schrodinger.job.remote_command module

exception schrodinger.job.remote_command.CommandError(sp_error=None, command='', errmsg=None, output='', userhost='', returncode=None)

Bases: Exception

Used to report external commands that fail.

When this is caught by the main cmdline driver, the error message will be printed and the usage message displayed.

__init__(sp_error=None, command='', errmsg=None, output='', userhost='', returncode=None)

The constructor takes a subprocess.CalledProcessError for the failed command, from which details of the command are extracted. A user- friendly error message will be composed from that information unless an explicit error message is provided.

__str__()

Return str(self).

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.job.remote_command', '__doc__': '\n Used to report external commands that fail.\n\n When this is caught by the main cmdline driver, the error message\n will be printed and the usage message displayed.\n ', '__init__': <function CommandError.__init__>, '__str__': <function CommandError.__str__>, '__weakref__': <attribute '__weakref__' of 'CommandError' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.job.remote_command'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__

__traceback__

__weakref__

list of weak references to the object (if defined)

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.job.remote_command.which(program, search_path=None)

Search for a file in the given list of directories. Use $PATH if no search path is specified.

Returns the absolute pathname for the first executable found.

Parameters:rogram – the executable to search for Return type:string Returns:the absolute pathname for the executable found, or None if the program could not be found.

schrodinger.job.remote_command.get_rsh_exec()

Return the name of the rsh-compatible program to use for executing remote commands.

schrodinger.job.remote_command.shell()

Return the pathname to a Bourne-compatible shell that can be used for running shell commands.

schrodinger.job.remote_command.remote_command(command, host, user=None, capture_stderr=False)

Execute a the given command on a particular host.

Returns a tuple containing the captured output and an error message.

Parameters:

• host (string) – the host on which to run the command
• user (string) – the user account under which to run the command
• command (string) – the command to be executed on the remote machine
• capture_stderr (boolean) – should stderr be captured along with stdout?

Return type:

string

Returns:

the captured output from the command

Raises:

CommandError – if the remote command fails

schrodinger.job.remote_command.rsh_put_cmd(remotehost, put_fn, remoteuser=None)

Returns the ‘scp’ command needed to execute to copy a file to a given remote host. The actual remote command needs to be appended to the returned string.

Parameters:

• remotehost (string) – string
• put_fn (string) – Path to the file that will be copied over. If it is a directory, it will be copied recursively
• remoteuser (string) – Remote username

Return type:

list

Returns:

the list of command args for the command, suitable for use in subprocess functions

schrodinger.job.remote_command.rsh_test(hosts)

Test remote commands to and from one or more hosts.