def test_get_build_info(self):
step = {
'uses': 'popperized/bin/sh@master',
'args': ['ls'],
'name': 'one',
'repo_dir': '/path/to/repo/dir',
'step_dir': 'sh'
}
with SingularityRunner() as sr:
build, img, build_sources = sr._get_build_info(step)
self.assertEqual(build, True)
self.assertEqual(img, 'popperized/bin')
self.assertEqual(build_sources, '/path/to/repo/dir/sh')
step = {
'uses': 'docker://alpine:3.9',
'runs': ['sh', '-c', 'echo $FOO > hello.txt ; pwd'],
'env': {
'FOO': 'bar'
},
'name': '1'
}
with SingularityRunner() as sr:
build, img, build_sources = sr._get_build_info(step)
self.assertEqual(build, False)
self.assertEqual(img, 'docker://alpine:3.9')
self.assertEqual(build_sources, None)
def test_get_build_info(self):
step = Box(
{"uses": "popperized/bin/sh@master", "args": ["ls"], "name": "one",},
default_box=True,
)
with SingularityRunner() as sr:
build, img, build_sources = sr._get_build_info(step)
self.assertEqual(build, True)
self.assertEqual(img, "popperized/bin")
self.assertTrue(f"{os.environ['HOME']}/.cache/popper" in build_sources)
self.assertTrue(f"github.com/popperized/bin/sh" in build_sources)
step = Box(
{
"uses": "docker://alpine:3.9",
"runs": ["sh", "-c", "echo $FOO > hello.txt ; pwd"],
"env": {"FOO": "bar"},
"name": "1",
},
default_box=True,
)
with SingularityRunner() as sr:
build, img, build_sources = sr._get_build_info(step)
self.assertEqual(build, False)
self.assertEqual(img, "docker://alpine:3.9")
self.assertEqual(build_sources, None)
def test_get_recipe_file(self):
repo = self.mk_repo()
build_ctx_path = repo.working_dir
with open(os.path.join(build_ctx_path, 'Dockerfile'), 'w') as f:
f.write("""
FROM alpine
RUN apk update && apk add bash
ADD README.md /
ENTRYPOINT ["/bin/bash"]""")
singularity_file = SingularityRunner._get_recipe_file(
build_ctx_path, 'sample.sif')
self.assertEqual(singularity_file,
os.path.join(build_ctx_path, 'Singularity.sample'))
self.assertEqual(os.path.exists(singularity_file), True)
with open(singularity_file) as f:
self.assertEqual(
f.read(), '''Bootstrap: docker
From: alpine
%files
README.md /
%post
apk update && apk add bash
%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"''')
os.remove(os.path.join(build_ctx_path, 'Dockerfile'))
self.assertRaises(SystemExit, SingularityRunner._get_recipe_file,
build_ctx_path, 'sample.sif')
def test_get_container_options(self):
config_dict = {
"engine": {
"name": "singularity",
"options": {
"hostname": "popper.local",
"ipc": True,
"bind": ["/path/in/host:/path/in/container"],
},
}
}
config = ConfigLoader.load(config_file=config_dict)
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
options = sr._get_container_options()
self.assertEqual(
options,
[
"--userns",
"--pwd",
"/workspace",
"--bind",
f"{os.getcwd()}:/workspace",
"--bind",
"/path/in/host:/path/in/container",
"--hostname",
"popper.local",
"--ipc",
],
)
def test_setup_singularity_cache(self):
config = PopperConfig()
config.wid = "abcd"
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
self.assertEqual(
f'{os.environ["HOME"]}/.cache/popper/singularity/abcd',
sr._singularity_cache)
def test_setup_singularity_cache(self):
config = ConfigLoader.load()
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
self.assertEqual(
f'{os.environ["HOME"]}/.cache/popper/singularity/{config.wid}',
sr._singularity_cache,
)
def test_create_container(self):
config = ConfigLoader.load()
step_one = Box(
{
"uses": "docker://*****:*****@master",
"args": ["ls"],
"id": "kontainer_two",
},
default_box=True,
)
cid_one = pu.sanitized_name(step_one.id, config.wid)
cid_two = pu.sanitized_name(step_two.id, config.wid)
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
sr._create_container(step_one, cid_one)
self.assertEqual(
os.path.exists(os.path.join(sr._singularity_cache, cid_one)),
True)
os.remove(os.path.join(sr._singularity_cache, cid_one))
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
sr._create_container(step_one, cid_two)
self.assertEqual(
os.path.exists(os.path.join(sr._singularity_cache, cid_two)),
True)
os.remove(os.path.join(sr._singularity_cache, cid_two))
def test_create_container(self):
config = PopperConfig()
config.wid = "abcd"
step_one = {
'uses': 'docker://*****:*****@master',
'args': ['ls'],
'name': 'kontainer_two',
'repo_dir':
f'{os.environ["HOME"]}/.cache/popper/abcd/github.com/popperized/bin',
'step_dir': 'sh'
}
cid_one = pu.sanitized_name(step_one['name'], config.wid)
cid_two = pu.sanitized_name(step_two['name'], config.wid)
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
c_one = sr._create_container(step_one, cid_one)
self.assertEqual(
os.path.exists(os.path.join(sr._singularity_cache, cid_one)),
True)
os.remove(os.path.join(sr._singularity_cache, cid_one))
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
c_two = sr._create_container(step_one, cid_two)
self.assertEqual(
os.path.exists(os.path.join(sr._singularity_cache, cid_two)),
True)
os.remove(os.path.join(sr._singularity_cache, cid_two))
def test_get_container_options(self):
config_dict = {
'engine': {
'name': 'singularity',
'options': {
'hostname': 'popper.local',
'ipc': True,
'bind': ['/path/in/host:/path/in/container']
}
}
}
config = PopperConfig(config_file=config_dict)
config.wid = "abcd"
with SingularityRunner(config=config) as sr:
sr._setup_singularity_cache()
options = sr._get_container_options()
self.assertEqual(options, [
'--userns', '--pwd', '/workspace', '--bind',
f'{os.getcwd()}:/workspace', '--bind',
'/path/in/host:/path/in/container', '--hostname',
'popper.local', '--ipc'
])
def test_singularity_start(self):
repo = self.mk_repo()
conf = PopperConfig(engine_name='singularity',
workspace_dir=repo.working_dir)
step = {
'uses': 'docker://*****:*****@master'
args: 'ls'
""")
wf.parse()
r.run(wf)
wf = YMLWorkflow("""
version: '1'
steps:
- uses: 'docker://alpine:3.9'
runs: ['sh', '-c', 'echo $FOO > hello.txt ; pwd']
env: {
FOO: bar
}
""")
wf.parse()
r.run(wf)
with open(os.path.join(repo.working_dir, 'hello.txt'), 'r') as f:
self.assertEqual(f.read(), 'bar\n')
wf = YMLWorkflow("""
version: '1'
steps:
- uses: 'docker://alpine:3.9'
runs: 'nocommandisnamedlikethis'
""")
wf.parse()
self.assertRaises(SystemExit, r.run, wf)
repo.close()
def test_singularity_start(self):
repo = self.mk_repo()
conf = ConfigLoader.load(engine_name="singularity",
workspace_dir=repo.working_dir)
step = Box(
{
"uses": "docker://*****:*****@master",
"args": ["ls"],
}]
}
r.run(WorkflowParser.parse(wf_data=wf_data))
wf_data = {
"steps": [{
"uses": "docker://alpine:3.9",
"args": ["sh", "-c", "echo $FOO > hello.txt ; pwd"],
"env": {
"FOO": "bar"
},
}]
}
r.run(WorkflowParser.parse(wf_data=wf_data))
with open(os.path.join(repo.working_dir, "hello.txt"), "r") as f:
self.assertEqual(f.read(), "bar\n")
wf_data = {
"steps": [{
"uses": "docker://alpine:3.9",
"args": ["nocommandisnamedlikethis"],
}]
}
self.assertRaises(SystemExit, r.run,
WorkflowParser.parse(wf_data=wf_data))
repo.close()