snakemake.remote package¶
Submodules¶
snakemake.remote.EGA module¶
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class
snakemake.remote.EGA.
EGAFile
(dataset, path)¶ Bases:
tuple
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dataset
¶ Alias for field number 0
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path
¶ Alias for field number 1
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class
snakemake.remote.EGA.
EGAFileInfo
(size, status, id, checksum)¶ Bases:
tuple
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checksum
¶ Alias for field number 3
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id
¶ Alias for field number 2
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size
¶ Alias for field number 0
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status
¶ Alias for field number 1
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class
snakemake.remote.EGA.
RemoteObject
(*args, protocol=None, keep_local=False, stay_on_remote=False, provider=None, **kwargs)[source]¶ Bases:
snakemake.remote.AbstractRemoteObject
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parts
¶
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class
snakemake.remote.EGA.
RemoteProvider
(*args, keep_local=False, stay_on_remote=False, is_default=False, retry=5, **kwargs)[source]¶ Bases:
snakemake.remote.AbstractRemoteProvider
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api_request
(url_suffix, url_prefix='https://ega.ebi.ac.uk:8051/elixir/', json=True, post=False, **params)[source]¶ Make an API request.
Parameters: - url_suffix (str) – Part of REST API URL right of https://ega.ebi.ac.uk:8051/elixir/
- params (dict) – Parameters to pass, except session
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available_protocols
¶ List of valid protocols for this remote provider.
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default_protocol
¶ The protocol that is prepended to the path when no protocol is specified.
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token
¶
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snakemake.remote.FTP module¶
snakemake.remote.GS module¶
snakemake.remote.HTTP module¶
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class
snakemake.remote.HTTP.
RemoteObject
(*args, keep_local=False, provider=None, additional_request_string='', allow_redirects=True, **kwargs)[source]¶ Bases:
snakemake.remote.DomainObject
This is a class to interact with an HTTP server.
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get_header_item
(httpr, header_name, default)[source]¶ Since HTTP header capitalization may differ, this returns a header value regardless of case
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list
¶
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class
snakemake.remote.HTTP.
RemoteProvider
(*args, keep_local=False, stay_on_remote=False, is_default=False, **kwargs)[source]¶ Bases:
snakemake.remote.AbstractRemoteProvider
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available_protocols
¶ List of valid protocols for this remote provider.
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default_protocol
¶ The protocol that is prepended to the path when no protocol is specified.
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snakemake.remote.NCBI module¶
snakemake.remote.S3 module¶
snakemake.remote.S3Mocked module¶
snakemake.remote.SFTP module¶
snakemake.remote.XRootD module¶
snakemake.remote.dropbox module¶
snakemake.remote.gfal module¶
snakemake.remote.gridftp module¶
snakemake.remote.iRODS module¶
snakemake.remote.webdav module¶
Module contents¶
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class
snakemake.remote.
AbstractRemoteObject
(*args, protocol=None, keep_local=False, stay_on_remote=False, provider=None, **kwargs)[source]¶ Bases:
object
This is an abstract class to be used to derive remote object classes for different cloud storage providers. For example, there could be classes for interacting with Amazon AWS S3 and Google Cloud Storage, both derived from this common base class.
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class
snakemake.remote.
AbstractRemoteProvider
(*args, keep_local=False, stay_on_remote=False, is_default=False, **kwargs)[source]¶ Bases:
object
This is an abstract class to be used to derive remote provider classes. These might be used to hold common credentials, and are then passed to RemoteObjects.
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allows_directories
= False¶
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default_protocol
()[source]¶ The protocol that is prepended to the path when no protocol is specified.
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supports_default
= False¶
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class
snakemake.remote.
DomainObject
(*args, **kwargs)[source]¶ Bases:
snakemake.remote.AbstractRemoteObject
This is a mixin related to parsing components out of a location path specified as (host|IP):port/remote/location
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host
¶
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local_path
¶
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name
¶
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path_prefix
¶
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path_remainder
¶
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port
¶
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remote_path
¶
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