aiida.transports package¶
Module for classes and utilities to define transports to other machines.
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class
aiida.transports.
Transport
(*args, **kwargs)[source]¶ Bases:
object
Abstract class for a generic transport (ssh, local, …) Contains the set of minimal methods
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_MAGIC_CHECK
= <_sre.SRE_Pattern object>¶
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__abstractmethods__
= frozenset([])¶
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__dict__
= dict_proxy({'rename': <function rename>, 'copyfile': <function copyfile>, '__module__': 'aiida.transports.transport', '__abstractmethods__': frozenset([]), 'putfile': <function putfile>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '__str__': <function __str__>, 'copy_from_remote_to_remote': <function copy_from_remote_to_remote>, '_MAGIC_CHECK': <_sre.SRE_Pattern object>, 'chmod': <function chmod>, '__dict__': <attribute '__dict__' of 'Transport' objects>, 'set_logger_extra': <function set_logger_extra>, 'copytree': <function copytree>, 'get_valid_auth_params': <classmethod object>, 'close': <function close>, '_common_auth_options': [('safe_interval', {'prompt': 'Connection cooldown time (sec)', 'type': <type 'int'>, 'help': 'Minimum time between connections in sec', 'non_interactive_default': True})], 'open': <function open>, 'listdir_withattributes': <function listdir_withattributes>, '__init__': <function __init__>, 'normalize': <function normalize>, '_valid_auth_params': None, 'isfile': <function isfile>, 'makedirs': <function makedirs>, '__enter__': <function __enter__>, 'mkdir': <function mkdir>, 'chown': <function chown>, '_exec_command_internal': <function _exec_command_internal>, 'getfile': <function getfile>, 'rmdir': <function rmdir>, '_abc_negative_cache_version': 39, 'get_mode': <function get_mode>, '__doc__': '\n Abstract class for a generic transport (ssh, local, ...)\n Contains the set of minimal methods\n ', 'isdir': <function isdir>, 'listdir': <function listdir>, '__exit__': <function __exit__>, 'get': <function get>, 'getcwd': <function getcwd>, 'glob': <function glob>, 'get_attribute': <function get_attribute>, 'has_magic': <function has_magic>, 'symlink': <function symlink>, 'get_safe_open_interval': <function get_safe_open_interval>, 'auth_options': <aiida.common.lang.classproperty object>, 'path_exists': <function path_exists>, '_get_safe_interval_suggestion_string': <classmethod object>, 'rmtree': <function rmtree>, 'put': <function put>, 'copy': <function copy>, 'logger': <property object>, 'glob1': <function glob1>, 'glob0': <function glob0>, 'gotocomputer_command': <function gotocomputer_command>, '_abc_cache': <_weakrefset.WeakSet object>, 'gettree': <function gettree>, 'exec_command_wait': <function exec_command_wait>, 'chdir': <function chdir>, 'get_valid_transports': <classmethod object>, 'remove': <function remove>, 'get_short_doc': <classmethod object>, 'iglob': <function iglob>, '__weakref__': <attribute '__weakref__' of 'Transport' objects>, 'puttree': <function puttree>, '__repr__': <function __repr__>, 'is_open': <property object>, '_abc_registry': <_weakrefset.WeakSet object>, 'whoami': <function whoami>, '_valid_auth_options': []})¶
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__enter__
()[source]¶ For transports that require opening a connection, opens all required channels (used in ‘with’ statements).
This object can be used in nested with statements and the connection will only be opened once and closed when the final with scope finishes e.g.:
t = Transport() with t: # Connection is now open.. with t: # ..still open.. pass # ..still open.. # ...closed
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__exit__
(type_, value, traceback)[source]¶ Closes connections, if needed (used in ‘with’ statements).
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__module__
= 'aiida.transports.transport'¶
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__weakref__
¶ list of weak references to the object (if defined)
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_abc_cache
= <_weakrefset.WeakSet object>¶
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_abc_negative_cache
= <_weakrefset.WeakSet object>¶
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_abc_negative_cache_version
= 39¶
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_abc_registry
= <_weakrefset.WeakSet object>¶
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_common_auth_options
= [('safe_interval', {'prompt': 'Connection cooldown time (sec)', 'type': <type 'int'>, 'help': 'Minimum time between connections in sec', 'non_interactive_default': True})]¶
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_exec_command_internal
(command, **kwargs)[source]¶ Execute the command on the shell, similarly to os.system.
Enforce the execution to be run from the cwd (as given by self.getcwd), if this is not None.
If possible, use the higher-level exec_command_wait function.
Parameters: command (str) – execute the command given as a string Returns: stdin, stdout, stderr and the session, when this exists (can be None).
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classmethod
_get_safe_interval_suggestion_string
(computer)[source]¶ Default time in seconds between consecutive checks.
Set to a non-zero value to be safe e.g. in the case of transports with a connection limit, to avoid overloading the server (and being banned). Should be overriden in plugins. This is anyway just a default, as the value can be changed by the user in the Computer properties, for instance. Currently both the local and the ssh transport override this value, so this is not used, but it will be the default for possible new plugins.
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_valid_auth_options
= []¶
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_valid_auth_params
= None¶
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auth_options
= {'safe_interval': {'help': 'Minimum time between connections in sec', 'non_interactive_default': True, 'prompt': 'Connection cooldown time (sec)', 'type': <type 'int'>}}¶
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chdir
(path)[source]¶ Change directory to ‘path’
Parameters: path (str) – path to change working directory into. Raises: IOError, if the requested path does not exist Return type: str
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chmod
(path, mode)[source]¶ Change permissions of a path.
Parameters: - path (str) – path to file
- mode (int) – new permissions
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chown
(path, uid, gid)[source]¶ Change the owner (uid) and group (gid) of a file. As with python’s os.chown function, you must pass both arguments, so if you only want to change one, use stat first to retrieve the current owner and group.
Parameters: - path (str) – path to the file to change the owner and group of
- uid (int) – new owner’s uid
- gid (int) – new group id
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copy
(remotesource, remotedestination, dereference=False, recursive=True)[source]¶ Copy a file or a directory from remote source to remote destination (On the same remote machine)
Parameters: - remotesource (str) – path of the remote source directory / file
- remotedestination (str) – path of the remote destination directory / file
- dereference (bool) – if True copy the contents of any symlinks found, otherwise copy the symlinks themselves
- recursive (bool) – if True copy directories recursively, otherwise only copy the specified file(s)
Raises: IOError, if one of src or dst does not exist
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copy_from_remote_to_remote
(transportdestination, remotesource, remotedestination, **kwargs)[source]¶ Copy files or folders from a remote computer to another remote computer.
Parameters: - transportdestination – transport to be used for the destination computer
- remotesource (str) – path to the remote source directory / file
- remotedestination (str) – path to the remote destination directory / file
- kwargs – keyword parameters passed to the call to transportdestination.put, except for ‘dereference’ that is passed to self.get
Note
the keyword ‘dereference’ SHOULD be set to False for the final put (onto the destination), while it can be set to the value given in kwargs for the get from the source. In that way, a symbolic link would never be followed in the final copy to the remote destination. That way we could avoid getting unknown (potentially malicious) files into the destination computer. HOWEVER, since dereference=False is currently NOT supported by all plugins, we still force it to True for the final put.
Note
the supported keys in kwargs are callback, dereference, overwrite and ignore_nonexisting.
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copyfile
(remotesource, remotedestination, dereference=False)[source]¶ Copy a file from remote source to remote destination (On the same remote machine)
Parameters: - remotesource (str) – path of the remote source directory / file
- remotedestination (str) – path of the remote destination directory / file
- dereference (bool) – if True copy the contents of any symlinks found, otherwise copy the symlinks themselves
Raises: IOError – if one of src or dst does not exist
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copytree
(remotesource, remotedestination, dereference=False)[source]¶ Copy a folder from remote source to remote destination (On the same remote machine)
Parameters: - remotesource (str) – path of the remote source directory / file
- remotedestination (str) – path of the remote destination directory / file
- dereference (bool) – if True copy the contents of any symlinks found, otherwise copy the symlinks themselves
Raises: IOError – if one of src or dst does not exist
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exec_command_wait
(command, **kwargs)[source]¶ Execute the command on the shell, waits for it to finish, and return the retcode, the stdout and the stderr.
Enforce the execution to be run from the pwd (as given by self.getcwd), if this is not None.
Parameters: command (str) – execute the command given as a string Returns: a list: the retcode (int), stdout (str) and stderr (str).
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get
(remotepath, localpath, *args, **kwargs)[source]¶ Retrieve a file or folder from remote source to local destination dst must be an absolute path (src not necessarily)
Parameters: - remotepath – (str) remote_folder_path
- localpath – (str) local_folder_path
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get_attribute
(path)[source]¶ Return an object FixedFieldsAttributeDict for file in a given path, as defined in aiida.common.extendeddicts Each attribute object consists in a dictionary with the following keys:
- st_size: size of files, in bytes
- st_uid: user id of owner
- st_gid: group id of owner
- st_mode: protection bits
- st_atime: time of most recent access
- st_mtime: time of most recent modification
Parameters: path (str) – path to file Returns: object FixedFieldsAttributeDict
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get_mode
(path)[source]¶ Return the portion of the file’s mode that can be set by chmod().
Parameters: path (str) – path to file Returns: the portion of the file’s mode that can be set by chmod()
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get_safe_open_interval
()[source]¶ Get an interval (in seconds) that suggests how long the user should wait between consecutive calls to open the transport. This can be used as a way to get the user to not swamp a limited number of connections, etc. However it is just advisory.
If returns 0, it is taken that there are no reasons to limit the frequency of open calls.
In the main class, it returns a default value (>0 for safety), set in the _DEFAULT_SAFE_OPEN_INTERVAL attribute of the class. Plugins should override it.
Returns: The safe interval between calling open, in seconds Return type: float
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classmethod
get_short_doc
()[source]¶ Return the first non-empty line of the class docstring, if available
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getfile
(remotepath, localpath, *args, **kwargs)[source]¶ Retrieve a file from remote source to local destination dst must be an absolute path (src not necessarily)
Parameters: - remotepath (str) – remote_folder_path
- localpath (str) – local_folder_path
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gettree
(remotepath, localpath, *args, **kwargs)[source]¶ Retrieve a folder recursively from remote source to local destination dst must be an absolute path (src not necessarily)
Parameters: - remotepath (str) – remote_folder_path
- localpath (str) – local_folder_path
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glob
(pathname)[source]¶ Return a list of paths matching a pathname pattern.
The pattern may contain simple shell-style wildcards a la fnmatch.
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glob0
(dirname, basename)[source]¶ Wrap basename i a list if it is empty or if dirname/basename is an existing path, else return empty list.
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gotocomputer_command
(remotedir)[source]¶ Return a string to be run using os.system in order to connect via the transport to the remote directory.
Expected behaviors:
- A new bash session is opened
- A reasonable error message is produced if the folder does not exist
Parameters: remotedir (str) – the full path of the remote directory
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iglob
(pathname)[source]¶ Return an iterator which yields the paths matching a pathname pattern.
The pattern may contain simple shell-style wildcards a la fnmatch.
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is_open
¶
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isdir
(path)[source]¶ True if path is an existing directory.
Parameters: path (str) – path to directory Returns: boolean
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isfile
(path)[source]¶ Return True if path is an existing file.
Parameters: path (str) – path to file Returns: boolean
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listdir
(path='.', pattern=None)[source]¶ Return a list of the names of the entries in the given path. The list is in arbitrary order. It does not include the special entries ‘.’ and ‘..’ even if they are present in the directory.
Parameters: - path (str) – path to list (default to ‘.’)
- pattern (str) – if used, listdir returns a list of files matching filters in Unix style. Unix only.
Returns: a list of strings
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listdir_withattributes
(path='.', pattern=None)[source]¶ Return a list of the names of the entries in the given path. The list is in arbitrary order. It does not include the special entries ‘.’ and ‘..’ even if they are present in the directory.
Parameters: - path (str) – path to list (default to ‘.’)
- pattern (str) – if used, listdir returns a list of files matching filters in Unix style. Unix only.
Returns: a list of dictionaries, one per entry. The schema of the dictionary is the following:
{ 'name': String, 'attributes': FileAttributeObject, 'isdir': Bool }
where ‘name’ is the file or folder directory, and any other information is metadata (if the file is a folder, a directory, …). ‘attributes’ behaves as the output of transport.get_attribute(); isdir is a boolean indicating if the object is a directory or not.
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logger
¶ Return the internal logger. If you have set extra parameters using set_logger_extra(), a suitable LoggerAdapter instance is created, bringing with itself also the extras.
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makedirs
(path, ignore_existing=False)[source]¶ Super-mkdir; create a leaf directory and all intermediate ones. Works like mkdir, except that any intermediate path segment (not just the rightmost) will be created if it does not exist.
Parameters: - path (str) – directory to create
- ignore_existing (bool) – if set to true, it doesn’t give any error if the leaf directory does already exist
Raises: OSError, if directory at path already exists
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mkdir
(path, ignore_existing=False)[source]¶ Create a folder (directory) named path.
Parameters: - path (str) – name of the folder to create
- ignore_existing (bool) – if True, does not give any error if the directory already exists
Raises: OSError, if directory at path already exists
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normalize
(path='.')[source]¶ Return the normalized path (on the server) of a given path. This can be used to quickly resolve symbolic links or determine what the server is considering to be the “current folder”.
Parameters: path (str) – path to be normalized Raises: IOError – if the path can’t be resolved on the server
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put
(localpath, remotepath, *args, **kwargs)[source]¶ Put a file or a directory from local src to remote dst. src must be an absolute path (dst not necessarily)) Redirects to putfile and puttree.
Parameters: - localpath (str) – absolute path to local source
- remotepath (str) – path to remote destination
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putfile
(localpath, remotepath, *args, **kwargs)[source]¶ Put a file from local src to remote dst. src must be an absolute path (dst not necessarily))
Parameters: - localpath (str) – absolute path to local file
- remotepath (str) – path to remote file
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puttree
(localpath, remotepath, *args, **kwargs)[source]¶ Put a folder recursively from local src to remote dst. src must be an absolute path (dst not necessarily))
Parameters: - localpath (str) – absolute path to local folder
- remotepath (str) – path to remote folder
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remove
(path)[source]¶ Remove the file at the given path. This only works on files; for removing folders (directories), use rmdir.
Parameters: path (str) – path to file to remove Raises: IOError – if the path is a directory
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rename
(oldpath, newpath)[source]¶ Rename a file or folder from oldpath to newpath.
Parameters: - oldpath (str) – existing name of the file or folder
- newpath (str) – new name for the file or folder
Raises: - IOError – if oldpath/newpath is not found
- ValueError – if oldpath/newpath is not a valid string
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rmdir
(path)[source]¶ Remove the folder named path. This works only for empty folders. For recursive remove, use rmtree.
Parameters: path (str) – absolute path to the folder to remove
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rmtree
(path)[source]¶ Remove recursively the content at path
Parameters: path (str) – absolute path to remove
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set_logger_extra
(logger_extra)[source]¶ Pass the data that should be passed automatically to self.logger as ‘extra’ keyword. This is typically useful if you pass data obtained using get_dblogger_extra in aiida.backends.djsite.utils, to automatically log also to the DbLog table.
Parameters: logger_extra – data that you want to pass as extra to the self.logger. To write to DbLog, it should be created by the aiida.backends.djsite.utils.get_dblogger_extra function. Pass None if you do not want to have extras passed.
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Subpackages¶
Submodules¶
Common cli utilities for transport plugins.
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aiida.transports.cli.
common_params
(command_func)[source]¶ Decorate a command function with common click parameters for all transport plugins.
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aiida.transports.cli.
configure_computer_main
(*args, **kwargs)[source]¶ Configure a computer via the CLI.
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aiida.transports.cli.
create_configure_cmd
(transport_type)[source]¶ Create verdi computer configure subcommand for a transport type.
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aiida.transports.cli.
create_option
(name, spec)[source]¶ Create a click option from a name and partial specs as used in transport auth_options.
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aiida.transports.cli.
interactive_default
(transport_type, key, also_noninteractive=False)[source]¶ Create a contextual_default value callback for an auth_param key.
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aiida.transports.cli.
match_comp_transport
(ctx, param, computer, transport_type)[source]¶ Check the computer argument against the transport type.
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aiida.transports.cli.
transport_option_default
(name, computer)[source]¶ Determine the default value for an auth_param key.
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aiida.transports.cli.
transport_options
(transport_type)[source]¶ Decorate a command with all options for a computer configure subcommand for transport_type.
Transport interface.
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class
aiida.transports.transport.
Transport
(*args, **kwargs)[source]¶ Bases:
object
Abstract class for a generic transport (ssh, local, …) Contains the set of minimal methods
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_MAGIC_CHECK
= <_sre.SRE_Pattern object>¶
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__abstractmethods__
= frozenset([])¶
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__dict__
= dict_proxy({'rename': <function rename>, 'copyfile': <function copyfile>, '__module__': 'aiida.transports.transport', '__abstractmethods__': frozenset([]), 'putfile': <function putfile>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '__str__': <function __str__>, 'copy_from_remote_to_remote': <function copy_from_remote_to_remote>, '_MAGIC_CHECK': <_sre.SRE_Pattern object>, 'chmod': <function chmod>, '__dict__': <attribute '__dict__' of 'Transport' objects>, 'set_logger_extra': <function set_logger_extra>, 'copytree': <function copytree>, 'get_valid_auth_params': <classmethod object>, 'close': <function close>, '_common_auth_options': [('safe_interval', {'prompt': 'Connection cooldown time (sec)', 'type': <type 'int'>, 'help': 'Minimum time between connections in sec', 'non_interactive_default': True})], 'open': <function open>, 'listdir_withattributes': <function listdir_withattributes>, '__init__': <function __init__>, 'normalize': <function normalize>, '_valid_auth_params': None, 'isfile': <function isfile>, 'makedirs': <function makedirs>, '__enter__': <function __enter__>, 'mkdir': <function mkdir>, 'chown': <function chown>, '_exec_command_internal': <function _exec_command_internal>, 'getfile': <function getfile>, 'rmdir': <function rmdir>, '_abc_negative_cache_version': 39, 'get_mode': <function get_mode>, '__doc__': '\n Abstract class for a generic transport (ssh, local, ...)\n Contains the set of minimal methods\n ', 'isdir': <function isdir>, 'listdir': <function listdir>, '__exit__': <function __exit__>, 'get': <function get>, 'getcwd': <function getcwd>, 'glob': <function glob>, 'get_attribute': <function get_attribute>, 'has_magic': <function has_magic>, 'symlink': <function symlink>, 'get_safe_open_interval': <function get_safe_open_interval>, 'auth_options': <aiida.common.lang.classproperty object>, 'path_exists': <function path_exists>, '_get_safe_interval_suggestion_string': <classmethod object>, 'rmtree': <function rmtree>, 'put': <function put>, 'copy': <function copy>, 'logger': <property object>, 'glob1': <function glob1>, 'glob0': <function glob0>, 'gotocomputer_command': <function gotocomputer_command>, '_abc_cache': <_weakrefset.WeakSet object>, 'gettree': <function gettree>, 'exec_command_wait': <function exec_command_wait>, 'chdir': <function chdir>, 'get_valid_transports': <classmethod object>, 'remove': <function remove>, 'get_short_doc': <classmethod object>, 'iglob': <function iglob>, '__weakref__': <attribute '__weakref__' of 'Transport' objects>, 'puttree': <function puttree>, '__repr__': <function __repr__>, 'is_open': <property object>, '_abc_registry': <_weakrefset.WeakSet object>, 'whoami': <function whoami>, '_valid_auth_options': []})¶
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__enter__
()[source]¶ For transports that require opening a connection, opens all required channels (used in ‘with’ statements).
This object can be used in nested with statements and the connection will only be opened once and closed when the final with scope finishes e.g.:
t = Transport() with t: # Connection is now open.. with t: # ..still open.. pass # ..still open.. # ...closed
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__exit__
(type_, value, traceback)[source]¶ Closes connections, if needed (used in ‘with’ statements).
-
__module__
= 'aiida.transports.transport'¶
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__weakref__
¶ list of weak references to the object (if defined)
-
_abc_cache
= <_weakrefset.WeakSet object>¶
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_abc_negative_cache
= <_weakrefset.WeakSet object>¶
-
_abc_negative_cache_version
= 39¶
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_abc_registry
= <_weakrefset.WeakSet object>¶
-
_common_auth_options
= [('safe_interval', {'prompt': 'Connection cooldown time (sec)', 'type': <type 'int'>, 'help': 'Minimum time between connections in sec', 'non_interactive_default': True})]¶
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_exec_command_internal
(command, **kwargs)[source]¶ Execute the command on the shell, similarly to os.system.
Enforce the execution to be run from the cwd (as given by self.getcwd), if this is not None.
If possible, use the higher-level exec_command_wait function.
Parameters: command (str) – execute the command given as a string Returns: stdin, stdout, stderr and the session, when this exists (can be None).
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classmethod
_get_safe_interval_suggestion_string
(computer)[source]¶ Default time in seconds between consecutive checks.
Set to a non-zero value to be safe e.g. in the case of transports with a connection limit, to avoid overloading the server (and being banned). Should be overriden in plugins. This is anyway just a default, as the value can be changed by the user in the Computer properties, for instance. Currently both the local and the ssh transport override this value, so this is not used, but it will be the default for possible new plugins.
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_valid_auth_options
= []¶
-
_valid_auth_params
= None¶
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auth_options
= {'safe_interval': {'help': 'Minimum time between connections in sec', 'non_interactive_default': True, 'prompt': 'Connection cooldown time (sec)', 'type': <type 'int'>}}¶
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chdir
(path)[source]¶ Change directory to ‘path’
Parameters: path (str) – path to change working directory into. Raises: IOError, if the requested path does not exist Return type: str
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chmod
(path, mode)[source]¶ Change permissions of a path.
Parameters: - path (str) – path to file
- mode (int) – new permissions
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chown
(path, uid, gid)[source]¶ Change the owner (uid) and group (gid) of a file. As with python’s os.chown function, you must pass both arguments, so if you only want to change one, use stat first to retrieve the current owner and group.
Parameters: - path (str) – path to the file to change the owner and group of
- uid (int) – new owner’s uid
- gid (int) – new group id
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copy
(remotesource, remotedestination, dereference=False, recursive=True)[source]¶ Copy a file or a directory from remote source to remote destination (On the same remote machine)
Parameters: - remotesource (str) – path of the remote source directory / file
- remotedestination (str) – path of the remote destination directory / file
- dereference (bool) – if True copy the contents of any symlinks found, otherwise copy the symlinks themselves
- recursive (bool) – if True copy directories recursively, otherwise only copy the specified file(s)
Raises: IOError, if one of src or dst does not exist
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copy_from_remote_to_remote
(transportdestination, remotesource, remotedestination, **kwargs)[source]¶ Copy files or folders from a remote computer to another remote computer.
Parameters: - transportdestination – transport to be used for the destination computer
- remotesource (str) – path to the remote source directory / file
- remotedestination (str) – path to the remote destination directory / file
- kwargs – keyword parameters passed to the call to transportdestination.put, except for ‘dereference’ that is passed to self.get
Note
the keyword ‘dereference’ SHOULD be set to False for the final put (onto the destination), while it can be set to the value given in kwargs for the get from the source. In that way, a symbolic link would never be followed in the final copy to the remote destination. That way we could avoid getting unknown (potentially malicious) files into the destination computer. HOWEVER, since dereference=False is currently NOT supported by all plugins, we still force it to True for the final put.
Note
the supported keys in kwargs are callback, dereference, overwrite and ignore_nonexisting.
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copyfile
(remotesource, remotedestination, dereference=False)[source]¶ Copy a file from remote source to remote destination (On the same remote machine)
Parameters: - remotesource (str) – path of the remote source directory / file
- remotedestination (str) – path of the remote destination directory / file
- dereference (bool) – if True copy the contents of any symlinks found, otherwise copy the symlinks themselves
Raises: IOError – if one of src or dst does not exist
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copytree
(remotesource, remotedestination, dereference=False)[source]¶ Copy a folder from remote source to remote destination (On the same remote machine)
Parameters: - remotesource (str) – path of the remote source directory / file
- remotedestination (str) – path of the remote destination directory / file
- dereference (bool) – if True copy the contents of any symlinks found, otherwise copy the symlinks themselves
Raises: IOError – if one of src or dst does not exist
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exec_command_wait
(command, **kwargs)[source]¶ Execute the command on the shell, waits for it to finish, and return the retcode, the stdout and the stderr.
Enforce the execution to be run from the pwd (as given by self.getcwd), if this is not None.
Parameters: command (str) – execute the command given as a string Returns: a list: the retcode (int), stdout (str) and stderr (str).
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get
(remotepath, localpath, *args, **kwargs)[source]¶ Retrieve a file or folder from remote source to local destination dst must be an absolute path (src not necessarily)
Parameters: - remotepath – (str) remote_folder_path
- localpath – (str) local_folder_path
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get_attribute
(path)[source]¶ Return an object FixedFieldsAttributeDict for file in a given path, as defined in aiida.common.extendeddicts Each attribute object consists in a dictionary with the following keys:
- st_size: size of files, in bytes
- st_uid: user id of owner
- st_gid: group id of owner
- st_mode: protection bits
- st_atime: time of most recent access
- st_mtime: time of most recent modification
Parameters: path (str) – path to file Returns: object FixedFieldsAttributeDict
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get_mode
(path)[source]¶ Return the portion of the file’s mode that can be set by chmod().
Parameters: path (str) – path to file Returns: the portion of the file’s mode that can be set by chmod()
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get_safe_open_interval
()[source]¶ Get an interval (in seconds) that suggests how long the user should wait between consecutive calls to open the transport. This can be used as a way to get the user to not swamp a limited number of connections, etc. However it is just advisory.
If returns 0, it is taken that there are no reasons to limit the frequency of open calls.
In the main class, it returns a default value (>0 for safety), set in the _DEFAULT_SAFE_OPEN_INTERVAL attribute of the class. Plugins should override it.
Returns: The safe interval between calling open, in seconds Return type: float
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classmethod
get_short_doc
()[source]¶ Return the first non-empty line of the class docstring, if available
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getfile
(remotepath, localpath, *args, **kwargs)[source]¶ Retrieve a file from remote source to local destination dst must be an absolute path (src not necessarily)
Parameters: - remotepath (str) – remote_folder_path
- localpath (str) – local_folder_path
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gettree
(remotepath, localpath, *args, **kwargs)[source]¶ Retrieve a folder recursively from remote source to local destination dst must be an absolute path (src not necessarily)
Parameters: - remotepath (str) – remote_folder_path
- localpath (str) – local_folder_path
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glob
(pathname)[source]¶ Return a list of paths matching a pathname pattern.
The pattern may contain simple shell-style wildcards a la fnmatch.
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glob0
(dirname, basename)[source]¶ Wrap basename i a list if it is empty or if dirname/basename is an existing path, else return empty list.
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gotocomputer_command
(remotedir)[source]¶ Return a string to be run using os.system in order to connect via the transport to the remote directory.
Expected behaviors:
- A new bash session is opened
- A reasonable error message is produced if the folder does not exist
Parameters: remotedir (str) – the full path of the remote directory
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iglob
(pathname)[source]¶ Return an iterator which yields the paths matching a pathname pattern.
The pattern may contain simple shell-style wildcards a la fnmatch.
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is_open
¶
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isdir
(path)[source]¶ True if path is an existing directory.
Parameters: path (str) – path to directory Returns: boolean
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isfile
(path)[source]¶ Return True if path is an existing file.
Parameters: path (str) – path to file Returns: boolean
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listdir
(path='.', pattern=None)[source]¶ Return a list of the names of the entries in the given path. The list is in arbitrary order. It does not include the special entries ‘.’ and ‘..’ even if they are present in the directory.
Parameters: - path (str) – path to list (default to ‘.’)
- pattern (str) – if used, listdir returns a list of files matching filters in Unix style. Unix only.
Returns: a list of strings
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listdir_withattributes
(path='.', pattern=None)[source]¶ Return a list of the names of the entries in the given path. The list is in arbitrary order. It does not include the special entries ‘.’ and ‘..’ even if they are present in the directory.
Parameters: - path (str) – path to list (default to ‘.’)
- pattern (str) – if used, listdir returns a list of files matching filters in Unix style. Unix only.
Returns: a list of dictionaries, one per entry. The schema of the dictionary is the following:
{ 'name': String, 'attributes': FileAttributeObject, 'isdir': Bool }
where ‘name’ is the file or folder directory, and any other information is metadata (if the file is a folder, a directory, …). ‘attributes’ behaves as the output of transport.get_attribute(); isdir is a boolean indicating if the object is a directory or not.
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logger
¶ Return the internal logger. If you have set extra parameters using set_logger_extra(), a suitable LoggerAdapter instance is created, bringing with itself also the extras.
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makedirs
(path, ignore_existing=False)[source]¶ Super-mkdir; create a leaf directory and all intermediate ones. Works like mkdir, except that any intermediate path segment (not just the rightmost) will be created if it does not exist.
Parameters: - path (str) – directory to create
- ignore_existing (bool) – if set to true, it doesn’t give any error if the leaf directory does already exist
Raises: OSError, if directory at path already exists
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mkdir
(path, ignore_existing=False)[source]¶ Create a folder (directory) named path.
Parameters: - path (str) – name of the folder to create
- ignore_existing (bool) – if True, does not give any error if the directory already exists
Raises: OSError, if directory at path already exists
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normalize
(path='.')[source]¶ Return the normalized path (on the server) of a given path. This can be used to quickly resolve symbolic links or determine what the server is considering to be the “current folder”.
Parameters: path (str) – path to be normalized Raises: IOError – if the path can’t be resolved on the server
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put
(localpath, remotepath, *args, **kwargs)[source]¶ Put a file or a directory from local src to remote dst. src must be an absolute path (dst not necessarily)) Redirects to putfile and puttree.
Parameters: - localpath (str) – absolute path to local source
- remotepath (str) – path to remote destination
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putfile
(localpath, remotepath, *args, **kwargs)[source]¶ Put a file from local src to remote dst. src must be an absolute path (dst not necessarily))
Parameters: - localpath (str) – absolute path to local file
- remotepath (str) – path to remote file
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puttree
(localpath, remotepath, *args, **kwargs)[source]¶ Put a folder recursively from local src to remote dst. src must be an absolute path (dst not necessarily))
Parameters: - localpath (str) – absolute path to local folder
- remotepath (str) – path to remote folder
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remove
(path)[source]¶ Remove the file at the given path. This only works on files; for removing folders (directories), use rmdir.
Parameters: path (str) – path to file to remove Raises: IOError – if the path is a directory
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rename
(oldpath, newpath)[source]¶ Rename a file or folder from oldpath to newpath.
Parameters: - oldpath (str) – existing name of the file or folder
- newpath (str) – new name for the file or folder
Raises: - IOError – if oldpath/newpath is not found
- ValueError – if oldpath/newpath is not a valid string
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rmdir
(path)[source]¶ Remove the folder named path. This works only for empty folders. For recursive remove, use rmtree.
Parameters: path (str) – absolute path to the folder to remove
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rmtree
(path)[source]¶ Remove recursively the content at path
Parameters: path (str) – absolute path to remove
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set_logger_extra
(logger_extra)[source]¶ Pass the data that should be passed automatically to self.logger as ‘extra’ keyword. This is typically useful if you pass data obtained using get_dblogger_extra in aiida.backends.djsite.utils, to automatically log also to the DbLog table.
Parameters: logger_extra – data that you want to pass as extra to the self.logger. To write to DbLog, it should be created by the aiida.backends.djsite.utils.get_dblogger_extra function. Pass None if you do not want to have extras passed.
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General utilities for Transport classes.
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class
aiida.transports.util.
FileAttribute
(init=None)[source]¶ Bases:
aiida.common.extendeddicts.FixedFieldsAttributeDict
A class, resembling a dictionary, to describe the attributes of a file, that is returned by get_attribute(). Possible keys: st_size, st_uid, st_gid, st_mode, st_atime, st_mtime
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__module__
= 'aiida.transports.util'¶
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_valid_fields
= ('st_size', 'st_uid', 'st_gid', 'st_mode', 'st_atime', 'st_mtime')¶
-
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class
aiida.transports.util.
_DetachedProxyCommand
(command_line)[source]¶ Bases:
paramiko.proxy.ProxyCommand
Modifies paramiko’s ProxyCommand by launching the process in a separate process group.
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__init__
(command_line)[source]¶ Create a new CommandProxy instance. The instance created by this class can be passed as an argument to the .Transport class.
Parameters: command_line (str) – the command that should be executed and used as the proxy.
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__module__
= 'aiida.transports.util'¶
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aiida.transports.util.
copy_from_remote_to_remote
(transportsource, transportdestination, remotesource, remotedestination, **kwargs)[source]¶ Copy files or folders from a remote computer to another remote computer.
Parameters: - transportsource – transport to be used for the source computer
- transportdestination – transport to be used for the destination computer
- remotesource (str) – path to the remote source directory / file
- remotedestination (str) – path to the remote destination directory / file
- kwargs – keyword parameters passed to the final put, except for ‘dereference’ that is passed to the initial get
Note
it uses the method transportsource.copy_from_remote_to_remote