de.mpg.biochem.mars.io

Interface MoleculeArchiveStorage

All Superinterfaces:

java.lang.AutoCloseable

All Known Subinterfaces:

MoleculeArchiveSource

All Known Implementing Classes:

MoleculeArchiveAmazonS3Source, MoleculeArchiveFSSource

public interface MoleculeArchiveStorage
extends java.lang.AutoCloseable

Location where Molecule Archives are stored. Follows structure of N5Source.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	MOLECULE_ARCHIVE_ENDING
static java.lang.String	MOLECULE_ARCHIVE_STORE_ENDING
static java.lang.String	N5_DATASET_DIRECTORY_ENDING Directory ending for n5 datasets.

Method Summary

Modifier and Type	Method and Description
default void	close() Default implementation of AutoCloseable.close() for all implementations that do not hold any closable resources.
static java.util.ArrayList<java.lang.String>	deepList(MoleculeArchiveStorage store, java.lang.String pathName, java.util.function.Predicate<java.lang.String> filter) Helper method to recursively list all groups and datasets.
default java.lang.String[]	deepList(java.lang.String pathName) Recursively list all groups and datasets in the given path.
default java.lang.String[]	deepList(java.lang.String pathName, java.util.concurrent.ExecutorService executor) Recursively list all groups (including datasets) in the given group, in parallel, using the given ExecutorService.
default java.lang.String[]	deepList(java.lang.String pathName, java.util.function.Predicate<java.lang.String> filter) Recursively list all groups and datasets in the given path.
default java.lang.String[]	deepList(java.lang.String pathName, java.util.function.Predicate<java.lang.String> filter, java.util.concurrent.ExecutorService executor) Recursively list all groups (including datasets) in the given group, in parallel, using the given ExecutorService.
static void	deepListHelper(MoleculeArchiveStorage store, java.lang.String path, java.util.function.Predicate<java.lang.String> filter, java.util.concurrent.ExecutorService executor, java.util.concurrent.LinkedBlockingQueue<java.util.concurrent.Future<java.lang.String>> datasetFutures) Helper method for parallel deep listing.
boolean	exists(java.lang.String pathName) Test whether a group or dataset exists at a given path.
default java.lang.String	getGroupSeparator() Returns the symbol that is used to separate nodes in a group path.
java.lang.String	getURI()
default java.lang.String	groupPath(java.lang.String... nodes) Creates a group path by concatenating all nodes with the node separator defined by getGroupSeparator().
java.lang.String[]	list(java.lang.String pathName) List all groups (including datasets) in a group.
java.lang.String[]	listDirectories(java.lang.String pathName) List all groups (including datasets) in a group.
java.lang.String[]	listFiles(java.lang.String pathName) List all groups (including datasets) in a group.

Field Detail

N5_DATASET_DIRECTORY_ENDING

static final java.lang.String N5_DATASET_DIRECTORY_ENDING

Directory ending for n5 datasets.

See Also:

Constant Field Values

MOLECULE_ARCHIVE_ENDING

static final java.lang.String MOLECULE_ARCHIVE_ENDING

See Also:

Constant Field Values

MOLECULE_ARCHIVE_STORE_ENDING

static final java.lang.String MOLECULE_ARCHIVE_STORE_ENDING

See Also:

Constant Field Values

Method Detail

getURI

java.lang.String getURI()

exists

boolean exists(java.lang.String pathName)
        throws java.io.IOException

Test whether a group or dataset exists at a given path.

Parameters:

pathName - group path

Returns:

true if the path exists

Throws:

java.io.IOException - an exception is thrown if the source is not accessible

list

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

List all groups (including datasets) in a group.

Parameters:

pathName - group path

Returns:

list of children

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

listDirectories

java.lang.String[] listDirectories(java.lang.String pathName)
                            throws java.io.IOException

List all groups (including datasets) in a group.

Parameters:

pathName - group path

Returns:

list of directories

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

listFiles

java.lang.String[] listFiles(java.lang.String pathName)
                      throws java.io.IOException

List all groups (including datasets) in a group.

Parameters:

pathName - group path

Returns:

list of files

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

deepList

default java.lang.String[] deepList(java.lang.String pathName,
                                    java.util.function.Predicate<java.lang.String> filter)
                             throws java.io.IOException

Recursively list all groups and datasets in the given path. Only paths that satisfy the provided filter will be included, but the children of paths that were excluded may be included (filter does not apply to the subtree).

Parameters:

pathName - base group path

filter - filter for children to be included

Returns:

list of child groups and datasets

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

deepList

default java.lang.String[] deepList(java.lang.String pathName)
                             throws java.io.IOException

Recursively list all groups and datasets in the given path.

Parameters:

pathName - base group path

Returns:

list of groups and datasets

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

deepList

static java.util.ArrayList<java.lang.String> deepList(MoleculeArchiveStorage store,
                                                      java.lang.String pathName,
                                                      java.util.function.Predicate<java.lang.String> filter)
                                               throws java.io.IOException

Helper method to recursively list all groups and datasets. This method is not part of the public API and is accessible only because Java 8 does not support private interface methods yet. TODO make private when committing to Java versions newer than 8

Parameters:

store - the MoleculeArchiveStore reader

pathName - the base group path

filter - a dataset filter

Returns:

the list of all children

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

deepList

default java.lang.String[] deepList(java.lang.String pathName,
                                    java.util.function.Predicate<java.lang.String> filter,
                                    java.util.concurrent.ExecutorService executor)
                             throws java.io.IOException,
                                    java.lang.InterruptedException,
                                    java.util.concurrent.ExecutionException

Recursively list all groups (including datasets) in the given group, in parallel, using the given ExecutorService. Only paths that satisfy the provided filter will be included, but the children of paths that were excluded may be included (filter does not apply to the subtree).

Parameters:

pathName - base group path

filter - filter for children to be included

executor - executor service

Returns:

list of datasets

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

java.util.concurrent.ExecutionException - the execution exception

java.lang.InterruptedException - the interrupted exception

deepList

default java.lang.String[] deepList(java.lang.String pathName,
                                    java.util.concurrent.ExecutorService executor)
                             throws java.io.IOException,
                                    java.lang.InterruptedException,
                                    java.util.concurrent.ExecutionException

Recursively list all groups (including datasets) in the given group, in parallel, using the given ExecutorService.

Parameters:

pathName - base group path

executor - executor service

Returns:

list of groups

Throws:

java.io.IOException - an exception is thrown if pathName is not a valid group

java.util.concurrent.ExecutionException - the execution exception

java.lang.InterruptedException - this exception is thrown if execution is interrupted

deepListHelper

static void deepListHelper(MoleculeArchiveStorage store,
                           java.lang.String path,
                           java.util.function.Predicate<java.lang.String> filter,
                           java.util.concurrent.ExecutorService executor,
                           java.util.concurrent.LinkedBlockingQueue<java.util.concurrent.Future<java.lang.String>> datasetFutures)

Helper method for parallel deep listing. This method is not part of the public API and is accessible only because Java 8 does not support private interface methods yet. TODO make private when committing to Java versions newer than 8

Parameters:

store - the MoleculeArchiveStore reader

path - the base path

filter - filter for datasets to be included

executor - the executor service

datasetFutures - result futures

getGroupSeparator

default java.lang.String getGroupSeparator()

Returns the symbol that is used to separate nodes in a group path.

Returns:

the group separator

groupPath

default java.lang.String groupPath(java.lang.String... nodes)

Creates a group path by concatenating all nodes with the node separator defined by getGroupSeparator(). The string will not have a leading or trailing node separator symbol.

Parameters:

nodes - a collection of child node names

Returns:

the full group path

close

default void close()

Default implementation of AutoCloseable.close() for all implementations that do not hold any closable resources.

Specified by:

close in interface java.lang.AutoCloseable