def create_container(app):
avail.get_image(image_version(app))
dirs = {
"output": fs.get_task_dir_path(app, 'tmp'),
"metadata": fs.get_task_dir_path(app, 'meta')
}
return image.create_container(image_version(app),
image_type(app).biobox_args(app), dirs,
image_task(app))
def test_executing_container():
out_dir = tempfile.mkdtemp()
cnt = exe.create_container(IMAGE, biobox_cfg(hlp.short_read_fastq()),
{"output": out_dir}, "default",
{"detach": False})
id_ = cnt['Id']
util.client().start(id_)
util.client().wait(id_)
assert funcy.get_in(util.client().inspect_container(id_),
['State', 'ExitCode']) == 0
assert os.path.isfile(os.path.join(out_dir, 'contigs.fa'))
hlp.clean_up_container(id_)
def test_create_container_with_cgroup_data():
# Currently {'cpuset' : "0"} is too hard to test because I don't know
# how to get the CPU IDs for the machine being used for testing
args = [{'cpu_shares' : 1}, {'mem_limit' : 10000000}]
out_dir = tempfile.mkdtemp()
for arg in args:
cnt = exe.create_container(
IMAGE,
CONFIG,
{"output" : out_dir},
"default",
arg)
helper.clean_up_container(cnt['Id'])
def test_executing_container():
out_dir = tempfile.mkdtemp()
cnt = exe.create_container(
IMAGE,
biobox_cfg(hlp.short_read_fastq()),
{"output" : out_dir},
"default",
{"detach" : False})
id_ = cnt['Id']
util.client().start(id_)
util.client().wait(id_)
assert funcy.get_in(util.client().inspect_container(id_), ['State', 'ExitCode']) == 0
assert os.path.isfile(os.path.join(out_dir, 'contigs.fa'))
hlp.clean_up_container(id_)
def run(self, argv):
doc = inspect.getdoc(inspect.getmodule(self))
opts = util.parse_docopt(doc, argv, False)
task = opts['--task']
image = opts['<image>']
output = opts['--output']
# Check the image exists
ctn.exit_if_no_image_available(image)
# Additional non-biobox args to pass to the docker daemon
docker_args = {'mem_limit': opts['--memory'],
'cpuset': opts['--cpuset'],
'cpu_shares': int_or_none(opts['--cpu-shares'])}
output_dir = tempfile.mkdtemp()
ctnr = biobox.create_container(image, self.prepare_config(opts), output_dir, task, docker_args)
ctn.run(ctnr)
self.after_run(output, output_dir)
return ctnr