Package fr.ens.biologie.genomique.eoulsan.data.protocols

Class StorageDataProtocol

java.lang.Object

fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol

All Implemented Interfaces:

DataProtocol

Direct Known Subclasses:

AdditionalAnnotationDataProtocol, GenomeDataProtocol, GFFDataProtocol, GTFDataProtocol

public abstract class StorageDataProtocol
extends Object

This abstract class define a storage protocol. It is useful to easily access common resources like genomes or annotations.

Since:

1.1

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
StorageDataProtocol()

Method Summary

Modifier and Type	Method	Description
boolean	canDelete()	Test if the delete() method is available with this protocol.
boolean	canList()	Test if the list() method is available with this protocol.
boolean	canMkdir()	Test if the mkdir() and mkdirs() methods are available with this protocol.
boolean	canRead()	Test if source is readable with this protocol.
boolean	canRename()	Test if the renameTo() method is available with this protocol.
boolean	canSymlink()	Test if the symlink() method is available with this protocol.
boolean	canWrite()	Test if source is writable with this protocol.
void	delete(DataFile file, boolean recursive)	Delete a file.
boolean	exists(DataFile src, boolean followLink)	Test a source exists.
protected abstract String	getBasePath()	Get the path where searching the files.
InputStream	getData(DataFile src)	Create an InputStream from the source.
DataFile	getDataFileParent(DataFile src)	Get the parent source of the source.
protected String	getExtension()	Get the file extensions of the files to search.
protected List<String>	getExtensions()	Get the list of the file extensions of the files to search.
DataFileMetadata	getMetadata(DataFile src)	Get the metadata for the source.
File	getSourceAsFile(DataFile src)	Get the underlying File object for the DataFile if the protocol allow it.
String	getSourceFilename(String source)	Get the name of the filename that correspond to the source.
DataFile	getUnderLyingData(DataFile src)	Get the underlying Data.
List<DataFile>	list(DataFile file)	List a directory.
void	mkdir(DataFile dir)	Create a directory.
void	mkdirs(DataFile dir)	Create a directory and its parents if not exists.
OutputStream	putData(DataFile dest)	Create an OutputStream from the source.
void	putData(DataFile src, DataFile dest)	Copy data from a source to a destination source
OutputStream	putData(DataFile src, DataFileMetadata md)	Create an OutputStream from the source.
void	rename(DataFile oldName, DataFile newName)	Rename a file.
void	symlink(DataFile target, DataFile link)	Create a symbolic link.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol

getName

Constructor Detail

StorageDataProtocol

public StorageDataProtocol()

Method Detail

getBasePath

protected abstract String getBasePath()

Get the path where searching the files.

Returns:

a string with the path where search the files

getExtension

protected String getExtension()

Get the file extensions of the files to search.

Returns:

a string with file extension of the files to search

getExtensions

protected List<String> getExtensions()

Get the list of the file extensions of the files to search.

Returns:

a list with file extensions of the files to search

getData

public InputStream getData(DataFile src)
                    throws IOException

Description copied from interface: DataProtocol

Create an InputStream from the source.

Parameters:

src - source to use

Returns:

an InputStream

Throws:

IOException - if an error occurs while creating the InputStream

putData

public OutputStream putData(DataFile dest)
                     throws IOException

Description copied from interface: DataProtocol

Create an OutputStream from the source.

Parameters:

dest - destination to use

Returns:

an OutputStream

Throws:

IOException - if an error occurs while creating the OutputStream

exists

public boolean exists(DataFile src,
                      boolean followLink)

Description copied from interface: DataProtocol

Test a source exists.

Parameters:

src - source to use

followLink - if the source is a symbolic file and followLink is true, it will check if the symbolic link target exists instead of the link

Returns:

true if the source exists

getMetadata

public DataFileMetadata getMetadata(DataFile src)
                             throws IOException

Description copied from interface: DataProtocol

Get the metadata for the source.

Parameters:

src - source to use

Returns:

always a metadataObject

Throws:

IOException - if an error occurs while getting metadata

canRead

public boolean canRead()

Description copied from interface: DataProtocol

Test if source is readable with this protocol.

Returns:

true if the source is readable

canWrite

public boolean canWrite()

Description copied from interface: DataProtocol

Test if source is writable with this protocol.

Returns:

true if the source is writable

getSourceAsFile

public File getSourceAsFile(DataFile src)

Description copied from interface: DataProtocol

Get the underlying File object for the DataFile if the protocol allow it.

Specified by:

getSourceAsFile in interface DataProtocol

Returns:

a File object or null if the protocol does not allow it

getUnderLyingData

public DataFile getUnderLyingData(DataFile src)
                           throws IOException

Get the underlying Data.

Parameters:

src - source to use

Returns:

a the underlying DataFile

Throws:

IOException - if an error occurs while getting the underlying DataFile

getSourceFilename

public String getSourceFilename(String source)

Description copied from interface: DataProtocol

Get the name of the filename that correspond to the source.

Specified by:

getSourceFilename in interface DataProtocol

Parameters:

source - the source

Returns:

a String with the filename

getDataFileParent

public DataFile getDataFileParent(DataFile src)

Description copied from interface: DataProtocol

Get the parent source of the source.

Specified by:

getDataFileParent in interface DataProtocol

Parameters:

src - source to use

Returns:

a String with the source of the parent or null if there is parent

putData

public OutputStream putData(DataFile src,
                            DataFileMetadata md)
                     throws IOException

Description copied from interface: DataProtocol

Create an OutputStream from the source.

Specified by:

putData in interface DataProtocol

Parameters:

src - source to use

md - metadata for the stream to write

Returns:

an OutputStream

Throws:

IOException - if an error occurs while creating the OutputStream

putData

public void putData(DataFile src,
                    DataFile dest)
             throws IOException

Description copied from interface: DataProtocol

Copy data from a source to a destination source

Specified by:

putData in interface DataProtocol

Parameters:

src - source source

dest - destination source

Throws:

IOException - if an error occurs while copying data

mkdir

public void mkdir(DataFile dir)
           throws IOException

Description copied from interface: DataProtocol

Create a directory.

Specified by:

mkdir in interface DataProtocol

Parameters:

dir - directory to create

Throws:

IOException - if an error occurs while creating the directory

mkdirs

public void mkdirs(DataFile dir)
            throws IOException

Description copied from interface: DataProtocol

Create a directory and its parents if not exists.

Specified by:

mkdirs in interface DataProtocol

Parameters:

dir - directory to create

Throws:

IOException - if an error occurs while creating the directory

canMkdir

public boolean canMkdir()

Description copied from interface: DataProtocol

Test if the mkdir() and mkdirs() methods are available with this protocol.

Specified by:

canMkdir in interface DataProtocol

Returns:

true if mkdir() and mkdirs() are available

symlink

public void symlink(DataFile target,
                    DataFile link)
             throws IOException

Description copied from interface: DataProtocol

Create a symbolic link.

Specified by:

symlink in interface DataProtocol

Parameters:

target - target file

link - symbolic link file

Throws:

IOException - if an error occurs while creating the symbolic link

canSymlink

public boolean canSymlink()

Description copied from interface: DataProtocol

Test if the symlink() method is available with this protocol.

Specified by:

canSymlink in interface DataProtocol

Returns:

true if symlink() is available

delete

public void delete(DataFile file,
                   boolean recursive)
            throws IOException

Description copied from interface: DataProtocol

Delete a file.

Specified by:

delete in interface DataProtocol

Parameters:

file - file to delete

recursive - recursive deletion

Throws:

IOException - if an error occurs while deleting the file

canDelete

public boolean canDelete()

Description copied from interface: DataProtocol

Test if the delete() method is available with this protocol.

Specified by:

canDelete in interface DataProtocol

Returns:

true if delete() is available

list

public List<DataFile> list(DataFile file)
                    throws IOException

Description copied from interface: DataProtocol

List a directory.

Specified by:

list in interface DataProtocol

Parameters:

file - directory to list

Returns:

a list of DataFile objects

Throws:

IOException - if an error occurs while listing the directory

canList

public boolean canList()

Description copied from interface: DataProtocol

Test if the list() method is available with this protocol.

Specified by:

canList in interface DataProtocol

Returns:

true if list() is available

canRename

public boolean canRename()

Description copied from interface: DataProtocol

Test if the renameTo() method is available with this protocol.

Specified by:

canRename in interface DataProtocol

Returns:

true if renameTo() is available

rename

public void rename(DataFile oldName,
                   DataFile newName)
            throws IOException

Description copied from interface: DataProtocol

Rename a file.

Specified by:

rename in interface DataProtocol

Parameters:

oldName - the file to rename

newName - the destination file

Throws:

IOException - if an error occurs while renaming the directory