fractal-server 2.14.4__py3-none-any.whl → 2.14.5__py3-none-any.whl

fractal_server/app/runner/executors/slurm_common/utils_executors.py

@@ -1,58 +0,0 @@
-from pathlib import Path
-from typing import Literal
-from typing import Optional
-
-
-def get_pickle_file_path(
-    *,
-    arg: str,
-    workflow_dir: Path,
-    subfolder_name: str,
-    in_or_out: Literal["in", "out"],
-    prefix: str,
-) -> Path:
-    if in_or_out in ["in", "out"]:
-        output = (
-            workflow_dir
-            / subfolder_name
-            / f"{prefix}_{in_or_out}_{arg}.pickle"
-        )
-        return output
-    else:
-        raise ValueError(
-            f"Missing or unexpected value in_or_out argument, {in_or_out=}"
-        )
-
-
-def get_slurm_script_file_path(
-    *, workflow_dir: Path, subfolder_name: str, prefix: Optional[str] = None
-) -> Path:
-    prefix = prefix or "_temp"
-    return workflow_dir / subfolder_name / f"{prefix}_slurm_submit.sbatch"
-
-
-def get_slurm_file_path(
-    *,
-    workflow_dir: Path,
-    subfolder_name: str,
-    arg: str = "%j",
-    out_or_err: Literal["out", "err"],
-    prefix: str,
-) -> Path:
-    if out_or_err == "out":
-        return (
-            workflow_dir
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.{out_or_err}"
-        )
-    elif out_or_err == "err":
-        return (
-            workflow_dir
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.{out_or_err}"
-        )
-    else:
-        raise ValueError(
-            "Missing or unexpected value out_or_err argument, "
-            f"{out_or_err=}"
-        )

fractal_server/app/runner/v2/runner_functions_low_level.py

@@ -1,122 +0,0 @@
-import json
-import logging
-import shutil
-import subprocess  # nosec
-from shlex import split
-from typing import Any
-
-from fractal_server.app.runner.exceptions import JobExecutionError
-from fractal_server.app.runner.exceptions import TaskExecutionError
-from fractal_server.string_tools import validate_cmd
-
-
-def _call_command_wrapper(cmd: str, log_path: str) -> None:
-    """
-    Call a command and write its stdout and stderr to files
-
-    Raises:
-        TaskExecutionError: If the `subprocess.run` call returns a positive
-                            exit code
-        JobExecutionError:  If the `subprocess.run` call returns a negative
-                            exit code (e.g. due to the subprocess receiving a
-                            TERM or KILL signal)
-    """
-    try:
-        validate_cmd(cmd)
-    except ValueError as e:
-        raise TaskExecutionError(f"Invalid command. Original error: {str(e)}")
-
-    # Verify that task command is executable
-    if shutil.which(split(cmd)[0]) is None:
-        msg = (
-            f'Command "{split(cmd)[0]}" is not valid. '
-            "Hint: make sure that it is executable."
-        )
-        raise TaskExecutionError(msg)
-
-    with open(log_path, "w") as fp_log:
-        try:
-            result = subprocess.run(  # nosec
-                split(cmd),
-                stderr=fp_log,
-                stdout=fp_log,
-            )
-        except Exception as e:
-            raise e
-
-    if result.returncode > 0:
-        with open(log_path, "r") as fp_stderr:
-            err = fp_stderr.read()
-        raise TaskExecutionError(err)
-    elif result.returncode < 0:
-        raise JobExecutionError(
-            info=f"Task failed with returncode={result.returncode}"
-        )
-
-
-def run_single_task(
-    # COMMON to all parallel tasks
-    command: str,
-    workflow_task_order: int,
-    workflow_task_id: int,
-    task_name: str,
-    # SPECIAL for each parallel task
-    parameters: dict[str, Any],
-    remote_files: dict[str, str],
-) -> dict[str, Any]:
-    """
-    Runs within an executor (AKA on the SLURM cluster).
-    """
-
-    try:
-        args_file_remote = remote_files["args_file_remote"]
-        metadiff_file_remote = remote_files["metadiff_file_remote"]
-        log_file_remote = remote_files["log_file_remote"]
-    except KeyError:
-        raise TaskExecutionError(
-            f"Invalid {remote_files=}",
-            workflow_task_order=workflow_task_order,
-            workflow_task_id=workflow_task_id,
-            task_name=task_name,
-        )
-
-    logger = logging.getLogger(None)
-    logger.debug(f"Now start running {command=}")
-
-    # Write arguments to args.json file
-    # NOTE: see issue 2346
-    with open(args_file_remote, "w") as f:
-        json.dump(parameters, f, indent=2)
-
-    # Assemble full command
-    # NOTE: this could be assembled backend-side
-    full_command = (
-        f"{command} "
-        f"--args-json {args_file_remote} "
-        f"--out-json {metadiff_file_remote}"
-    )
-
-    try:
-        _call_command_wrapper(
-            full_command,
-            log_path=log_file_remote,
-        )
-    except TaskExecutionError as e:
-        e.workflow_task_order = workflow_task_order
-        e.workflow_task_id = workflow_task_id
-        e.task_name = task_name
-        raise e
-
-    try:
-        with open(metadiff_file_remote, "r") as f:
-            out_meta = json.load(f)
-    except FileNotFoundError as e:
-        logger.debug(
-            "Task did not produce output metadata. "
-            f"Original FileNotFoundError: {str(e)}"
-        )
-        out_meta = None
-
-    if out_meta == {}:
-        return None
-    return out_meta