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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,157 @@ | ||
| from .helpers import execute | ||
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| from pathlib import Path | ||
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| class Environment: | ||
| """ | ||
| Base class for environments that are used to execute tasks. | ||
| Right now it is asssumed that the environment, including container images, | ||
| are available and are not removed at the end | ||
| TODO: add setup and teardown methods | ||
| """ | ||
|
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| def setup(self): | ||
| pass | ||
|
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| def execute(self, task): | ||
| """ | ||
| Execute the task in the environment. | ||
| Parameters | ||
| ---------- | ||
| task : TaskBase | ||
| the task to execute | ||
| Returns | ||
| ------- | ||
| output | ||
| Output of the task. | ||
| """ | ||
| raise NotImplementedError | ||
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| def teardown(self): | ||
| pass | ||
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| class Native(Environment): | ||
| """ | ||
| Native environment, i.e. the tasks are executed in the current python environment. | ||
| """ | ||
|
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| def execute(self, task): | ||
| keys = ["return_code", "stdout", "stderr"] | ||
| values = execute(task.command_args(), strip=task.strip) | ||
| output = dict(zip(keys, values)) | ||
| if output["return_code"]: | ||
| msg = f"Error running '{task.name}' task with {task.command_args()}:" | ||
| if output["stderr"]: | ||
| msg += "\n\nstderr:\n" + output["stderr"] | ||
| if output["stdout"]: | ||
| msg += "\n\nstdout:\n" + output["stdout"] | ||
| raise RuntimeError(msg) | ||
| return output | ||
|
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|
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| class Container(Environment): | ||
| """ | ||
| Base class for container environments used by Docker and Singularity. | ||
| Parameters | ||
| ---------- | ||
| image : str | ||
| Name of the container image | ||
| tag : str | ||
| Tag of the container image | ||
| root : str | ||
| Base path for mounting host directories into the container | ||
| xargs : Union[str, List[str]] | ||
| Extra arguments to be passed to the container | ||
| """ | ||
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| def __init__(self, image, tag="latest", root="/mnt/pydra", xargs=None): | ||
| self.image = image | ||
| self.tag = tag | ||
| if xargs is None: | ||
| xargs = [] | ||
| elif isinstance(xargs, str): | ||
| xargs = xargs.split() | ||
| self.xargs = xargs | ||
| self.root = root | ||
|
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| def bind(self, loc, mode="ro"): | ||
| loc_abs = Path(loc).absolute() | ||
| return f"{loc_abs}:{self.root}{loc_abs}:{mode}" | ||
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| class Docker(Container): | ||
| """Docker environment.""" | ||
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| def execute(self, task): | ||
| docker_img = f"{self.image}:{self.tag}" | ||
| # mounting all input locations | ||
| mounts = task.get_bindings(root=self.root) | ||
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| docker_args = [ | ||
| "docker", | ||
| "run", | ||
| "-v", | ||
| self.bind(task.cache_dir, "rw"), | ||
| *self.xargs, | ||
| ] | ||
| docker_args.extend( | ||
| " ".join( | ||
| [f"-v {key}:{val[0]}:{val[1]}" for (key, val) in mounts.items()] | ||
| ).split() | ||
| ) | ||
| docker_args.extend(["-w", f"{self.root}{task.output_dir}"]) | ||
| keys = ["return_code", "stdout", "stderr"] | ||
|
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| values = execute( | ||
| docker_args + [docker_img] + task.command_args(root=self.root), | ||
| strip=task.strip, | ||
| ) | ||
| output = dict(zip(keys, values)) | ||
| if output["return_code"]: | ||
| if output["stderr"]: | ||
| raise RuntimeError(output["stderr"]) | ||
| else: | ||
| raise RuntimeError(output["stdout"]) | ||
| return output | ||
|
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|
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| class Singularity(Container): | ||
| """Singularity environment.""" | ||
|
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| def execute(self, task): | ||
| singularity_img = f"{self.image}:{self.tag}" | ||
| # mounting all input locations | ||
| mounts = task.get_bindings(root=self.root) | ||
|
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| # todo adding xargsy etc | ||
| singularity_args = [ | ||
| "singularity", | ||
| "exec", | ||
| "-B", | ||
| self.bind(task.cache_dir, "rw"), | ||
| *self.xargs, | ||
| ] | ||
| singularity_args.extend( | ||
| " ".join( | ||
| [f"-B {key}:{val[0]}:{val[1]}" for (key, val) in mounts.items()] | ||
| ).split() | ||
| ) | ||
| singularity_args.extend(["--pwd", f"{self.root}{task.output_dir}"]) | ||
| keys = ["return_code", "stdout", "stderr"] | ||
|
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| values = execute( | ||
| singularity_args + [singularity_img] + task.command_args(root=self.root), | ||
| strip=task.strip, | ||
| ) | ||
| output = dict(zip(keys, values)) | ||
| if output["return_code"]: | ||
| if output["stderr"]: | ||
| raise RuntimeError(output["stderr"]) | ||
| else: | ||
| raise RuntimeError(output["stdout"]) | ||
| return output | ||
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