fractal-server 1.4.9__py3-none-any.whl → 2.0.0a0__py3-none-any.whl

fractal_server/app/runner/_slurm/__init__.py

@@ -1,150 +0,0 @@
-# Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and
-# University of Zurich
-#
-# Original authors:
-# Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
-# Tommaso Comparin <tommaso.comparin@exact-lab.it>
-# Marco Franzon <marco.franzon@exact-lab.it>
-#
-# This file is part of Fractal and was originally developed by eXact lab S.r.l.
-# <exact-lab.it> under contract with Liberali Lab from the Friedrich Miescher
-# Institute for Biomedical Research and Pelkmans Lab from the University of
-# Zurich.
-"""
-Slurm Bakend
-
-This backend runs fractal workflows in a SLURM cluster using Clusterfutures
-Executor objects.
-"""
-from pathlib import Path
-from typing import Any
-from typing import Optional
-from typing import Union
-
-from ...models import Workflow
-from .._common import execute_tasks
-from ..common import async_wrap
-from ..common import set_start_and_last_task_index
-from ..common import TaskParameters
-from ._submit_setup import _slurm_submit_setup
-from .executor import FractalSlurmExecutor
-
-
-def _process_workflow(
-    *,
-    workflow: Workflow,
-    input_paths: list[Path],
-    output_path: Path,
-    input_metadata: dict[str, Any],
-    input_history: list[dict[str, Any]],
-    logger_name: str,
-    workflow_dir: Path,
-    workflow_dir_user: Path,
-    first_task_index: int,
-    last_task_index: int,
-    slurm_user: Optional[str] = None,
-    slurm_account: Optional[str] = None,
-    user_cache_dir: str,
-    worker_init: Optional[Union[str, list[str]]] = None,
-) -> dict[str, Any]:
-    """
-    Internal processing routine for the SLURM backend
-
-    This function initialises the a FractalSlurmExecutor, setting logging,
-    workflow working dir and user to impersonate. It then schedules the
-    workflow tasks and returns the output dataset metadata.
-
-    Cf. [process_workflow][fractal_server.app.runner._local.process_workflow]
-
-    Returns:
-        output_dataset_metadata: Metadata of the output dataset
-    """
-
-    if not slurm_user:
-        raise RuntimeError(
-            "slurm_user argument is required, for slurm backend"
-        )
-
-    if isinstance(worker_init, str):
-        worker_init = worker_init.split("\n")
-
-    with FractalSlurmExecutor(
-        debug=True,
-        keep_logs=True,
-        slurm_user=slurm_user,
-        user_cache_dir=user_cache_dir,
-        working_dir=workflow_dir,
-        working_dir_user=workflow_dir_user,
-        common_script_lines=worker_init,
-        slurm_account=slurm_account,
-    ) as executor:
-        output_task_pars = execute_tasks(
-            executor=executor,
-            task_list=workflow.task_list[
-                first_task_index : (last_task_index + 1)  # noqa
-            ],  # noqa
-            task_pars=TaskParameters(
-                input_paths=input_paths,
-                output_path=output_path,
-                metadata=input_metadata,
-                history=input_history,
-            ),
-            workflow_dir=workflow_dir,
-            workflow_dir_user=workflow_dir_user,
-            submit_setup_call=_slurm_submit_setup,
-            logger_name=logger_name,
-        )
-    output_dataset_metadata_history = dict(
-        metadata=output_task_pars.metadata, history=output_task_pars.history
-    )
-    return output_dataset_metadata_history
-
-
-async def process_workflow(
-    *,
-    workflow: Workflow,
-    input_paths: list[Path],
-    output_path: Path,
-    input_metadata: dict[str, Any],
-    input_history: list[dict[str, Any]],
-    logger_name: str,
-    workflow_dir: Path,
-    workflow_dir_user: Optional[Path] = None,
-    user_cache_dir: Optional[str] = None,
-    slurm_user: Optional[str] = None,
-    slurm_account: Optional[str] = None,
-    worker_init: Optional[str] = None,
-    first_task_index: Optional[int] = None,
-    last_task_index: Optional[int] = None,
-) -> dict[str, Any]:
-    """
-    Process workflow (SLURM backend public interface)
-
-    Cf. [process_workflow][fractal_server.app.runner._local.process_workflow]
-    """
-
-    # Set values of first_task_index and last_task_index
-    num_tasks = len(workflow.task_list)
-    first_task_index, last_task_index = set_start_and_last_task_index(
-        num_tasks,
-        first_task_index=first_task_index,
-        last_task_index=last_task_index,
-    )
-
-    output_dataset_metadata_history = await async_wrap(_process_workflow)(
-        workflow=workflow,
-        input_paths=input_paths,
-        output_path=output_path,
-        input_metadata=input_metadata,
-        input_history=input_history,
-        logger_name=logger_name,
-        workflow_dir=workflow_dir,
-        workflow_dir_user=workflow_dir_user,
-        slurm_user=slurm_user,
-        slurm_account=slurm_account,
-        user_cache_dir=user_cache_dir,
-        worker_init=worker_init,
-        first_task_index=first_task_index,
-        last_task_index=last_task_index,
-    )
-    return output_dataset_metadata_history

fractal_server/app/runner/common.py

@@ -1,311 +0,0 @@
-"""
-Common utilities and routines for runner backends (public API)
-
-This module includes utilities and routines that are of use to implement
-runner backends but that should also be exposed to the other components of
-`Fractal Server`.
-"""
-import asyncio
-import json
-import os
-from functools import partial
-from functools import wraps
-from json import JSONEncoder
-from pathlib import Path
-from typing import Any
-from typing import Callable
-from typing import Optional
-
-from pydantic import BaseModel
-
-from ...logger import close_logger as close_job_logger  # noqa F401
-from ..models import Dataset
-from ..models.workflow import Workflow
-
-
-class TaskExecutionError(RuntimeError):
-    """
-    Forwards errors occurred during the execution of a task
-
-    This error wraps and forwards errors occurred during the execution of
-    tasks, when the exit code is larger than 0 (i.e. the error took place
-    within the task). This error also adds information that is useful to track
-    down and debug the failing task within a workflow.
-
-    Attributes:
-        workflow_task_id:
-            ID of the workflow task that failed.
-        workflow_task_order:
-            Order of the task within the workflow.
-        task_name:
-            Human readable name of the failing task.
-    """
-
-    workflow_task_id: Optional[int] = None
-    workflow_task_order: Optional[int] = None
-    task_name: Optional[str] = None
-
-    def __init__(
-        self,
-        *args,
-        workflow_task_id: Optional[int] = None,
-        workflow_task_order: Optional[int] = None,
-        task_name: Optional[str] = None,
-    ):
-        super().__init__(*args)
-        self.workflow_task_id = workflow_task_id
-        self.workflow_task_order = workflow_task_order
-        self.task_name = task_name
-
-
-class JobExecutionError(RuntimeError):
-    """
-    Forwards errors in the execution of a task that are due to external factors
-
-    This error wraps and forwards errors occurred during the execution of
-    tasks, but related to external factors like:
-
-    1. A negative exit code (e.g. because the task received a TERM or KILL
-       signal);
-    2. An error on the executor side (e.g. the SLURM executor could not
-       find the pickled file with task output).
-
-    This error also adds information that is useful to track down and debug the
-    failing task within a workflow.
-
-    Attributes:
-        info:
-            A free field for additional information
-        cmd_file:
-            Path to the file of the command that was executed (e.g. a SLURM
-            submission script).
-        stdout_file:
-            Path to the file with the command stdout
-        stderr_file:
-            Path to the file with the command stderr
-    """
-
-    cmd_file: Optional[str] = None
-    stdout_file: Optional[str] = None
-    stderr_file: Optional[str] = None
-    info: Optional[str] = None
-
-    def __init__(
-        self,
-        *args,
-        cmd_file: Optional[str] = None,
-        stdout_file: Optional[str] = None,
-        stderr_file: Optional[str] = None,
-        info: Optional[str] = None,
-    ):
-        super().__init__(*args)
-        self.cmd_file = cmd_file
-        self.stdout_file = stdout_file
-        self.stderr_file = stderr_file
-        self.info = info
-
-    def _read_file(self, filepath: str) -> str:
-        """
-        Return the content of a text file, and handle the cases where it is
-        empty or missing
-        """
-        if os.path.exists(filepath):
-            with open(filepath, "r") as f:
-                content = f.read()
-                if content:
-                    return f"Content of {filepath}:\n{content}"
-                else:
-                    return f"File {filepath} is empty\n"
-        else:
-            return f"File {filepath} is missing\n"
-
-    def assemble_error(self) -> str:
-        """
-        Read the files that are specified in attributes, and combine them in an
-        error message.
-        """
-        if self.cmd_file:
-            content = self._read_file(self.cmd_file)
-            cmd_content = f"COMMAND:\n{content}\n\n"
-        else:
-            cmd_content = ""
-        if self.stdout_file:
-            content = self._read_file(self.stdout_file)
-            out_content = f"STDOUT:\n{content}\n\n"
-        else:
-            out_content = ""
-        if self.stderr_file:
-            content = self._read_file(self.stderr_file)
-            err_content = f"STDERR:\n{content}\n\n"
-        else:
-            err_content = ""
-
-        content = f"{cmd_content}{out_content}{err_content}"
-        if self.info:
-            content = f"{content}ADDITIONAL INFO:\n{self.info}\n\n"
-
-        if not content:
-            content = str(self)
-        message = f"JobExecutionError\n\n{content}"
-        return message
-
-
-class TaskParameterEncoder(JSONEncoder):
-    """
-    Convenience JSONEncoder that serialises `Path`s as strings
-    """
-
-    def default(self, value):
-        if isinstance(value, Path):
-            return value.as_posix()
-        return JSONEncoder.default(self, value)
-
-
-class TaskParameters(BaseModel):
-    """
-    Wrapper for task input parameters
-
-    Instances of this class are used to pass parameters from the output of a
-    task to the input of the next one.
-
-    Attributes:
-        input_paths:
-            Input paths as derived by the input dataset.
-        output_paths:
-            Output path as derived from the output dataset.
-        metadata:
-            Dataset metadata, as found in the input dataset or as updated by
-            the previous task.
-        history:
-            Dataset history, as found in the input dataset or as updated by
-            the previous task.
-    """
-
-    input_paths: list[Path]
-    output_path: Path
-    metadata: dict[str, Any]
-    history: list[dict[str, Any]]
-
-    class Config:
-        arbitrary_types_allowed = True
-        extra = "forbid"
-
-
-def validate_workflow_compatibility(
-    *,
-    input_dataset: Dataset,
-    workflow: Workflow,
-    output_dataset: Dataset,
-    first_task_index: int,
-    last_task_index: int,
-) -> None:
-    """
-    Check compatibility of workflow and input / ouptut dataset
-    """
-    # Check input_dataset type
-    workflow_input_type = workflow.task_list[first_task_index].task.input_type
-    if (
-        workflow_input_type != "Any"
-        and workflow_input_type != input_dataset.type
-    ):
-        raise TypeError(
-            f"Incompatible types `{workflow_input_type}` of workflow "
-            f"`{workflow.name}` and `{input_dataset.type}` of dataset "
-            f"`{input_dataset.name}`"
-        )
-
-    # Check output_dataset type
-    workflow_output_type = workflow.task_list[last_task_index].task.output_type
-    if (
-        workflow_output_type != "Any"
-        and workflow_output_type != output_dataset.type
-    ):
-        raise TypeError(
-            f"Incompatible types `{workflow_output_type}` of workflow "
-            f"`{workflow.name}` and `{output_dataset.type}` of dataset "
-            f"`{output_dataset.name}`"
-        )
-
-
-def async_wrap(func: Callable) -> Callable:
-    """
-    Wrap a synchronous callable in an async task
-
-    Ref: [issue #140](https://github.com/fractal-analytics-platform/fractal-server/issues/140)
-    and [this StackOverflow answer](https://stackoverflow.com/q/43241221/19085332).
-
-    Returns:
-        async_wrapper:
-            A factory that allows wrapping a blocking callable within a
-            coroutine.
-    """  # noqa: E501
-
-    @wraps(func)
-    async def async_wrapper(*args, loop=None, executor=None, **kwargs):
-        if loop is None:
-            loop = asyncio.get_event_loop()
-        pfunc = partial(func, *args, **kwargs)
-        return await loop.run_in_executor(executor, pfunc)
-
-    return async_wrapper
-
-
-def write_args_file(
-    *args: dict[str, Any],
-    path: Path,
-):
-    """
-    Merge arbitrary dictionaries and write to file
-
-    Args:
-        *args:
-            One or more dictionaries that will be merged into one respecting
-            the order with which they are passed in, i.e., last in overrides
-            previous ones.
-        path:
-            Destination for serialised file.
-    """
-    out = {}
-    for d in args:
-        out.update(d)
-
-    with open(path, "w") as f:
-        json.dump(out, f, cls=TaskParameterEncoder, indent=4)
-
-
-def set_start_and_last_task_index(
-    num_tasks: int,
-    first_task_index: Optional[int] = None,
-    last_task_index: Optional[int] = None,
-) -> tuple[int, int]:
-    """
-    Handle `first_task_index` and `last_task_index`, by setting defaults and
-    validating values.
-
-    num_tasks:
-        Total number of tasks in a workflow task list
-    first_task_index:
-        Positional index of the first task to execute
-    last_task_index:
-        Positional index of the last task to execute
-    """
-    # Set default values
-    if first_task_index is None:
-        first_task_index = 0
-    if last_task_index is None:
-        last_task_index = num_tasks - 1
-
-    # Perform checks
-    if first_task_index < 0:
-        raise ValueError(f"{first_task_index=} cannot be negative")
-    if last_task_index < 0:
-        raise ValueError(f"{last_task_index=} cannot be negative")
-    if last_task_index > num_tasks - 1:
-        raise ValueError(
-            f"{last_task_index=} cannot be larger than {(num_tasks-1)=}"
-        )
-    if first_task_index > last_task_index:
-        raise ValueError(
-            f"{first_task_index=} cannot be larger than {last_task_index=}"
-        )
-    return (first_task_index, last_task_index)

fractal_server-1.4.9.dist-info/RECORD

@@ -1,97 +0,0 @@
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