genomespaceclient package¶

genomespaceclient module¶

class genomespaceclient.client.GSAceObject(permission, sid, ace_id=None)[source]¶

Bases: object

See: http://www.genomespace.org/support/api/restful-access-to-dm#ace

__init__(permission, sid, ace_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class genomespaceclient.client.GSAclObject(object_id, object_type)[source]¶

Bases: object

See: http://www.genomespace.org/support/api/restful-access-to-dm#acl

__init__(object_id, object_type)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class genomespaceclient.client.GSDataFormat(name, url, file_extension, description)[source]¶

Bases: object

See: http://www.genomespace.org/support/api/restful-access-to-dm#appendix_c

__init__(name, url, file_extension, description)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class genomespaceclient.client.GSDirectoryListing(contents, directory)[source]¶

Bases: object

See: http://www.genomespace.org/support/api/restful-access-to-dm#appendix_b

__init__(contents, directory)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class genomespaceclient.client.GSEffectiveAcl(access_control_entries, effective_acl_object, effective_acl_id=None)[source]¶

Bases: object

See: http://www.genomespace.org/support/api/restful-access-to-dm#appendix_f

__init__(access_control_entries, effective_acl_object, effective_acl_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class genomespaceclient.client.GSFileMetadata(name, path, url, parentUrl, size, owner, is_directory, is_link, target_path, last_modified, data_format, available_data_formats, effective_acl)[source]¶

Bases: object

See: http://www.genomespace.org/support/api/restful-access-to-dm#appendix_a

__init__(name, path, url, parentUrl, size, owner, is_directory, is_link, target_path, last_modified, data_format, available_data_formats, effective_acl)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class genomespaceclient.client.GSSidObject(name, sid_type, sid_id=None)[source]¶

Bases: object

See: http://www.genomespace.org/support/api/restful-access-to-dm#sid

__init__(name, sid_type, sid_id=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

class genomespaceclient.client.GenomeSpaceClient(username=None, password=None, token=None)[source]¶

Bases: object

A simple GenomeSpace client

__init__(username=None, password=None, token=None)[source]¶

Constructs a new GenomeSpace client. A username/password combination or a token must be supplied.

Parameters:	username (`str`) – GenomeSpace username password (`str`) – GenomeSpace password token (`str`) – A GenomeSpace auth token. If supplied, the token will be used instead of the username/password.

copy(source, destination, recurse=False)[source]¶

Copies a file to/from/within GenomeSpace.

E.g. .. code-block:: python

client.copy(“/tmp/local_file.txt”,

“https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/hello.txt”)

Parameters:	source (`str`) – Local filename or GenomeSpace URL of source file. destination (`str`) – Local filename or GenomeSpace URL of destination file.

delete(genomespace_url, recurse=False)[source]¶

Deletes a file within a GenomeSpace folder.

E.g. .. code-block:: python

client.delete(“https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt”)

Parameters:	genomespace_url (`str`) – GenomeSpace URL of file to delete.

get_metadata(genomespace_url)[source]¶

Gets metadata information of a genomespace file/folder. See: http://www.genomespace.org/support/api/restful-access-to-dm#file_metadata

E.g.

client.get_metadata("https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt")

Parameters:	genomespace_url (`str`) – GenomeSpace URL of file to delete.
Return type:	`dict`
Returns:	a JSON dict in the format documented here: http://www.genomespace.org/support/api/restful-access-to-dm#appendix_b

get_remaining_token_time(genomespace_url)[source]¶

Gets the time to live for the gs-token if you have one. If you don’t have one, will return 0, as the non existent token has no time left to live. See: http://www.genomespace.org/support/api/restful-access-to-identity-server#get_token_time

E.g.

client.get_remaining_token_time('https://genomespace.genome.edu.au/')

Parameters:	genomespace_url (`str`) – GenomeSpace URL.
Return type:	`int`
Returns:	the time the token has left to live in milliseconds.

isdir(genomespace_url)[source]¶

Returns True if a given genomespace_url is a directory

Parameters:	genomespace_url (`str`) – GenomeSpace URL of file to delete.
Return type:	`bool`
Returns:	True if the url is a directory. False otherwise.

list(genomespace_url)[source]¶

Returns a list of files within a GenomeSpace folder.

E.g. .. code-block:: python

client.list(“https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/”)

Parameters:	genomespace_url (`str`) – GenomeSpace URL of folder to list.
Return type:	`dict`
Returns:	a JSON dict in the format documented here: http://www.genomespace.org/support/api/restful-access-to-dm#appendix_b

mkdir(genomespace_url, create_path=True)[source]¶

Creates a folder at a given location.

E.g. .. code-block:: python

client.mkdir(“https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/Folder1”)

Parameters:	genomespace_url (`str`) – GenomeSpace URL of file to delete. create_path (`boolean`) – Create intermediate directories as required.

move(source, destination)[source]¶

Moves a file within GenomeSpace.

E.g. .. code-block:: python

client.move(“https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/hello.txt”,

“https://dm.genomespace.org/datamanager/v1.0/file/Home/MyBucket/world.txt”)

Parameters:	source – GenomeSpace URL of source file. Cannot be a local file. destination – Local filename or GenomeSpace URL of destination file. If destination is a local file, the file will be copied to the destination and the source file deleted.