fractal-server 2.14.4a0__py3-none-any.whl → 2.14.5__py3-none-any.whl

{fractal_server-2.14.4a0.dist-info → fractal_server-2.14.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=ogag4AVsfl_E8OtJRekIRakeld3q5BpgpzxnhBgTkfs,25
+fractal_server/__init__.py,sha256=UajcJi63hxo1f0KVwKUKBcFjbKvBho3JgZuYlujcsDA,23
 fractal_server/__main__.py,sha256=rkM8xjY1KeS3l63irB8yCrlVobR-73uDapC4wvrIlxI,6957
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -67,45 +67,44 @@ fractal_server/app/routes/aux/validate_user_settings.py,sha256=FLVi__8YFcm_6c_K5
 fractal_server/app/routes/pagination.py,sha256=L8F5JqekF39qz-LpeScdlhb57MQnSRXjK4ZEtsZqYLk,1210
 fractal_server/app/runner/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/components.py,sha256=-Ii5l8d_V6f5DFOd-Zsr8VYmOsyqw0Hox9fEFQiuqxY,66
-fractal_server/app/runner/exceptions.py,sha256=JC5ufHyeA1hYD_rkZUscI30DD8D903ncag7Z3AArmUY,4215
+fractal_server/app/runner/exceptions.py,sha256=OPUWt8DV0V5iK5xPK8AhbJ3j3llrpmQM0pvgBCW4EqY,4033
 fractal_server/app/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/runner/executors/base_runner.py,sha256=4xxMpYycIeAOz5niaJj2xtVW_Cq-shCxP1qk4g-KwOM,5137
+fractal_server/app/runner/executors/base_runner.py,sha256=QOs9AWtT3G3XxIWBNamWpH94mAzuwWMzLXpCCkOiD-0,5459
+fractal_server/app/runner/executors/call_command_wrapper.py,sha256=6ykSnuC3u0eqvVE6vEcAL5CjQwphoIf-ZoadevUWOTU,1424
 fractal_server/app/runner/executors/local/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/local/get_local_config.py,sha256=KiakXxOahaLgWvQJ1LVGYGXht6DMGR9x8Xu-TuT9aY4,3628
-fractal_server/app/runner/executors/local/runner.py,sha256=AfJ2KDUBdLqkeJTdRzYCkfJh4LiGbdnsHROko_Pk9vA,9587
+fractal_server/app/runner/executors/local/runner.py,sha256=0b98oB9HX-1GS41M6yJ6KnL1MQxYjNtJPzF7u06Jcoc,10721
 fractal_server/app/runner/executors/slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_common/_batching.py,sha256=ZY020JZlDS5mfpgpWTChQkyHU7iLE5kx2HVd57_C6XA,8850
 fractal_server/app/runner/executors/slurm_common/_job_states.py,sha256=nuV-Zba38kDrRESOVB3gaGbrSPZc4q7YGichQaeqTW0,238
 fractal_server/app/runner/executors/slurm_common/_slurm_config.py,sha256=_feRRnVVnvQa3AsOQqfULfOgaoj2o6Ze0-fwXwic8p4,15795
-fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py,sha256=bqFD9uZfwXqmVXsScrgANp09zvbuc_LSGCDAmBV0wqo,33379
+fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py,sha256=M7liHYIo7r0Ej70uxQF8eg-J5Ag4HM92uSMoveBB05I,34729
 fractal_server/app/runner/executors/slurm_common/get_slurm_config.py,sha256=BW6fDpPyB0VH5leVxvwzkVH3r3hC7DuSyoWmRzHITWg,7305
-fractal_server/app/runner/executors/slurm_common/remote.py,sha256=Z7cnAlhYi9Orgeq6UGCl3cnWq9DX_sPrc6X1p40hVFE,5364
-fractal_server/app/runner/executors/slurm_common/slurm_job_task_models.py,sha256=RoxHLKOn0_wGjnY0Sv0a9nDSiqxYZHKRoMkT3p9_G1E,3607
-fractal_server/app/runner/executors/slurm_common/utils_executors.py,sha256=naPyJI0I3lD-sYHbSXbMFGUBK4h_SggA5V91Z1Ch1Xg,1416
+fractal_server/app/runner/executors/slurm_common/remote.py,sha256=hKnNph1aSTLw1o33jHxoKhku5w_-vw5Y_bHr4J87KWc,3775
+fractal_server/app/runner/executors/slurm_common/slurm_job_task_models.py,sha256=ZYi8pDKBX4fnBzJ82njH9U9uV6VbSSK1cjKav_ei8uo,3554
 fractal_server/app/runner/executors/slurm_ssh/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_ssh/run_subprocess.py,sha256=vlkJ0S37wYOmLG6gKC5-x8mBivYcgK7HTVvaroBnqLk,1030
-fractal_server/app/runner/executors/slurm_ssh/runner.py,sha256=IJ6fHidj8Yv0H59NzOgd3ZIgYuCiOmlkB1_Rt8Jt-Qo,7901
+fractal_server/app/runner/executors/slurm_ssh/runner.py,sha256=1Tf-Sx8u-6yKpIdwE7BTsfxN2VwRAs0CMc0CVoIgcOM,7826
 fractal_server/app/runner/executors/slurm_ssh/tar_commands.py,sha256=g173siyv7qtjov5i-CjTVRT8d19ibK8re3RVWbsdHYA,1845
 fractal_server/app/runner/executors/slurm_sudo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/runner/executors/slurm_sudo/_subprocess_run_as_user.py,sha256=BlOz4NElv3v7rUYefyeki33uaJxcSDk6rPuVZx9ocdw,2776
-fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=zT-DH61oPEq4dvo08EMnXv3QMYpwAZ3teY7R3MJ5G_8,6291
+fractal_server/app/runner/executors/slurm_sudo/_subprocess_run_as_user.py,sha256=Lolm9nNk810wpJmPIXPK-Op7Wt0Oj4btT6tEVO0gfjc,2607
+fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=vif3PO55mfpGMiRUzkEPSsHxazj6cBbTPpbV-UuQjEk,5907
 fractal_server/app/runner/filenames.py,sha256=lPnxKHtdRizr6FqG3zOdjDPyWA7GoaJGTtiuJV0gA8E,70
 fractal_server/app/runner/set_start_and_last_task_index.py,sha256=-q4zVybAj8ek2XlbENKlfOAJ39hT_zoJoZkqzDqiAMY,1254
 fractal_server/app/runner/shutdown.py,sha256=9pfSKHDNdIcm0eY-opgRTi7y0HmvfPmYiu9JR6Idark,2082
-fractal_server/app/runner/task_files.py,sha256=27xFuPzSJc1Pw912CfSMPOhOIpvNwpkyLCnycqdo9lw,4365
+fractal_server/app/runner/task_files.py,sha256=VR6JD5jPaZZof28j6GfkFnn_hF1DR1Om1YV8NUtslvA,4106
 fractal_server/app/runner/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/v2/_local.py,sha256=fJfSpY72BJeO_hGISIK1jE5q7lx3z3fv9_hlhNcJHLM,3072
-fractal_server/app/runner/v2/_slurm_ssh.py,sha256=zQYvuTF_pNuBm9t73CSnhxvh1z_fgp2EkXJWclHiI5I,3306
-fractal_server/app/runner/v2/_slurm_sudo.py,sha256=KmRBGFw9NDNMuMLp4H72iSj4NA3hm9f6OHJHkrMQmHM,3021
+fractal_server/app/runner/v2/_slurm_ssh.py,sha256=evhY0Ec4Foa9CXkZWC5YHkD1phrpVIxBwsxHwgLCK5E,3268
+fractal_server/app/runner/v2/_slurm_sudo.py,sha256=0g96dQ7Xj8om14Lcr2vQuBDrHSmQc8L4O1rD421Kd5w,2983
 fractal_server/app/runner/v2/db_tools.py,sha256=du5dKhMMFMErQXbGIgu9JvO_vtMensodyPsyDeqz1yQ,3324
 fractal_server/app/runner/v2/deduplicate_list.py,sha256=IVTE4abBU1bUprFTkxrTfYKnvkNTanWQ-KWh_etiT08,645
 fractal_server/app/runner/v2/merge_outputs.py,sha256=D1L4Taieq9i71SPQyNc1kMokgHh-sV_MqF3bv7QMDBc,907
 fractal_server/app/runner/v2/runner.py,sha256=2NQhcaGDw6XJ6Mnmiubru0yq2PpgF6fWFIE5hOVnOY0,17701
-fractal_server/app/runner/v2/runner_functions.py,sha256=AzsE7VF6NMz_5qc0htQkfow5_2rr-wkx50vFJTndj8I,19250
-fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=_h_OOffq3d7V0uHa8Uvs0mj31y1GSZBUXjDDF3WjVjY,3620
+fractal_server/app/runner/v2/runner_functions.py,sha256=78tJEjeN_NKVwrMJjzMvS2Bu2bYoO5Cerh8QdC3T2nw,18865
 fractal_server/app/runner/v2/submit_workflow.py,sha256=QywUGIoHAHnrWgfnyX8W9kVqKY-RvVyNLpzrbsXZOZ4,13075
 fractal_server/app/runner/v2/task_interface.py,sha256=vVNSLiUTnImo82dp910KqP4gYLX3aoiLSJsfvdzGems,2561
-fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
+fractal_server/app/runner/versions.py,sha256=cgKICSTSf9mPq0gSNi1fpnk2oKSHItcxDynipT9hvo8,429
 fractal_server/app/schemas/__init__.py,sha256=stURAU_t3AOBaH0HSUbV-GKhlPKngnnIMoqWc3orFyI,135
 fractal_server/app/schemas/user.py,sha256=0e4fWin0EdStjlbUnNWl7GsvnVfKMJPmVPCt-Mm_9tg,1945
 fractal_server/app/schemas/user_group.py,sha256=ejk5qHLbmmDotXT6_--kkoDHVm-T5nS9GDtivJ4LjZU,1456
@@ -127,7 +126,7 @@ fractal_server/app/schemas/v2/workflowtask.py,sha256=Q_2wM89QLMX19uthrnOigh-bxLY
 fractal_server/app/security/__init__.py,sha256=e2cveg5hQpieGD3bSPd5GTOMthvJ-HXH3buSb9WVfEU,14096
 fractal_server/app/security/signup_email.py,sha256=Xd6QYxcdmg0PHpDwmUE8XQmPcOj3Xjy5oROcIMhmltM,1472
 fractal_server/app/user_settings.py,sha256=OP1yiYKtPadxwM51_Q0hdPk3z90TCN4z1BLpQsXyWiU,1316
-fractal_server/config.py,sha256=McwfsTwRUzQOfN97ZjTLOHVyUvJKBqKY8xc9vK_eACA,26437
+fractal_server/config.py,sha256=7njTJrbddEckO8VZjeO5_V7l9v8gCk9JwtfzYKTXvzA,26046
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
@@ -176,7 +175,7 @@ fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.p
 fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py,sha256=TDWCaIoM0Q4SpRWmR9zr_rdp3lJXhCfBPTMhtrP5xYE,3950
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
-fractal_server/ssh/_fabric.py,sha256=jF7Nny0r3_PL1WjM1Zlw1I73Uqerx-mTaDWQlOaOpa0,23324
+fractal_server/ssh/_fabric.py,sha256=wLjOh2kBnaBjpmGB6lbrPdcWq9D5BzbaS2vKYwOfxEo,23498
 fractal_server/string_tools.py,sha256=niViRrrZAOo0y6pEFI9L_eUYS1PoOiQZUBtngiLc2_k,1877
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
@@ -211,8 +210,8 @@ fractal_server/types/validators/_workflow_task_arguments_validators.py,sha256=HL
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=PMwrxWFxRTQRl1b9h-NRIbFGPKqpH_hXnkAT3NfZdpY,3571
 fractal_server/zip_tools.py,sha256=GjDgo_sf6V_DDg6wWeBlZu5zypIxycn_l257p_YVKGc,4876
-fractal_server-2.14.4a0.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.14.4a0.dist-info/METADATA,sha256=Hl3iQzK2CtzTsqeTm4h_I4DZOX318S_WRsFjGmDEwhQ,4562
-fractal_server-2.14.4a0.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
-fractal_server-2.14.4a0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.14.4a0.dist-info/RECORD,,
+fractal_server-2.14.5.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.14.5.dist-info/METADATA,sha256=UZkyF3UKy2ONKfsIYsUrS7u0ha7kdkeudbUet6_ZUu4,4294
+fractal_server-2.14.5.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
+fractal_server-2.14.5.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.14.5.dist-info/RECORD,,

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