirectory(java.lang.String rootInArchive,
                                                java.io.File directory,
                                                ArchivingStrategy strategy,
                                                IArchiveEntryVisitor visitor)

Archive the content below directory from the filesystem.

Parameters:

rootInArchive - The root directory of path in the archive. Example: If path=/home/joe/work/a/b/c and rootInArchive=/t, then c will end up in the archive at the path /t/c. If rootInArchive is the last part of the parent directory of path on the filesystem, then its metadata will be taken from the filesystem.

directory - The directory to archive the content of. It is an error if this is not an existing directory.

strategy - The archiving strategy to use. This strategy object determines which files to include and to exclude and which files to compress.

visitor - The IArchiveEntryVisitor to use. Can be null.

archiveFile

IHDF5Archiver archiveFile(java.lang.String path,
                        byte[] data)

Archive the data as file in the archive.

Parameters:

path - The path to archive the data at.

data - The bytes to archive as file content.

archiveFile

IHDF5Archiver archiveFile(java.lang.String path,
                        java.io.InputStream input)

Archive the input as file in the archive.

Parameters:

path - The path to archive the data at.

input - The input stream to get the file content from.

archiveFile

IHDF5Archiver archiveFile(NewArchiveEntry.NewFileArchiveEntry entry,
                        java.io.InputStream input)

Archive the input as file in the archive.

Parameters:

entry - The archive entry (defining the path) to archive the data at.

input - The input stream to get the file content from.

archiveFile

IHDF5Archiver archiveFile(NewArchiveEntry.NewFileArchiveEntry entry,
                        byte[] data)

Archive the data as file in the archive.

Parameters:

entry - The archive entry (defining the path) to archive the data at.

data - The bytes to archive as file content.

archiveFileAsIOutputStream

ch.systemsx.cisd.base.io.IOutputStream archiveFileAsIOutputStream(NewArchiveEntry.NewFileArchiveEntry entry)

Return an IOutputStream that can be used to write the content of a file into the archive.

Parameters:

entry - The archive entry (defining the path) to archive the data at.

Returns:

The output stream that the file content is written to.

archiveFileAsOutputStream

java.io.OutputStream archiveFileAsOutputStream(NewArchiveEntry.NewFileArchiveEntry entry)

Return an OutputStream that can be used to write the content of a file into the archive.

Parameters:

entry - The archive entry (defining the path) to archive the data at.

Returns:

The output stream that the file content is written to.

archiveSymlink

IHDF5Archiver archiveSymlink(java.lang.String path,
                           java.lang.String linkTarget)

Add a new symbolic link to the archive.

Parameters:

path - The path where the symbolic link resides.

linkTarget - The target where the symbolic link points to.

archiveSymlink

IHDF5Archiver archiveSymlink(NewArchiveEntry.NewSymLinkArchiveEntry entry)

Add a new symbolic link to the archive.

Parameters:

entry - The archive entry describing the symbolic link.

archiveDirectory

IHDF5Archiver archiveDirectory(java.lang.String path)

Add a new directory to the archive.

Parameters:

path - The path in the archive where the directory resides.

archiveDirectory

IHDF5Archiver archiveDirectory(NewArchiveEntry.NewDirectoryArchiveEntry entry)

Add a new directory to the archive.

Parameters:

entry - The archive entry describing the directory.

delete

IHDF5Archiver delete(java.lang.String path)

Deletes a path from the archive.

Parameters:

path - The path to delete.

delete

IHDF5Archiver delete(java.util.List<java.lang.String> paths)

Deletes a list of paths from the archive.

Parameters:

paths - The paths to delete.

delete

IHDF5Archiver delete(java.util.List<java.lang.String> paths,
                   IArchiveEntryVisitor entryVisitorOrNull)

Deletes a list of paths from the archive.

Parameters:

paths - The paths to delete.

entryVisitorOrNull - The visitor for each archive entry which is actually deleted. If no errors occur, the visitor will be called once for each path in the list of paths.

list

IHDF5Archiver list(java.lang.String fileOrDir,
                 IArchiveEntryVisitor visitor)

Description copied from interface: IHDF5ArchiveInfoProvider

Returns the list of all entries below fileOrDir in the archive recursively.

Specified by:

list in interface IHDF5ArchiveInfoProvider

Parameters:

fileOrDir - The file to list or the directory to list the entries from recursively.

visitor - The archive entry visitor to call for each entry.

Returns:

This archive info provider.

list

IHDF5Archiver list(java.lang.String fileOrDir,
                 IArchiveEntryVisitor visitor,
                 ListParameters params)

Description copied from interface: IHDF5ArchiveInfoProvider

Returns the list of entries below fileOrDir in the archive.

Specified by:

list in interface IHDF5ArchiveInfoProvider

Parameters:

fileOrDir - The file to list or the directory to list the entries from.

visitor - The archive entry visitor to call for each entry.

params - the parameters to modify the listing behavior.

Returns:

This archive info provider.

verifyAgainstFilesystem

IHDF5Archiver verifyAgainstFilesystem(java.lang.String fileOrDir,
                                    java.io.File rootDirectoryOnFS,
                                    java.lang.String rootDirectoryInArchive,
                                    IArchiveEntryVisitor visitor,
                                    IArchiveEntryVisitor missingArchiveEntryVisitor,
                                    VerifyParameters params)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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

IHDF5Archiver verifyAgainstFilesystem(java.lang.String fileOrDir,
                                    java.io.File rootDirectoryOnFS,
                                    java.lang.String rootDirectoryInArchive,
                                    IArchiveEntryVisitor visitor,
                                    VerifyParameters params)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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

IHDF5Archiver verifyAgainstFilesystem(java.lang.String fileOrDir,
                                    java.io.File rootDirectoryOnFS,
                                    IArchiveEntryVisitor visitor,
                                    IArchiveEntryVisitor missingArchiveEntryVisitor,
                                    VerifyParameters params)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the complete archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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

IHDF5Archiver verifyAgainstFilesystem(java.lang.String fileOrDir,
                                    java.io.File rootDirectoryOnFS,
                                    IArchiveEntryVisitor visitor,
                                    VerifyParameters params)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the complete archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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

IHDF5Archiver verifyAgainstFilesystem(java.lang.String fileOrDir,
                                    java.io.File rootDirectoryOnFS,
                                    IArchiveEntryVisitor visitor,
                                    IArchiveEntryVisitor missingArchiveEntryVisitor)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the complete archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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

IHDF5Archiver verifyAgainstFilesystem(java.lang.String fileOrDir,
                                    java.io.File rootDirectoryOnFS,
                                    IArchiveEntryVisitor visitor)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the complete archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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,
                                                   java.lang.String rootDirectoryInArchive)

Description copied from interface: IHDF5ArchiveReader

Verifies the content of the archive against the filesystem.

Specified by:

verifyAgainstFilesystem in interface IHDF5ArchiveReader

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

IHDF5Archiver extractFile(java.lang.String path,
                        java.io.OutputStream out)
                          throws ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

Description copied from interface: IHDF5ArchiveReader

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

Specified by:

extractFile in interface IHDF5ArchiveReader

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.

Throws:

ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked

extractToFilesystem

IHDF5Archiver extractToFilesystem(java.io.File rootDirectory)

Description copied from interface: IHDF5ArchiveReader

Extracts the complete archive to the file system.

Specified by:

extractToFilesystem in interface IHDF5ArchiveReader

Parameters:

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

Returns:

This archive reader.

extractToFilesystem

IHDF5Archiver extractToFilesystem(java.io.File rootDirectory,
                                java.lang.String path)
                                  throws java.lang.IllegalStateException

Description copied from interface: IHDF5ArchiveReader

Extracts a path from the archive to the file system.

Specified by:

extractToFilesystem in interface IHDF5ArchiveReader

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.

Throws:

java.lang.IllegalStateException

extractToFilesystem

IHDF5Archiver extractToFilesystem(java.io.File rootDirectory,
                                java.lang.String path,
                                IArchiveEntryVisitor visitor)
                                  throws java.lang.IllegalStateException

Description copied from interface: IHDF5ArchiveReader

Extracts a path from the archive to the file system.

Specified by:

extractToFilesystem in interface IHDF5ArchiveReader

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.

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

Returns:

This archive reader.

Throws:

java.lang.IllegalStateException

extractToFilesystem

IHDF5Archiver extractToFilesystem(java.io.File rootDirectory,
                                java.lang.String path,
                                ArchivingStrategy strategy,
                                IArchiveEntryVisitor visitor)
                                  throws java.lang.IllegalStateException

Description copied from interface: IHDF5ArchiveReader

Extracts a path from the archive to the file system.

Specified by:

extractToFilesystem in interface IHDF5ArchiveReader

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.

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

Returns:

This archive reader.

Throws:

java.lang.IllegalStateException

extractToFilesystemBelowDirectory

IHDF5Archiver extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                              java.lang.String rootPathInArchive)

Description copied from interface: IHDF5ArchiveReader

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

Specified by:

extractToFilesystemBelowDirectory in interface IHDF5ArchiveReader

Parameters:

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

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

Returns:

This archive reader.

extractToFilesystemBelowDirectory

IHDF5Archiver extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                              java.lang.String rootPathInArchive,
                                              IArchiveEntryVisitor visitorOrNull)

Description copied from interface: IHDF5ArchiveReader

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

Specified by:

extractToFilesystemBelowDirectory in interface IHDF5ArchiveReader

Parameters:

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

rootPathInArchive - 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

IHDF5Archiver extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                              java.lang.String rootPathInArchive,
                                              ArchivingStrategy strategy,
                                              IArchiveEntryVisitor visitorOrNull)

Description copied from interface: IHDF5ArchiveReader

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

Specified by:

extractToFilesystemBelowDirectory in interface IHDF5ArchiveReader

Parameters:

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

rootPathInArchive - 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

IHDF5Archiver extractToFilesystemBelowDirectory(java.io.File rootDirectory,
                                              java.lang.String rootPathInArchive,
                                              java.lang.String path,
                                              ArchivingStrategy strategy,
                                              IArchiveEntryVisitor visitorOrNull)
                                                throws java.lang.IllegalStateException

Description copied from interface: IHDF5ArchiveReader

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

Specified by:

extractToFilesystemBelowDirectory in interface IHDF5ArchiveReader

Parameters:

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

rootPathInArchive - 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.

Throws:

java.lang.IllegalStateException