Source code for singularitytarget

# Copyright 2011-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.

The module containing the classes describing the targets.

import os
import subprocess

import fastr
from fastr import exceptions
from import SubprocessBasedTarget

class SingularityTarget(SubprocessBasedTarget):
    A tool target that is run using a singularity container,
    see the `singulary website <>`_

    * ``binary (required)``: the name of the binary/script to call, can also be called ``bin``
      for backwards compatibility.
    * ``container (required)``: the singularity container to run, this can be in url form for singularity
                                pull or as a path to a local container

    * ``interpreter``: the interpreter to use to call the binary e.g. ``python``

    SINGULARITY_BIN = 'singularity'

[docs] def __init__(self, binary, container, interpreter=None): """ Define a new local binary target. Must be defined either using paths and optionally environment_variables and initscripts, or enviroment modules. """ self.binary = binary self.container = container self.interpreter = interpreter
[docs] def __enter__(self): """ Set the environment in such a way that the target will be on the path. """ super(SingularityTarget, self).__enter__() # TODO Make sure the container is present, otherwise download the container return self
[docs] def __exit__(self, exc_type, exc_value, traceback): """ Cleanup the environment """ # TODO We could potentially remove the container again if we downloaded it in the first place? pass
[docs] @classmethod def test(cls): """ Test if singularity is availble on the path """ try: subprocess.check_output([cls.SINGULARITY_BIN, '--help'], stderr=subprocess.STDOUT) except OSError: raise exceptions.FastrExecutableNotFoundError(cls.SINGULARITY_BIN)
[docs] def run_command(self, command): # Add interpreter if needed if self.interpreter is not None: command = [self.interpreter] + command # Bind all fastr mounts mounts = fastr.config.mounts.values() binds = [] for mount in mounts: if not os.path.exists(mount): continue binds.append('--bind') binds.append('{x}:{x}'.format(x=mount))'Singularity binds: {}'.format(binds)) # Compose the singularity command singularity_command = [self.SINGULARITY_BIN, 'exec'] singularity_command.extend(binds) singularity_command.append(self.container) singularity_command.extend(command) # Create final command fastr.log.debug('Command: {}'.format(command)) fastr.log.debug('Singularity command: {}'.format(singularity_command)) return self.call_subprocess(singularity_command)