# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# 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 fastr.core.target import SubprocessBasedTarget
class SingularityTarget(SubprocessBasedTarget):
"""
A tool target that is run using a singularity container,
see the `singulary website <http://singularity.lbl.gov/>`_
* ``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))
fastr.log.info('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)