fractal-server 2.14.0a10__py3-none-any.whl → 2.14.0a11__py3-none-any.whl

fractal_server/app/runner/executors/local/_submit_setup.py

@@ -1,46 +0,0 @@
-from pathlib import Path
-from typing import Any
-from typing import Literal
-
-from ...task_files import TaskFiles
-from ._local_config import get_local_backend_config
-from fractal_server.app.models.v2 import WorkflowTaskV2
-
-
-def _local_submit_setup(
-    *,
-    wftask: WorkflowTaskV2,
-    root_dir_local: Path,
-    root_dir_remote: Path,
-    which_type: Literal["non_parallel", "parallel"],
-) -> dict[str, Any]:
-    """
-    Collect WorkflowTask-specific configuration parameters from different
-    sources, and inject them for execution.
-
-    FIXME
-
-    Arguments:
-        wftask: WorkflowTask for which the configuration is to be assembled
-        root_dir_local:
-        root_dir_rempote: Not used in this function.
-        which_type: Whether it is a parallel or non-parallel task.
-    """
-
-    local_backend_config = get_local_backend_config(
-        wftask=wftask,
-        which_type=which_type,
-    )
-
-    # Get TaskFiles object
-    task_files = TaskFiles(
-        root_dir_local=root_dir_local,
-        root_dir_remote=root_dir_local,
-        task_order=wftask.order,
-        task_name=wftask.task.name,
-    )
-
-    return dict(
-        local_backend_config=local_backend_config,
-        task_files=task_files,
-    )

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

@@ -1,84 +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>
-#
-# 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.
-"""
-Submodule to define _slurm_submit_setup, which is also the reference
-implementation of `submit_setup_call`.
-"""
-from pathlib import Path
-from typing import Any
-from typing import Literal
-
-from ...task_files import TaskFiles
-from fractal_server.app.models.v2 import WorkflowTaskV2
-from fractal_server.app.runner.executors.slurm_common.get_slurm_config import (
-    get_slurm_config,
-)
-
-
-def _slurm_submit_setup(
-    *,
-    wftask: WorkflowTaskV2,
-    root_dir_local: Path,
-    root_dir_remote: Path,
-    which_type: Literal["non_parallel", "parallel"],
-) -> dict[str, Any]:
-    """
-    Collect WorkflowTask-specific configuration parameters from different
-    sources, and inject them for execution.
-
-    FIXME
-
-    Here goes all the logic for reading attributes from the appropriate sources
-    and transforming them into an appropriate `SlurmConfig` object (encoding
-    SLURM configuration) and `TaskFiles` object (with details e.g. about file
-    paths or filename prefixes).
-
-    For now, this is the reference implementation for the argument
-    `submit_setup_call` of
-    [fractal_server.app.runner.v2.runner][].
-
-    Arguments:
-        wftask:
-            WorkflowTask for which the configuration is to be assembled
-        workflow_dir_local:
-            Server-owned directory to store all task-execution-related relevant
-            files (inputs, outputs, errors, and all meta files related to the
-            job execution). Note: users cannot write directly to this folder.
-        workflow_dir_remote:
-            User-side directory with the same scope as `workflow_dir_local`,
-            and where a user can write.
-
-    Returns:
-        submit_setup_dict:
-            A dictionary that will be passed on to
-            `FractalSlurmExecutor.submit` and `FractalSlurmExecutor.map`, so
-            as to set extra options.
-    """
-
-    # Get SlurmConfig object
-    slurm_config = get_slurm_config(
-        wftask=wftask,
-        which_type=which_type,
-    )
-
-    # Get TaskFiles object
-    task_files = TaskFiles(
-        root_dir_local=root_dir_local,
-        root_dir_remote=root_dir_remote,
-        task_order=wftask.order,
-        task_name=wftask.task.name,
-    )
-
-    return dict(
-        slurm_config=slurm_config,
-        task_files=task_files,
-    )

fractal_server/app/runner/v2/_db_tools.py

@@ -1,48 +0,0 @@
-from typing import Any
-
-from sqlalchemy.dialects.postgresql import insert as pg_insert
-from sqlalchemy.orm import Session
-
-from fractal_server.app.models.v2 import HistoryImageCache
-
-
-def bulk_upsert_image_cache_fast(
-    *,
-    list_upsert_objects: list[dict[str, Any]],
-    db: Session,
-) -> None:
-    """
-    Insert or update many objects into `HistoryImageCache` and commit
-
-    This function is an optimized version of
-
-    ```python
-    for obj in list_upsert_objects:
-        db.merge(**obj)
-    db.commit()
-    ```
-
-    See docs at
-    https://docs.sqlalchemy.org/en/20/dialects/postgresql.html#insert-on-conflict-upsert
-
-    FIXME: we tried to replace `index_elements` with
-    `constraint="pk_historyimagecache"`, but it did not work as expected.
-
-    Arguments:
-        list_upsert_objects:
-            List of dictionaries for objects to be upsert-ed.
-        db: A sync database session
-    """
-    if len(list_upsert_objects) == 0:
-        return None
-    stmt = pg_insert(HistoryImageCache).values(list_upsert_objects)
-    stmt = stmt.on_conflict_do_update(
-        index_elements=[
-            HistoryImageCache.zarr_url,
-            HistoryImageCache.dataset_id,
-            HistoryImageCache.workflowtask_id,
-        ],
-        set_=dict(latest_history_unit_id=stmt.excluded.latest_history_unit_id),
-    )
-    db.execute(stmt)
-    db.commit()