Source code for aiida.transports.plugins.ssh

# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved.                     #
# This file is part of the AiiDA code.                                    #
#                                                                         #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
# For further information on the license, see the LICENSE.txt file        #
# For further information please visit http://www.aiida.net               #
###########################################################################
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import

import io
import os
import click
import glob
from stat import S_ISDIR, S_ISREG

import six
from six.moves import cStringIO as StringIO

from aiida.cmdline.params import options
from aiida.cmdline.params.types.path import AbsolutePathParamType
from aiida.common.escaping import escape_for_bash
from ..transport import Transport, TransportInternalError


__all__ = ('parse_sshconfig', 'convert_to_bool', 'SshTransport')


# TODO : callback functions in paramiko are currently not used much and probably broken
[docs]def parse_sshconfig(computername): import paramiko config = paramiko.SSHConfig() try: config.parse(io.open(os.path.expanduser('~/.ssh/config'), encoding='utf8')) except IOError: # No file found, so empty configuration pass return config.lookup(computername)
[docs]def convert_to_bool(string): upstring = str(string).upper() if upstring in ['Y', 'YES', 'T', 'TRUE']: return True elif upstring in ['N', 'NO', 'F', 'FALSE']: return False else: raise ValueError('Invalid boolean value provided')
[docs]class SshTransport(Transport): """ Support connection, command execution and data transfer to remote computers via SSH+SFTP. """ # Valid keywords accepted by the connect method of paramiko.SSHClient # I disable 'password' and 'pkey' to avoid these data to get logged in the # aiida log file. _valid_connect_options = [ ('username', {'prompt': 'User name', 'help': 'user name for the computer', 'non_interactive_default': True}), ('port', {'option': options.PORT, 'prompt': 'port Nr', 'non_interactive_default': True}), ('look_for_keys', {'switch': True, 'prompt': 'Look for keys', 'help': 'switch automatic key file discovery on / off', 'non_interactive_default': True}), ('key_filename', {'type': AbsolutePathParamType(dir_okay=False, exists=True), 'prompt': 'SSH key file', 'help': 'Manually pass a key file if default path is not set in ssh config', 'non_interactive_default': True}), ('timeout', {'type': int, 'prompt': 'Connection timeout in s', 'help': 'time in seconds to wait for connection before giving up', 'non_interactive_default': True}), ('allow_agent', {'switch': True, 'prompt': 'Allow ssh agent', 'help': 'switch to allow or disallow ssh agent', 'non_interactive_default': True}), ('proxy_command', {'prompt': 'SSH proxy command', 'help': 'SSH proxy command', 'non_interactive_default': True}), # Managed 'manually' in connect ('compress', {'switch': True, 'prompt': 'Compress file transfers', 'help': 'switch file transfer compression on / off', 'non_interactive_default': True}), ('gss_auth', {'type': bool, 'prompt': 'GSS auth', 'help': 'GSS auth for kerberos', 'non_interactive_default': True}), ('gss_kex', {'type': bool, 'prompt': 'GSS kex', 'help': 'GSS kex for kerberos', 'non_interactive_default': True}), ('gss_deleg_creds', {'type': bool, 'prompt': 'GSS deleg_creds', 'help': 'GSS deleg_creds for kerberos', 'non_interactive_default': True}), ('gss_host', {'prompt': 'GSS host', 'help': 'GSS host for kerberos', 'non_interactive_default': True}), # for Kerberos support through python-gssapi ] _valid_connect_params = [i[0] for i in _valid_connect_options] # Valid parameters for the ssh transport # For each param, a class method with name # _convert_PARAMNAME_fromstring # should be defined, that returns the value converted from a string to # a correct type, or raise a ValidationError # # moreover, if you want to help in the default configuration, you can # define a _get_PARAMNAME_suggestion_string # to return a suggestion; it must accept only one parameter, being a Computer # instance _valid_auth_options = _valid_connect_options + [ ('load_system_host_keys', {'switch': True, 'prompt': 'Load system host keys', 'help': 'switch loading system host keys on / off', 'non_interactive_default': True}), ('key_policy', {'type': click.Choice(['RejectPolicy', 'WarningPolicy', 'AutoAddPolicy']), 'prompt': 'Key policy', 'help': 'SSH key policy', 'non_interactive_default': True}) ] # I set the (default) value here to 5 secs between consecutive SSH checks. # This should be incremented to 30, probably. _DEFAULT_SAFE_OPEN_INTERVAL = 5
[docs] @classmethod def _get_username_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ import getpass config = parse_sshconfig(computer.hostname) # Either the configured user in the .ssh/config, or the current username return str(config.get('user', getpass.getuser()))
[docs] @classmethod def _get_port_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) # Either the configured user in the .ssh/config, or the default SSH port return str(config.get('port', 22))
[docs] @classmethod def _get_key_filename_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) try: identities = config['identityfile'] # In paramiko > 0.10, identity file is a list of strings. if isinstance(identities, six.string_types): identity = identities elif isinstance(identities, (list, tuple)): if not identities: # An empty list should not be provided; to be sure, # anyway, behave as if no identityfile were defined raise KeyError # By default we suggest only the first one identity = identities[0] else: # If the parser provides an unknown type, just skip to # the 'except KeyError' section, as if no identityfile # were provided (hopefully, this should never happen) raise KeyError except KeyError: # No IdentityFile defined: return an empty string return '' return os.path.expanduser(identity)
[docs] @classmethod def _get_timeout_suggestion_string(cls, computer): """ Return a suggestion for the specific field. Provide 60s as a default timeout for connections. """ config = parse_sshconfig(computer.hostname) return str(config.get('connecttimeout', '60'))
[docs] @classmethod def _get_allow_agent_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) return convert_to_bool(str(config.get('allow_agent', 'no')))
[docs] @classmethod def _get_look_for_keys_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) return convert_to_bool(str(config.get('look_for_keys', 'no')))
[docs] @classmethod def _get_proxy_command_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) # Either the configured user in the .ssh/config, or the default SSH port raw_string = str(config.get('proxycommand', '')) # Note: %h and %p get already automatically substituted with # hostname and port by the config parser! pieces = raw_string.split() new_pieces = [] for piece in pieces: if '>' in piece: # If there is a piece with > to readdress stderr or stdout, # skip from here on (anything else can only be readdressing) break else: new_pieces.append(piece) return' '.join(new_pieces)
[docs] @classmethod def _get_compress_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ return 'True'
[docs] @classmethod def _get_load_system_host_keys_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ return 'True'
[docs] @classmethod def _get_key_policy_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ return 'RejectPolicy'
[docs] @classmethod def _get_gss_auth_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) return convert_to_bool(str(config.get('gssapiauthentication', 'no')))
[docs] @classmethod def _get_gss_kex_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) return convert_to_bool(str(config.get('gssapikeyexchange', 'no')))
[docs] @classmethod def _get_gss_deleg_creds_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) return convert_to_bool(str(config.get('gssapidelegatecredentials', 'no')))
[docs] @classmethod def _get_gss_host_suggestion_string(cls, computer): """ Return a suggestion for the specific field. """ config = parse_sshconfig(computer.hostname) return str(config.get('gssapihostname', computer.hostname))
[docs] @classmethod def _get_safe_interval_suggestion_string(cls, computer): return cls._DEFAULT_SAFE_OPEN_INTERVAL
[docs] def __init__(self, machine, **kwargs): """ Initialize the SshTransport class. :param machine: the machine to connect to :param load_system_host_keys: (optional, default False) if False, do not load the system host keys :param key_policy: (optional, default = paramiko.RejectPolicy()) the policy to use for unknown keys Other parameters valid for the ssh connect function (see the self._valid_connect_params list) are passed to the connect function (as port, username, password, ...); taken from the accepted paramiko.SSHClient.connect() params. """ import paramiko super(SshTransport, self).__init__() self._is_open = False self._sftp = None self._proxy = None self._machine = machine self._client = paramiko.SSHClient() self._load_system_host_keys = kwargs.pop('load_system_host_keys', False) if self._load_system_host_keys: self._client.load_system_host_keys() self._safe_open_interval = kwargs.pop('safe_interval', self._DEFAULT_SAFE_OPEN_INTERVAL) self._missing_key_policy = kwargs.pop('key_policy', 'RejectPolicy') # This is paramiko default if self._missing_key_policy == 'RejectPolicy': self._client.set_missing_host_key_policy(paramiko.RejectPolicy()) elif self._missing_key_policy == 'WarningPolicy': self._client.set_missing_host_key_policy(paramiko.WarningPolicy()) elif self._missing_key_policy == 'AutoAddPolicy': self._client.set_missing_host_key_policy(paramiko.AutoAddPolicy()) else: raise ValueError('Unknown value of the key policy, allowed values ' 'are: RejectPolicy, WarningPolicy, AutoAddPolicy') self._connect_args = {} for k in self._valid_connect_params: try: self._connect_args[k] = kwargs.pop(k) except KeyError: pass if kwargs: raise ValueError('The following parameters were not accepted by ' 'the transport: {}'.format(','.join(str(k) for k in kwargs)))
[docs] def open(self): """ Open a SSHClient to the machine possibly using the parameters given in the __init__. Also opens a sftp channel, ready to be used. The current working directory is set explicitly, so it is not None. :raise aiida.common.InvalidOperation: if the channel is already open """ from aiida.common.exceptions import InvalidOperation from aiida.transports.util import _DetachedProxyCommand if self._is_open: raise InvalidOperation('Cannot open the transport twice') # Open a SSHClient connection_arguments = self._connect_args proxystring = connection_arguments.pop('proxy_command', None) if proxystring: self._proxy = _DetachedProxyCommand(proxystring) connection_arguments['sock'] = self._proxy try: self._client.connect(self._machine, **connection_arguments) except Exception as exc: self.logger.error("Error connecting to '{}' through SSH: ".format(self._machine) + '[{}] {}, '.format(self.__class__.__name__, exc) + 'connect_args were: {}'.format(self._connect_args)) raise # Open also a SFTPClient self._sftp = self._client.open_sftp() # Set the current directory to a explicit path, and not to None self._sftp.chdir(self._sftp.normalize('.')) self._is_open = True return self
[docs] def close(self): """ Close the SFTP channel, and the SSHClient. :todo: correctly manage exceptions :raise aiida.common.InvalidOperation: if the channel is already open """ from aiida.common.exceptions import InvalidOperation if not self._is_open: raise InvalidOperation('Cannot close the transport: it is already closed') self._sftp.close() self._client.close() self._is_open = False
@property def sshclient(self): if not self._is_open: raise TransportInternalError('Error, ssh method called for SshTransport without opening the channel first') return self._client @property def sftp(self): if not self._is_open: raise TransportInternalError('Error, sftp method called for SshTransport without opening the channel first') return self._sftp
[docs] def __str__(self): """ Return a useful string. """ conn_info = self._machine try: conn_info = '{}@{}'.format(self._connect_args['username'], conn_info) except KeyError: # No username explicitly defined: ignore pass try: conn_info += ':{}'.format(self._connect_args['port']) except KeyError: # No port explicitly defined: ignore pass return '{} [{}]'.format('OPEN' if self._is_open else 'CLOSED', conn_info)
[docs] def chdir(self, path): """ Change directory of the SFTP session. Emulated internally by paramiko. Differently from paramiko, if you pass None to chdir, nothing happens and the cwd is unchanged. """ from paramiko.sftp import SFTPError old_path = self.sftp.getcwd() if path is not None: try: self.sftp.chdir(path) except SFTPError as e: # e.args[0] is an error code. For instance, # 20 is 'the object is not a directory' # Here I just re-raise the message as IOError raise IOError(e.args[1]) # Paramiko already checked that path is a folder, otherwise I would # have gotten an exception. Now, I want to check that I have read # permissions in this folder (nothing is said on write permissions, # though). # Otherwise, if I do _exec_command_internal, that as a first operation # cd's in a folder, I get a wrong retval, that is an unwanted behavior. # # Note: I don't store the result of the function; if I have no # read permissions, this will raise an exception. try: self.sftp.stat('.') except IOError as exc: if 'Permission denied' in str(exc): self.chdir(old_path) raise IOError(str(exc))
[docs] def normalize(self, path): """ Returns the normalized path (removing double slashes, etc...) """ return self.sftp.normalize(path)
[docs] def getcwd(self): """ Return the current working directory for this SFTP session, as emulated by paramiko. If no directory has been set with chdir, this method will return None. But in __enter__ this is set explicitly, so this should never happen within this class. """ return self.sftp.getcwd()
[docs] def makedirs(self, path, ignore_existing=False): """ 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. NOTE: since os.path.split uses the separators as the host system (that could be windows), I assume the remote computer is Linux-based and use '/' as separators! :param path: directory to create (string) :param ignore_existing: if set to true, it doesn't give any error if the leaf directory does already exist (bool) :raise OSError: If the directory already exists. """ # check to avoid creation of empty dirs path = os.path.normpath(path) if path.startswith('/'): to_create = path.strip().split('/')[1:] this_dir = '/' else: to_create = path.strip().split('/') this_dir = '' for count, element in enumerate(to_create): if count > 0: this_dir += '/' this_dir += element if count + 1 == len(to_create) and self.isdir(this_dir) and ignore_existing: return if count + 1 == len(to_create) and self.isdir(this_dir) and not ignore_existing: self.mkdir(this_dir) if not self.isdir(this_dir): self.mkdir(this_dir)
[docs] def mkdir(self, path, ignore_existing=False): """ Create a folder (directory) named path. :param path: name of the folder to create :param ignore_existing: if True, does not give any error if the directory already exists :raise OSError: If the directory already exists. """ if ignore_existing and self.isdir(path): return try: self.sftp.mkdir(path) except IOError as exc: if os.path.isabs(path): raise OSError("Error during mkdir of '{}', " "maybe you don't have the permissions to do it, " 'or the directory already exists? ({})'.format(path, exc)) else: raise OSError("Error during mkdir of '{}' from folder '{}', " "maybe you don't have the permissions to do it, " 'or the directory already exists? ({})'.format(path, self.getcwd(), exc))
# TODO : implement rmtree
[docs] def rmtree(self, path): """ Remove a file or a directory at path, recursively Flags used: -r: recursive copy; -f: force, makes the command non interactive; :param path: remote path to delete :raise IOError: if the rm execution failed. """ # Assuming linux rm command! # TODO : do we need to avoid the aliases when calling rm_exe='rm'? Call directly /bin/rm? rm_exe = 'rm' rm_flags = '-r -f' # if in input I give an invalid object raise ValueError if not path: raise ValueError('Input to rmtree() must be a non empty string. ' + 'Found instead %s as path' % path) command = '{} {} {}'.format(rm_exe, rm_flags, escape_for_bash(path)) retval, stdout, stderr = self.exec_command_wait(command) if retval == 0: if stderr.strip(): self.logger.warning('There was nonempty stderr in the rm command: {}'.format(stderr)) return True else: self.logger.error("Problem executing rm. Exit code: {}, stdout: '{}', " "stderr: '{}'".format(retval, stdout, stderr)) raise IOError('Error while executing rm. Exit code: {}'.format(retval))
[docs] def rmdir(self, path): """ Remove the folder named 'path' if empty. """ self.sftp.rmdir(path)
[docs] def isdir(self, path): """ Return True if the given path is a directory, False otherwise. Return False also if the path does not exist. """ # Return False on empty string (paramiko would map this to the local # folder instead) if not path: return False try: return S_ISDIR(self.sftp.stat(path).st_mode) except IOError as e: if getattr(e, 'errno', None) == 2: # errno=2 means path does not exist: I return False return False else: raise # Typically if I don't have permissions (errno=13)
[docs] def chmod(self, path, mode): """ Change permissions to path :param path: path to file :param mode: new permission bits (integer) """ if not path: raise IOError('Input path is an empty argument.') return self.sftp.chmod(path, mode)
[docs] def _os_path_split_asunder(self, path): """ Used by makedirs. Takes path (a str) and returns a list deconcatenating the path """ parts = [] while True: newpath, tail = os.path.split(path) if newpath == path: assert not tail if path: parts.append(path) break parts.append(tail) path = newpath parts.reverse() return parts
[docs] def put(self, localpath, remotepath, callback=None, dereference=True, overwrite=True, ignore_nonexisting=False): """ Put a file or a folder from local to remote. Redirects to putfile or puttree. :param localpath: an (absolute) local path :param remotepath: a remote path :param dereference: follow symbolic links (boolean). Default = True (default behaviour in paramiko). False is not implemented. :param overwrite: if True overwrites files and folders (boolean). Default = False. :raise ValueError: if local path is invalid :raise OSError: if the localpath does not exist """ # TODO: flag confirm exists since v1.7.7. What is the paramiko # version supported? # TODO : add dereference if not dereference: raise NotImplementedError if not os.path.isabs(localpath): raise ValueError('The localpath must be an absolute path') if self.has_magic(localpath): if self.has_magic(remotepath): raise ValueError('Pathname patterns are not allowed in the destination') # use the imported glob to analyze the path locally to_copy_list = glob.glob(localpath) rename_remote = False if len(to_copy_list) > 1: # I can't scp more than one file on a single file if self.isfile(remotepath): raise OSError('Remote destination is not a directory') # I can't scp more than one file in a non existing directory elif not self.path_exists(remotepath): # questo dovrebbe valere solo per file raise OSError('Remote directory does not exist') else: # the remote path is a directory rename_remote = True for s in to_copy_list: if os.path.isfile(s): if rename_remote: # copying more than one file in one directory # here is the case isfile and more than one file r = os.path.join(remotepath, os.path.split(s)[1]) self.putfile(s, r, callback, dereference, overwrite) elif self.isdir(remotepath): # one file to copy in '.' r = os.path.join(remotepath, os.path.split(s)[1]) self.putfile(s, r, callback, dereference, overwrite) else: # one file to copy on one file self.putfile(s, remotepath, callback, dereference, overwrite) else: self.puttree(s, remotepath, callback, dereference, overwrite) else: if os.path.isdir(localpath): self.puttree(localpath, remotepath, callback, dereference, overwrite) elif os.path.isfile(localpath): if self.isdir(remotepath): r = os.path.join(remotepath, os.path.split(localpath)[1]) self.putfile(localpath, r, callback, dereference, overwrite) else: self.putfile(localpath, remotepath, callback, dereference, overwrite) else: if ignore_nonexisting: pass else: raise OSError('The local path {} does not exist'.format(localpath))
[docs] def putfile(self, localpath, remotepath, callback=None, dereference=True, overwrite=True): """ Put a file from local to remote. :param localpath: an (absolute) local path :param remotepath: a remote path :param overwrite: if True overwrites files and folders (boolean). Default = True. :raise ValueError: if local path is invalid :raise OSError: if the localpath does not exist, or unintentionally overwriting """ # TODO : add dereference if not dereference: raise NotImplementedError # TODO : check what happens if I give in input a directory if not os.path.isabs(localpath): raise ValueError('The localpath must be an absolute path') if self.isfile(remotepath) and not overwrite: raise OSError('Destination already exists: not overwriting it') return self.sftp.put(localpath, remotepath, callback=callback)
[docs] def puttree(self, localpath, remotepath, callback=None, dereference=True, overwrite=True): # by default overwrite """ Put a folder recursively from local to remote. :param localpath: an (absolute) local path :param remotepath: a remote path :param dereference: follow symbolic links (boolean) Default = True (default behaviour in paramiko). False is not implemented. :param overwrite: if True overwrites files and folders (boolean). Default = True :raise ValueError: if local path is invalid :raise OSError: if the localpath does not exist, or trying to overwrite :raise IOError: if remotepath is invalid .. note:: setting dereference equal to True could cause infinite loops. see os.walk() documentation """ # TODO : add dereference if not dereference: raise NotImplementedError if not os.path.isabs(localpath): raise ValueError('The localpath must be an absolute path') if not os.path.exists(localpath): raise OSError('The localpath does not exists') if not os.path.isdir(localpath): raise ValueError('Input localpath is not a folder: {}'.format(localpath)) if not remotepath: raise IOError('remotepath must be a non empty string') if self.path_exists(remotepath) and not overwrite: raise OSError("Can't overwrite existing files") if self.isfile(remotepath): raise OSError('Cannot copy a directory into a file') if not self.isdir(remotepath): # in this case copy things in the remotepath directly self.mkdir(remotepath) # and make a directory at its place else: # remotepath exists already: copy the folder inside of it! remotepath = os.path.join(remotepath, os.path.split(localpath)[1]) self.mkdir(remotepath) # create a nested folder # TODO, NOTE: we are not using 'onerror' because we checked above that # the folder exists, but it would be better to use it for this_source in os.walk(localpath): # Get the relative path this_basename = os.path.relpath(path=this_source[0], start=localpath) try: self.sftp.stat(os.path.join(remotepath, this_basename)) except IOError as e: import errno if e.errno == errno.ENOENT: # Missing file self.mkdir(os.path.join(remotepath, this_basename)) else: raise for this_file in this_source[2]: this_local_file = os.path.join(localpath, this_basename, this_file) this_remote_file = os.path.join(remotepath, this_basename, this_file) self.putfile(this_local_file, this_remote_file)
[docs] def get(self, remotepath, localpath, callback=None, dereference=True, overwrite=True, ignore_nonexisting=False): """ Get a file or folder from remote to local. Redirects to getfile or gettree. :param remotepath: a remote path :param localpath: an (absolute) local path :param dereference: follow symbolic links. Default = True (default behaviour in paramiko). False is not implemented. :param overwrite: if True overwrites files and folders. Default = False :raise ValueError: if local path is invalid :raise IOError: if the remotepath is not found """ # TODO : add dereference if not dereference: raise NotImplementedError if not os.path.isabs(localpath): raise ValueError('The localpath must be an absolute path') if self.has_magic(remotepath): if self.has_magic(localpath): raise ValueError('Pathname patterns are not allowed in the destination') # use the self glob to analyze the path remotely to_copy_list = self.glob(remotepath) rename_local = False if len(to_copy_list) > 1: # I can't scp more than one file on a single file if os.path.isfile(localpath): raise IOError('Remote destination is not a directory') # I can't scp more than one file in a non existing directory elif not os.path.exists(localpath): # this should hold only for files raise OSError('Remote directory does not exist') else: # the remote path is a directory rename_local = True for s in to_copy_list: if self.isfile(s): if rename_local: # copying more than one file in one directory # here is the case isfile and more than one file r = os.path.join(localpath, os.path.split(s)[1]) self.getfile(s, r, callback, dereference, overwrite) else: # one file to copy on one file self.getfile(s, localpath, callback, dereference, overwrite) else: self.gettree(s, localpath, callback, dereference, overwrite) else: if self.isdir(remotepath): self.gettree(remotepath, localpath, callback, dereference, overwrite) elif self.isfile(remotepath): if os.path.isdir(localpath): r = os.path.join(localpath, os.path.split(remotepath)[1]) self.getfile(remotepath, r, callback, dereference, overwrite) else: self.getfile(remotepath, localpath, callback, dereference, overwrite) else: if ignore_nonexisting: pass else: raise IOError('The remote path {} does not exist'.format(remotepath))
[docs] def getfile(self, remotepath, localpath, callback=None, dereference=True, overwrite=True): """ Get a file from remote to local. :param remotepath: a remote path :param localpath: an (absolute) local path :param overwrite: if True overwrites files and folders. Default = False :raise ValueError: if local path is invalid :raise OSError: if unintentionally overwriting """ # TODO : add dereference if not os.path.isabs(localpath): raise ValueError('localpath must be an absolute path') if os.path.isfile(localpath) and not overwrite: raise OSError('Destination already exists: not overwriting it') if not dereference: raise NotImplementedError # Workaround for bug #724 in paramiko -- remove localpath on IOError try: return self.sftp.get(remotepath, localpath, callback) except IOError: try: os.remove(localpath) except OSError: pass raise
[docs] def gettree(self, remotepath, localpath, callback=None, dereference=True, overwrite=True): """ Get a folder recursively from remote to local. :param remotepath: a remote path :param localpath: an (absolute) local path :param dereference: follow symbolic links. Default = True (default behaviour in paramiko). False is not implemented. :param overwrite: if True overwrites files and folders. Default = False :raise ValueError: if local path is invalid :raise IOError: if the remotepath is not found :raise OSError: if unintentionally overwriting """ # TODO : add dereference if not dereference: raise NotImplementedError if not remotepath: raise IOError('Remotepath must be a non empty string') if not localpath: raise ValueError('Localpaths must be a non empty string') if not os.path.isabs(localpath): raise ValueError('Localpaths must be an absolute path') if not self.isdir(remotepath): raise IOError('Input remotepath is not a folder: {}'.format(localpath)) if os.path.exists(localpath) and not overwrite: raise OSError("Can't overwrite existing files") if os.path.isfile(localpath): raise OSError('Cannot copy a directory into a file') if not os.path.isdir(localpath): # in this case copy things in the remotepath directly os.mkdir(localpath) # and make a directory at its place else: # localpath exists already: copy the folder inside of it! localpath = os.path.join(localpath, os.path.split(remotepath)[1]) os.mkdir(localpath) # create a nested folder item_list = self.listdir(remotepath) dest = str(localpath) for item in item_list: item = str(item) if self.isdir(os.path.join(remotepath, item)): self.gettree(os.path.join(remotepath, item), os.path.join(dest, item)) else: self.getfile(os.path.join(remotepath, item), os.path.join(dest, item))
[docs] def get_attribute(self, path): """ Returns the object Fileattribute, specified in aiida.transports Receives in input the path of a given file. """ from aiida.transports.util import FileAttribute paramiko_attr = self.sftp.lstat(path) aiida_attr = FileAttribute() # map the paramiko class into the aiida one # note that paramiko object contains more informations than the aiida for key in aiida_attr._valid_fields: aiida_attr[key] = getattr(paramiko_attr, key) return aiida_attr
[docs] def copyfile(self, remotesource, remotedestination, dereference=False): return self.copy(remotesource, remotedestination, dereference)
[docs] def copytree(self, remotesource, remotedestination, dereference=False): return self.copy(remotesource, remotedestination, dereference, recursive=True)
[docs] def copy(self, remotesource, remotedestination, dereference=False, recursive=True): """ Copy a file or a directory from remote source to remote destination. Flags used: ``-r``: recursive copy; ``-f``: force, makes the command non interactive; ``-L`` follows symbolic links :param remotesource: file to copy from :param remotedestination: file to copy to :param dereference: if True, copy content instead of copying the symlinks only Default = False. :param recursive: if True copy directories recursively, otherwise only copy the specified file(s) :type recursive: bool :raise IOError: if the cp execution failed. .. note:: setting dereference equal to True could cause infinite loops. """ # In the majority of cases, we should deal with linux cp commands # TODO : do we need to avoid the aliases when calling cp_exe='cp'? Call directly /bin/cp? cp_flags = '-f' if recursive: cp_flags += ' -r' # For the moment, this is hardcoded. May become a parameter cp_exe = 'cp' # To evaluate if we also want -p: preserves mode,ownership and timestamp if dereference: # use -L; --dereference is not supported on mac cp_flags += ' -L' # if in input I give an invalid object raise ValueError if not remotesource: raise ValueError( 'Input to copy() must be a non empty string. ' + 'Found instead %s as remotesource' % remotesource) if not remotedestination: raise ValueError('Input to copy() must be a non empty string. ' + 'Found instead %s as remotedestination' % remotedestination) if self.has_magic(remotedestination): raise ValueError('Pathname patterns are not allowed in the destination') if self.has_magic(remotesource): to_copy_list = self.glob(remotesource) if len(to_copy_list) > 1: if not self.path_exists(remotedestination) or self.isfile(remotedestination): raise OSError("Can't copy more than one file in the same destination file") for s in to_copy_list: self._exec_cp(cp_exe, cp_flags, s, remotedestination) else: self._exec_cp(cp_exe, cp_flags, remotesource, remotedestination)
[docs] def _exec_cp(self, cp_exe, cp_flags, src, dst): # to simplify writing the above copy function command = '{} {} {} {}'.format(cp_exe, cp_flags, escape_for_bash(src), escape_for_bash(dst)) retval, stdout, stderr = self.exec_command_wait(command) # TODO : check and fix below if retval == 0: if stderr.strip(): self.logger.warning('There was nonempty stderr in the cp command: {}'.format(stderr)) else: self.logger.error("Problem executing cp. Exit code: {}, stdout: '{}', " "stderr: '{}', command: '{}'".format(retval, stdout, stderr, command)) raise IOError('Error while executing cp. Exit code: {}, ' "stdout: '{}', stderr: '{}', " "command: '{}'".format(retval, stdout, stderr, command))
[docs] def _local_listdir(self, path, pattern=None): """ Acts on the local folder, for the rest, same as listdir """ if not pattern: return os.listdir(path) else: import re if path.startswith('/'): # always this is the case in the local case base_dir = path else: base_dir = os.path.join(os.getcwd(), path) filtered_list = glob.glob(os.path.join(base_dir, pattern)) if not base_dir.endswith(os.sep): base_dir += os.sep return [re.sub(base_dir, '', i) for i in filtered_list]
[docs] def listdir(self, path='.', pattern=None): """ Get the list of files at path. :param path: default = '.' :param pattern: returns the list of files matching pattern. Unix only. (Use to emulate ``ls *`` for example) """ if not pattern: return self.sftp.listdir(path) else: import re if path.startswith('/'): base_dir = path else: base_dir = os.path.join(self.getcwd(), path) filtered_list = glob.glob(os.path.join(base_dir, pattern)) if not base_dir.endswith('/'): base_dir += '/' return [re.sub(base_dir, '', i) for i in filtered_list]
[docs] def remove(self, path): """ Remove a single file at 'path' """ return self.sftp.remove(path)
[docs] def rename(self, src, dst): """ Rename a file or folder from src to dst. :param str oldpath: existing name of the file or folder :param str newpath: new name for the file or folder :raises IOError: if src/dst is not found :raises ValueError: if src/dst is not a valid string """ if not src: raise ValueError('Source {} is not a valid string'.format(src)) if not dst: raise ValueError('Destination {} is not a valid string'.format(dst)) if not self.isfile(src): if not self.isdir(src): raise IOError('Source {} does not exist'.format(src)) if not self.isfile(dst): if not self.isdir(dst): raise IOError('Destination {} does not exist'.format(dst)) return self.sftp.rename(src, dst)
[docs] def isfile(self, path): """ Return True if the given path is a file, False otherwise. Return False also if the path does not exist. """ # This should not be needed for files, since an empty string should # be mapped by paramiko to the local directory - which is not a file - # but this is just to be sure if not path: return False try: self.logger.debug("stat for path '{}' ('{}'): {} [{}]".format(path, self.sftp.normalize(path), self.sftp.stat(path), self.sftp.stat(path).st_mode)) return S_ISREG(self.sftp.stat(path).st_mode) except IOError as e: if getattr(e, 'errno', None) == 2: # errno=2 means path does not exist: I return False return False else: raise # Typically if I don't have permissions (errno=13)
[docs] def _exec_command_internal(self, command, combine_stderr=False, bufsize=-1): """ Executes the specified command in bash login shell. Before the command is executed, changes directory to the current working directory as returned by self.getcwd(). For executing commands and waiting for them to finish, use exec_command_wait. :param command: the command to execute. The command is assumed to be already escaped using :py:func:`aiida.common.escaping.escape_for_bash`. :param combine_stderr: (default False) if True, combine stdout and stderr on the same buffer (i.e., stdout). Note: If combine_stderr is True, stderr will always be empty. :param bufsize: same meaning of the one used by paramiko. :return: a tuple with (stdin, stdout, stderr, channel), where stdin, stdout and stderr behave as file-like objects, plus the methods provided by paramiko, and channel is a paramiko.Channel object. """ channel = self.sshclient.get_transport().open_session() channel.set_combine_stderr(combine_stderr) if self.getcwd() is not None: escaped_folder = escape_for_bash(self.getcwd()) command_to_execute = ('cd {escaped_folder} && ' '{real_command}'.format(escaped_folder=escaped_folder, real_command=command)) else: command_to_execute = command self.logger.debug('Command to be executed: {}'.format(command_to_execute)) # Note: The default shell will eat one level of escaping, while # 'bash -l -c ...' will eat another. Thus, we need to escape again. channel.exec_command('bash -l -c ' + escape_for_bash(command_to_execute)) stdin = channel.makefile('wb', bufsize) stdout = channel.makefile('rb', bufsize) stderr = channel.makefile_stderr('rb', bufsize) return stdin, stdout, stderr, channel
[docs] def exec_command_wait(self, command, stdin=None, combine_stderr=False, bufsize=-1): """ Executes the specified command and waits for it to finish. :param command: the command to execute :param stdin: (optional,default=None) can be a string or a file-like object. :param combine_stderr: (optional, default=False) see docstring of self._exec_command_internal() :param bufsize: same meaning of paramiko. :return: a tuple with (return_value, stdout, stderr) where stdout and stderr are strings. """ # TODO: To see if like this it works or hangs because of buffer problems. ssh_stdin, stdout, stderr, channel = self._exec_command_internal(command, combine_stderr, bufsize=bufsize) if stdin is not None: if isinstance(stdin, six.string_types): filelike_stdin = StringIO(stdin) else: filelike_stdin = stdin try: for l in filelike_stdin.readlines(): ssh_stdin.write(l) except AttributeError: raise ValueError('stdin can only be either a string of a file-like object!') # I flush and close them anyway; important to call shutdown_write # to avoid hangouts ssh_stdin.flush() ssh_stdin.channel.shutdown_write() # I get the return code (blocking) retval = channel.recv_exit_status() # needs to be after 'recv_exit_status', otherwise it might hang output_text = stdout.read().decode('utf-8') stderr_text = stderr.read().decode('utf-8') return retval, output_text, stderr_text
[docs] def gotocomputer_command(self, remotedir): """ Specific gotocomputer string to connect to a given remote computer via ssh and directly go to the calculation folder. """ # TODO: add also ProxyCommand and Timeout support further_params = [] if 'username' in self._connect_args: further_params.append('-l {}'.format(escape_for_bash(self._connect_args['username']))) if 'port' in self._connect_args: further_params.append('-p {}'.format(self._connect_args['port'])) if 'key_filename' in self._connect_args: further_params.append('-i {}'.format(escape_for_bash(self._connect_args['key_filename']))) further_params_str = ' '.join(further_params) connect_string = """ssh -t {machine} {further_params} "if [ -d {escaped_remotedir} ] ; then cd {escaped_remotedir} ; bash -l ; else echo ' ** The directory' ; echo ' ** {remotedir}' ; echo ' ** seems to have been deleted, I logout...' ; fi" """.format( further_params=further_params_str, machine=self._machine, escaped_remotedir="'{}'".format(remotedir), remotedir=remotedir) # print connect_string return connect_string
[docs] def path_exists(self, path): """ Check if path exists """ import errno try: self.sftp.stat(path) except IOError as e: if e.errno == errno.ENOENT: return False raise else: return True