def test_instance_cmds(self, docker_container):
image = docker_container[1]
myinstance = Client.instance(image)
assert myinstance.get_uri().startswith("instance://")
print("...Case 2: List instances")
instances = Client.instances()
assert len(instances) == 1
instances = Client.instances(return_json=True)
assert len(instances) == 1
assert isinstance(instances[0], dict)
print("...Case 3: Commands to instances")
result = Client.execute(myinstance, ["echo", "hello"])
assert result == "hello\n"
print("...Case 4: Return value from instance")
result = Client.execute(myinstance, "ls /", return_result=True)
print(result)
assert "tmp\nusr\nvar" in result["message"]
assert result["return_code"] == 0
print("...Case 5: Stop instances")
myinstance.stop()
instances = Client.instances()
assert instances == []
myinstance1 = Client.instance(image)
myinstance2 = Client.instance(image)
assert myinstance1 is not None
assert myinstance2 is not None
instances = Client.instances()
assert len(instances) == 2
Client.instance_stopall()
instances = Client.instances()
assert instances == []
def test_instance_cmds(self, docker_container):
image = docker_container[1]
myinstance = Client.instance(image)
assert myinstance.get_uri().startswith('instance://')
print("...Case 2: List instances")
instances = Client.instances()
assert len(instances) == 1
instances = Client.instances(return_json=True)
assert len(instances) == 1
assert isinstance(instances[0], dict)
print("...Case 3: Commands to instances")
result = Client.execute(myinstance, ['echo', 'hello'])
assert result == 'hello\n'
print('...Case 4: Return value from instance')
result = Client.execute(myinstance, 'ls /', return_result=True)
print(result)
assert 'tmp\nusr\nvar' in result['message']
assert result['return_code'] == 0
print("...Case 5: Stop instances")
myinstance.stop()
instances = Client.instances()
assert instances == []
myinstance1 = Client.instance(image)
myinstance2 = Client.instance(image)
assert myinstance1 is not None
assert myinstance2 is not None
instances = Client.instances()
assert len(instances) == 2
Client.instance_stopall()
instances = Client.instances()
assert instances == []
def test_instance_class():
instance = Client.instance("docker://ubuntu", start=False)
assert instance.get_uri() == "instance://" + instance.name
assert instance.name != ""
name = "coolName"
instance = Client.instance("docker://busybox:1.30.1",
start=False,
name=name)
assert instance.get_uri() == "instance://" + instance.name
assert instance.name == name
def test_instance_class():
instance = Client.instance('docker://ubuntu', start=False)
assert instance.get_uri() == 'instance://' + instance.name
assert instance.name != ''
name = 'coolName'
instance = Client.instance('docker://busybox:1.30.1',
start=False,
name=name)
assert instance.get_uri() == 'instance://' + instance.name
assert instance.name == name
def get_instance(instanceDict):
try:
t_ins = Client.instance(image=instanceDict["image"],
name=instanceDict["ins_name"],
options=instanceDict["options"])
return t_ins
except Exception as e:
logging.error(e)
return None
def __init__(self, mode, container_image, volumes, extra_kwargs):
assert mode in ('docker', 'singularity')
self.mode = mode
if mode == 'docker':
import docker
client = docker.from_env()
if extra_kwargs.get('requires_gpu', False):
extra_kwargs.pop('requires_gpu')
extra_kwargs["device_requests"] = [
docker.types.DeviceRequest(count=-1,
capabilities=[['gpu']])
]
# check if the image is already present locally
repo_tags = []
for image in client.images.list():
repo_tags.extend(image.attrs['RepoTags'])
if container_image not in repo_tags:
client.images.pull(container_image)
self.docker_container = client.containers.create(container_image,
tty=True,
volumes=volumes,
**extra_kwargs)
elif mode == 'singularity':
from spython.main import Client
# load local image file if it exists, otherwise search dockerhub
if Path(container_image).exists():
self.singularity_image = container_image
else:
self.singularity_image = Client.pull(
f'docker://{container_image}')
if not Path(self.singularity_image).exists():
raise FileNotFoundError(
f'Unable to locate container image {container_image}')
# bin options
singularity_bind = ','.join([
f'{volume_src}:{volume["bind"]}'
for volume_src, volume in volumes.items()
])
options = ['--bind', singularity_bind]
# gpu options
if extra_kwargs.get('requires_gpu', False):
# only nvidia at the moment
options += ['--nv']
self.client_instance = Client.instance(self.singularity_image,
start=False,
options=options)
def test_AFNI_libraries():
SINGULARITY_IMAGE_PATH = '/home/circleci/project/C-PAC-CI.simg'
if not os.path.exists(SINGULARITY_IMAGE_PATH):
try:
SINGULARITY_IMAGE_PATH = [
d for d in os.listdir(str(Path(__file__).parent.parent.parent))
if (d.endswith('.simg') or d.endswith('.sif'))
][0]
except:
raise Exception("Singularity image not in expected location.")
if os.path.exists(SINGULARITY_IMAGE_PATH):
afni_libraries = Client.execute(
Client.instance(SINGULARITY_IMAGE_PATH),
['./dev/circleci_data/AFNI_libraries.sh'])
assert "not found" not in afni_libraries, '\n'.join([
line.strip() for line in afni_libraries.split('\n')
if "not found" in line
])
def _try_to_stream(self, args, stream_command='run'):
self._bindings_as_option()
try:
if stream_command == 'run':
for line in Client.run(Client.instance(self.image),
args=args,
options=self.options,
stream=True,
return_result=True):
yield line
elif stream_command == 'execute':
for line in Client.execute(self.image,
command=args['command'].split(' '),
options=self.options,
stream=True,
quiet=False):
yield line
except CalledProcessError: # pragma: no cover
return
