def test_with_input(self):
r = self.runner.clone()
r.with_input("file:///tmp/input", "/mnt/input")
r.with_input("file:///tmp/input2", "./input2")
expected = [
tes.Input(
url="file:///tmp/input",
path="/mnt/input",
type="FILE"
),
tes.Input(
url="file:///tmp/input2",
path="/tmp/tesseract/input2",
type="FILE"
)
]
print("ACTUAL", r.input_files)
print("EXPECTED", expected)
self.assertEqual(
r.input_files,
expected
)
with self.assertRaises(ValueError):
self.runner.with_input("fake://tmp/input", "/mnt/input")
with self.assertRaises(ValueError):
self.runner.with_input("file://tmp/input", "../input")
def create_input(self, name, d):
if "contents" in d:
return tes.Input(name=name,
description="cwl_input:%s" % (name),
path=d["path"],
content=d["contents"],
type=d["class"].upper())
return tes.Input(name=name,
description="cwl_input:%s" % (name),
url=d["location"],
path=d["path"],
type=d["class"].upper())
def create_input_parameter(self, key, value):
if "contents" in value:
return tes.Input(name=key,
description="cwl_input:%s" % (key),
path=value["path"],
contents=value["contents"],
type=value["class"].upper())
else:
return tes.Input(name=key,
description="cwl_input:%s" % (key),
url=value["location"],
path=value["path"],
type=value["class"].upper())
def parse_listing(self, listing, inputs):
for item in listing:
if "writable" in item:
raise UnsupportedRequirement(
"The TES spec does not allow for writable inputs")
if "contents" in item:
loc = self.fs_access.join(self.tmpdir, item["basename"])
with self.fs_access.open(loc, "wb") as gen:
gen.write(item["contents"])
else:
loc = item["location"]
parameter = tes.Input(
name=item["basename"],
description="InitialWorkDirRequirement:cwl_input:%s" %
(item["basename"]),
url=file_uri(loc),
path=self.fs_access.join(self.docker_workdir,
item["basename"]),
type=item["class"].upper())
inputs.append(parameter)
return inputs
def with_input(self, url, path):
u = urlparse(process_url(url))
if u.scheme not in self.file_store.supported:
raise ValueError("Unsupported scheme - must be one of %s" %
(self.file_store.supported))
if u.scheme == "file" and self.file_store.scheme != "file":
raise ValueError("please upload your input file to the file store")
u = urlparse(path)
if u.scheme not in ["file", ""]:
raise ValueError("runtime path must be defined as a local path")
if u.scheme == "file":
path = os.path.join(u.netloc, u.path)
if path.startswith("./"):
pass
elif not os.path.isabs(path):
raise ValueError(
"runtime path must be an absolute path or start with './'")
self.input_files.append(
tes.Input(path=os.path.join("/tmp/tesseract",
re.sub("^./", "", path)),
url=url,
type="FILE"))
def _create_task_msg(self, input_cp_url, output_cp_url):
runner = pkg_resources.resource_string(__name__, "resources/runner.py")
if isinstance(runner, bytes):
runner = runner.decode("utf8")
cmd_install_reqs = "pip install %s" % (" ".join(self.libraries))
cmd_tesseract = "python tesseract.py func.pickle"
if len(self.libraries) == 0:
cmd = cmd_tesseract
else:
cmd = cmd_install_reqs + " && " + cmd_tesseract
task = tes.Task(name="tesseract remote execution",
inputs=self.input_files + [
tes.Input(name="pickled function",
url=input_cp_url,
path="/tmp/tesseract/func.pickle",
type="FILE"),
tes.Input(name="tesseract runner script",
path="/tmp/tesseract/tesseract.py",
type="FILE",
content=str(runner))
],
outputs=self.output_files + [
tes.Output(name="pickled result",
url=output_cp_url,
path="/tmp/tesseract/result.pickle",
type="FILE")
],
resources=tes.Resources(cpu_cores=self.cpu_cores,
ram_gb=self.ram_gb,
disk_gb=self.disk_gb),
executors=[
tes.Executor(image=self.docker,
command=["sh", "-c", cmd],
stdout="/tmp/tesseract/stdout",
stderr="/tmp/tesseract/stderr",
workdir="/tmp/tesseract")
])
return task
def _mount_local_path_if_possible(self, local_path: str,
container_path: str) -> None:
"""
Internal function. Should not be called outside this class.
If a local path is somewhere the server thinks it can access, mount it
into all the tasks.
"""
# TODO: We aren't going to work well with linked imports if we're mounting the job store into the container...
path_url = 'file://' + os.path.abspath(local_path)
if os.path.exists(local_path) and self._server_can_mount(path_url):
# We can access this file from the server. Probably.
self.mounts.append(
tes.Input(
url=path_url,
path=container_path,
type="DIRECTORY" if os.path.isdir(local_path) else "FILE"))