def test_docker_image_saved(bwamem_help):
client = docker.from_env()
container = client.containers.run(
"biocontainers/bwa:v0.7.17_cv1",
entrypoint=["sleep", "999999999"],
detach=True,
)
exec = DockerExecutor(container)
cmd = exec.convert(["bwa", "mem"])
assert cmd.docker_image == "biocontainers/bwa:v0.7.17_cv1"
def test_docker(bwamem_help):
client = docker.from_env()
container = client.containers.run(
"biocontainers/bwa:v0.7.17_cv1",
entrypoint=["sleep", "999999999"],
detach=True,
)
exec = DockerExecutor(container)
output = exec.execute(["bwa", "mem"])
assert output == bwamem_help
container.kill()
def test_no_output():
# Check that it doesn't crash when no output is received
client = docker.from_env()
container = client.containers.run(
"quay.io/biocontainers/gadem:1.3.1--h516909a_2",
entrypoint=["sleep", "9999999"],
detach=True,
)
exec = DockerExecutor(container)
output = exec.execute(["gadem"])
container.kill()
assert output is not None
def test_infinite_output():
"""
Test that the DockerExecutor can kill the command if it's constantly producing output
"""
client = docker.from_env(timeout=99999)
container = client.containers.run(
"ubuntu:latest",
entrypoint=["sleep", "999999999"],
detach=True,
)
exec = DockerExecutor(container)
output = exec.execute(["yes"])
container.kill()
assert output.startswith("y")
def test_docker_kill():
"""
Test that the DockerExecutor can kill the command if it times out
"""
client = docker.from_env(timeout=99999)
container = client.containers.run(
"ubuntu:latest",
entrypoint=["sleep", "999999999"],
detach=True,
)
exec = DockerExecutor(container)
output = exec.execute(["sleep", "999999"])
container.kill()
assert output == ""