de.mpg.biochem.mars.io

Class MoleculeArchiveAmazonS3KeyValueAccess

java.lang.Object

de.mpg.biochem.mars.io.MoleculeArchiveAmazonS3KeyValueAccess

public class MoleculeArchiveAmazonS3KeyValueAccess
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
MoleculeArchiveAmazonS3KeyValueAccess(com.amazonaws.services.s3.AmazonS3 s3, java.lang.String bucketName) Opens an AmazonS3 client and a given bucket name.

Method Summary

Modifier and Type	Method and Description
static java.lang.String	addTrailingSlash(java.lang.String path) When listing children objects for a group, must append a delimiter to the path (e.g.
java.lang.String[]	components(java.lang.String path)
java.lang.String	compose(java.lang.String... components)
void	createDirectories(java.lang.String normalPath)
void	delete(java.lang.String normalPath)
boolean	exists(java.lang.String normalPath) Test whether the normalPath exists.
boolean	isDirectory(java.lang.String normalPath) Test whether the path is a directory.
boolean	isFile(java.lang.String normalPath) Test whether the path is a file.
java.lang.String[]	list(java.lang.String normalPath)
java.lang.String[]	listDirectories(java.lang.String normalPath)
java.util.List<java.lang.String>	listObjectKeys(java.lang.String normalPath)
LockedChannel	lockForReading(java.lang.String normalPath)
LockedChannel	lockForWriting(java.lang.String normalPath)
java.lang.String	normalize(java.lang.String path)
static java.lang.String	normalizeGroupPath(java.lang.String path) Normalize a group path relative to a container's root, resulting in removal of redundant "/", "./", resolution of relative "../", and removal of leading slashes.
java.lang.String	parent(java.lang.String path)
static java.lang.String	removeLeadingSlash(java.lang.String path) When absolute paths are passed (e.g.

Methods inherited from class java.lang.Object

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

Constructor Detail

MoleculeArchiveAmazonS3KeyValueAccess

public MoleculeArchiveAmazonS3KeyValueAccess(com.amazonaws.services.s3.AmazonS3 s3,
                                             java.lang.String bucketName)
                                      throws java.io.IOException

Opens an AmazonS3 client and a given bucket name.

Parameters:

s3 - the s3 instance

bucketName - the bucket name

Throws:

java.io.IOException - if the access could not be created

Method Detail

components

public java.lang.String[] components(java.lang.String path)

compose

public java.lang.String compose(java.lang.String... components)

parent

public java.lang.String parent(java.lang.String path)

normalize

public java.lang.String normalize(java.lang.String path)

normalizeGroupPath

public static java.lang.String normalizeGroupPath(java.lang.String path)

Normalize a group path relative to a container's root, resulting in removal of redundant "/", "./", resolution of relative "../", and removal of leading slashes.

Parameters:

path - to normalize

Returns:

the normalized path

exists

public boolean exists(java.lang.String normalPath)

Test whether the normalPath exists.

Removes leading slash from normalPath, and then checks whether either path or path + "/" is a key.

Parameters:

normalPath - is expected to be in normalized form, no further efforts are made to normalize it.

Returns:

true if path exists, false otherwise

addTrailingSlash

public static java.lang.String addTrailingSlash(java.lang.String path)

When listing children objects for a group, must append a delimiter to the path (e.g. group/data/). This is necessary for not including wrong objects in the filtered set (e.g. group/data-2/attributes.json when group/data is passed without the last slash).

Parameters:

path - the path

Returns:

the path with a trailing slash

removeLeadingSlash

public static java.lang.String removeLeadingSlash(java.lang.String path)

When absolute paths are passed (e.g. /group/data), AWS S3 service creates an additional root folder with an empty name. This method removes the root slash symbol and returns the corrected path.

Parameters:

path - the path

Returns:

the path without the leading slash

isDirectory

public boolean isDirectory(java.lang.String normalPath)

Test whether the path is a directory.

Appends trailing "/" to normalPath if there is none, removes leading "/", and then checks whether resulting path is a key.

Parameters:

normalPath - is expected to be in normalized form, no further efforts are made to normalize it.

Returns:

true if path (with trailing "/") exists as a key, false otherwise

isFile

public boolean isFile(java.lang.String normalPath)

Test whether the path is a file.

Checks whether normalPath has no trailing "/", then removes leading "/" and checks whether the resulting path is a key.

Parameters:

normalPath - is expected to be in normalized form, no further efforts are made to normalize it.

Returns:

true if path exists as a key and has no trailing slash, false otherwise

lockForReading

public LockedChannel lockForReading(java.lang.String normalPath)
                             throws java.io.IOException

Throws:

java.io.IOException

lockForWriting

public LockedChannel lockForWriting(java.lang.String normalPath)
                             throws java.io.IOException

Throws:

java.io.IOException

listObjectKeys

public java.util.List<java.lang.String> listObjectKeys(java.lang.String normalPath)

listDirectories

public java.lang.String[] listDirectories(java.lang.String normalPath)

list

public java.lang.String[] list(java.lang.String normalPath)
                        throws java.io.IOException

Throws:

java.io.IOException

createDirectories

public void createDirectories(java.lang.String normalPath)
                       throws java.io.IOException

Throws:

java.io.IOException

delete

public void delete(java.lang.String normalPath)
            throws java.io.IOException

Throws:

java.io.IOException