fractal-server 2.3.3__py3-none-any.whl → 2.3.5__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.3.3"
+__VERSION__ = "2.3.5"

fractal_server/app/routes/api/__init__.py

@@ -2,9 +2,12 @@
 `api` module
 """
 from fastapi import APIRouter
+from fastapi import Depends
 
 from ....config import get_settings
 from ....syringe import Inject
+from ...models.security import UserOAuth
+from ...security import current_active_superuser
 
 
 router_api = APIRouter()
@@ -17,3 +20,9 @@ async def alive():
         alive=True,
         version=settings.PROJECT_VERSION,
     )
+
+
+@router_api.get("/settings/")
+async def view_settings(user: UserOAuth = Depends(current_active_superuser)):
+    settings = Inject(get_settings)
+    return settings.get_sanitized()

fractal_server/app/routes/api/v1/project.py

@@ -250,9 +250,18 @@ async def apply_workflow(
     db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ApplyWorkflowReadV1]:
 
+    settings = Inject(get_settings)
+    if settings.FRACTAL_API_V1_MODE == "include_without_submission":
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                "Legacy API is still accessible, "
+                "but the submission of legacy jobs is not available."
+            ),
+        )
+
     # Remove non-submitted V1 jobs from the app state when the list grows
     # beyond a threshold
-    settings = Inject(get_settings)
     if (
         len(request.app.state.jobsV1)
         > settings.FRACTAL_API_MAX_JOB_LIST_LENGTH

fractal_server/app/runner/compress_folder.py

@@ -1,120 +1,132 @@
-import shlex
-import subprocess  # nosec
+"""
+Wrap `tar` compression command.
+
+This module is used both locally (in the environment where `fractal-server`
+is running) and remotely (as a standalon Python module, executed over SSH).
+
+This is a twin-module of `extract_archive.py`.
+
+The reason for using the `tar` command via `subprocess` rather than Python
+built-in `tarfile` library has to do with performance issues we observed
+when handling files which were just created within a SLURM job, and in the
+context of a CephFS filesystem.
+"""
+import shutil
 import sys
-import tarfile
-import time
 from pathlib import Path
-from typing import Optional
 
+from fractal_server.app.runner.run_subprocess import run_subprocess
+from fractal_server.logger import get_logger
+from fractal_server.logger import set_logger
+
+
+def copy_subfolder(src: Path, dest: Path, logger_name: str):
+    cmd_cp = f"cp -r {src.as_posix()} {dest.as_posix()}"
+    logger = get_logger(logger_name=logger_name)
+    logger.debug(f"{cmd_cp=}")
+    res = run_subprocess(cmd=cmd_cp, logger_name=logger_name)
+    return res
+
+
+def create_tar_archive(
+    tarfile_path: Path,
+    subfolder_path_tmp_copy: Path,
+    logger_name: str,
+    remote_to_local: bool,
+):
+    logger = get_logger(logger_name)
+
+    if remote_to_local:
+        exclude_options = "--exclude *sbatch --exclude *_in_*.pickle "
+    else:
+        exclude_options = ""
+
+    cmd_tar = (
+        f"tar czf {tarfile_path} "
+        f"{exclude_options} "
+        f"--directory={subfolder_path_tmp_copy.as_posix()} "
+        "."
+    )
+    logger.debug(f"cmd tar:\n{cmd_tar}")
+    run_subprocess(cmd=cmd_tar, logger_name=logger_name)
 
-# COMPRESS_FOLDER_MODALITY = "python"
-COMPRESS_FOLDER_MODALITY = "cp-tar-rmtree"
 
+def remove_temp_subfolder(subfolder_path_tmp_copy: Path, logger_name: str):
+    logger = get_logger(logger_name)
+    try:
+        logger.debug(f"Now remove {subfolder_path_tmp_copy}")
+        shutil.rmtree(subfolder_path_tmp_copy)
+    except Exception as e:
+        logger.debug(f"ERROR during shutil.rmtree: {e}")
 
-def _filter(info: tarfile.TarInfo) -> Optional[tarfile.TarInfo]:
-    if info.name.endswith(".pickle"):
-        filename = info.name.split("/")[-1]
-        parts = filename.split("_")
-        if len(parts) == 3 and parts[1] == "in":
-            return None
-        elif len(parts) == 5 and parts[3] == "in":
-            return None
-    elif info.name.endswith("slurm_submit.sbatch"):
-        return None
-    return info
 
+def compress_folder(
+    subfolder_path: Path, remote_to_local: bool = False
+) -> str:
+    """
+    Compress e.g. `/path/archive` into `/path/archive.tar.gz`
 
-if __name__ == "__main__":
-    help_msg = (
-        "Expected use:\n"
-        "python -m fractal_server.app.runner.compress_folder "
-        "path/to/folder"
-    )
+    Note that `/path/archive.tar.gz` may already exist. In this case, it will
+    be overwritten.
 
-    if len(sys.argv[1:]) != 1:
-        raise ValueError(
-            "Invalid argument(s).\n" f"{help_msg}\n" f"Provided: {sys.argv=}"
-        )
+    Args:
+        subfolder_path: Absolute path to the folder to compress.
+        remote_to_local: If `True`, exclude some files from the tar.gz archive.
+
+    Returns:
+        Absolute path to the tar.gz archive.
+    """
 
-    subfolder_path = Path(sys.argv[1])
-    t_0 = time.perf_counter()
-    print("[compress_folder.py] START")
-    print(f"[compress_folder.py] {COMPRESS_FOLDER_MODALITY=}")
-    print(f"[compress_folder.py] {subfolder_path=}")
+    logger_name = "compress_folder"
+    logger = set_logger(logger_name)
 
-    job_folder = subfolder_path.parent
+    logger.debug("START")
+    logger.debug(f"{subfolder_path=}")
+    parent_dir = subfolder_path.parent
     subfolder_name = subfolder_path.name
-    tarfile_path = (job_folder / f"{subfolder_name}.tar.gz").as_posix()
-    print(f"[compress_folder.py] {tarfile_path=}")
-
-    if COMPRESS_FOLDER_MODALITY == "python":
-        raise NotImplementedError()
-        with tarfile.open(tarfile_path, "w:gz") as tar:
-            tar.add(
-                subfolder_path,
-                arcname=".",  # ????
-                recursive=True,
-                filter=_filter,
-            )
-    elif COMPRESS_FOLDER_MODALITY == "cp-tar-rmtree":
-        import shutil
-        import time
-
-        subfolder_path_tmp_copy = (
-            subfolder_path.parent / f"{subfolder_path.name}_copy"
-        )
+    tarfile_path = (parent_dir / f"{subfolder_name}.tar.gz").as_posix()
+    logger.debug(f"{tarfile_path=}")
 
-        t0 = time.perf_counter()
-        # shutil.copytree(subfolder_path, subfolder_path_tmp_copy)
-        cmd_cp = (
-            "cp -r "
-            f"{subfolder_path.as_posix()} "
-            f"{subfolder_path_tmp_copy.as_posix()}"
-        )
-        res = subprocess.run(  # nosec
-            shlex.split(cmd_cp),
-            check=True,
-            capture_output=True,
-            encoding="utf-8",
+    subfolder_path_tmp_copy = (
+        subfolder_path.parent / f"{subfolder_path.name}_copy"
+    )
+    try:
+        copy_subfolder(
+            subfolder_path, subfolder_path_tmp_copy, logger_name=logger_name
         )
-        t1 = time.perf_counter()
-        print("[compress_folder.py] `cp -r` END - " f"elapsed: {t1-t0:.3f} s")
-
-        cmd_tar = (
-            "tar czf "
-            f"{tarfile_path} "
-            "--exclude *sbatch --exclude *_in_*.pickle "
-            f"--directory={subfolder_path_tmp_copy.as_posix()} "
-            "."
+        create_tar_archive(
+            tarfile_path,
+            subfolder_path_tmp_copy,
+            logger_name=logger_name,
+            remote_to_local=remote_to_local,
         )
+        return tarfile_path
 
-        print(f"[compress_folder.py] cmd tar:\n{cmd_tar}")
-        t0 = time.perf_counter()
-        res = subprocess.run(  # nosec
-            shlex.split(cmd_tar),
-            capture_output=True,
-            encoding="utf-8",
-        )
-        t1 = time.perf_counter()
-        t_1 = time.perf_counter()
-        print(f"[compress_folder.py] tar END - elapsed: {t1-t0:.3f} s")
+    except Exception as e:
+        logger.debug(f"ERROR: {e}")
+        sys.exit(1)
 
-        print(f"[compress_folder] END - elapsed {t_1 - t_0:.3f} seconds")
+    finally:
+        remove_temp_subfolder(subfolder_path_tmp_copy, logger_name=logger_name)
 
-        if res.returncode != 0:
-            print("[compress_folder.py] ERROR in tar")
-            print(f"[compress_folder.py] tar stdout:\n{res.stdout}")
-            print(f"[compress_folder.py] tar stderr:\n{res.stderr}")
 
-            shutil.rmtree(subfolder_path_tmp_copy)
-            sys.exit(1)
+def main(sys_argv: list[str]):
+
+    help_msg = (
+        "Expected use:\n"
+        "python -m fractal_server.app.runner.compress_folder "
+        "path/to/folder [--remote-to-local]\n"
+    )
+    num_args = len(sys_argv[1:])
+    if num_args == 0:
+        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
+    elif num_args == 1:
+        compress_folder(subfolder_path=Path(sys_argv[1]))
+    elif num_args == 2 and sys_argv[2] == "--remote-to-local":
+        compress_folder(subfolder_path=Path(sys_argv[1]), remote_to_local=True)
+    else:
+        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
 
-        t0 = time.perf_counter()
-        shutil.rmtree(subfolder_path_tmp_copy)
-        t1 = time.perf_counter()
-        print(
-            f"[compress_folder.py] shutil.rmtree END - elapsed: {t1-t0:.3f} s"
-        )
 
-    t_1 = time.perf_counter()
-    print(f"[compress_folder] END - elapsed {t_1 - t_0:.3f} seconds")
+if __name__ == "__main__":
+    main(sys.argv)

fractal_server/app/runner/executors/slurm/_slurm_config.py

@@ -62,6 +62,8 @@ class _SlurmConfigSet(BaseModel, extra=Extra.forbid):
     time: Optional[str]
     account: Optional[str]
     extra_lines: Optional[list[str]]
+    pre_submission_commands: Optional[list[str]]
+    gpus: Optional[str]
 
 
 class _BatchingConfigSet(BaseModel, extra=Extra.forbid):
@@ -219,6 +221,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
         constraint: Corresponds to SLURM option.
         gres: Corresponds to SLURM option.
         account: Corresponds to SLURM option.
+        gpus: Corresponds to SLURM option.
         time: Corresponds to SLURM option (WARNING: not fully supported).
         prefix: Prefix of configuration lines in SLURM submission scripts.
         shebang_line: Shebang line for SLURM submission scripts.
@@ -240,6 +243,8 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
             Key-value pairs to be included as `export`-ed variables in SLURM
             submission script, after prepending values with the user's cache
             directory.
+        pre_submission_commands: List of commands to be prepended to the sbatch
+            command.
     """
 
     # Required SLURM parameters (note that the integer attributes are those
@@ -254,6 +259,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
     job_name: Optional[str] = None
     constraint: Optional[str] = None
     gres: Optional[str] = None
+    gpus: Optional[str] = None
     time: Optional[str] = None
     account: Optional[str] = None
 
@@ -274,6 +280,8 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
     target_num_jobs: int
     max_num_jobs: int
 
+    pre_submission_commands: list[str] = Field(default_factory=list)
+
     def _sorted_extra_lines(self) -> list[str]:
         """
         Return a copy of `self.extra_lines`, where lines starting with
@@ -340,7 +348,14 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
             f"{self.prefix} --cpus-per-task={self.cpus_per_task}",
             f"{self.prefix} --mem={mem_per_job_MB}M",
         ]
-        for key in ["job_name", "constraint", "gres", "time", "account"]:
+        for key in [
+            "job_name",
+            "constraint",
+            "gres",
+            "gpus",
+            "time",
+            "account",
+        ]:
             value = getattr(self, key)
             if value is not None:
                 # Handle the `time` parameter

fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -13,7 +13,6 @@
 import json
 import math
 import sys
-import tarfile
 import threading
 import time
 from concurrent.futures import Future
@@ -38,9 +37,11 @@ from ...slurm._slurm_config import SlurmConfig
 from .._batching import heuristics
 from ._executor_wait_thread import FractalSlurmWaitThread
 from fractal_server.app.runner.components import _COMPONENT_KEY_
+from fractal_server.app.runner.compress_folder import compress_folder
 from fractal_server.app.runner.exceptions import JobExecutionError
 from fractal_server.app.runner.exceptions import TaskExecutionError
 from fractal_server.app.runner.executors.slurm.ssh._slurm_job import SlurmJob
+from fractal_server.app.runner.extract_archive import extract_archive
 from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
 from fractal_server.ssh._fabric import FractalSSH
@@ -822,17 +823,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
 
         # Create compressed subfolder archive (locally)
         local_subfolder = self.workflow_dir_local / subfolder_name
-        tarfile_name = f"{subfolder_name}.tar.gz"
-        tarfile_path_local = (
-            self.workflow_dir_local / tarfile_name
-        ).as_posix()
+        tarfile_path_local = compress_folder(local_subfolder)
+        tarfile_name = Path(tarfile_path_local).name
+        logger.info(f"Subfolder archive created at {tarfile_path_local}")
         tarfile_path_remote = (
             self.workflow_dir_remote / tarfile_name
         ).as_posix()
-        with tarfile.open(tarfile_path_local, "w:gz") as tar:
-            for this_file in local_subfolder.glob("*"):
-                tar.add(this_file, arcname=this_file.name)
-        logger.info(f"Subfolder archive created at {tarfile_path_local}")
 
         # Transfer archive
         t_0_put = time.perf_counter()
@@ -873,9 +869,22 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
 
         # Submit job to SLURM, and get jobid
         sbatch_command = f"sbatch --parsable {job.slurm_script_remote}"
-        sbatch_stdout = self.fractal_ssh.run_command(
-            cmd=sbatch_command,
-        )
+        pre_submission_cmds = job.slurm_config.pre_submission_commands
+        if len(pre_submission_cmds) == 0:
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=sbatch_command)
+        else:
+            logger.debug(f"Now using {pre_submission_cmds=}")
+            script_lines = pre_submission_cmds + [sbatch_command]
+            script_content = "\n".join(script_lines)
+            script_content = f"{script_content}\n"
+            script_path_remote = (
+                f"{job.slurm_script_remote.as_posix()}_wrapper.sh"
+            )
+            self.fractal_ssh.write_remote_file(
+                path=script_path_remote, content=script_content
+            )
+            cmd = f"bash {script_path_remote}"
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=cmd)
 
         # Extract SLURM job ID from stdout
         try:
@@ -885,7 +894,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             error_msg = (
                 f"Submit command `{sbatch_command}` returned "
                 f"`{stdout=}` which cannot be cast to an integer "
-                f"SLURM-job ID. Original error:\n{str(e)}"
+                f"SLURM-job ID.\n"
+                f"Note that {pre_submission_cmds=}.\n"
+                f"Original error:\n{str(e)}"
             )
             logger.error(error_msg)
             raise JobExecutionError(info=error_msg)
@@ -1222,7 +1233,8 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         tar_command = (
             f"{self.python_remote} "
             "-m fractal_server.app.runner.compress_folder "
-            f"{(self.workflow_dir_remote / subfolder_name).as_posix()}"
+            f"{(self.workflow_dir_remote / subfolder_name).as_posix()} "
+            "--remote-to-local"
         )
         stdout = self.fractal_ssh.run_command(cmd=tar_command)
         print(stdout)
@@ -1240,8 +1252,7 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         )
 
         # Extract tarfile locally
-        with tarfile.open(tarfile_path_local) as tar:
-            tar.extractall(path=(self.workflow_dir_local / subfolder_name))
+        extract_archive(Path(tarfile_path_local))
 
         t_1 = time.perf_counter()
         logger.info("[_get_subfolder_sftp] End - " f"elapsed: {t_1-t_0:.3f} s")

fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -1121,6 +1121,12 @@ class FractalSlurmExecutor(SlurmExecutor):
             slurm_err_path=str(job.slurm_stderr),
         )
 
+        # Print warning for ignored parameter
+        if len(job.slurm_config.pre_submission_commands) > 0:
+            logger.warning(
+                f"Ignoring {job.slurm_config.pre_submission_commands=}."
+            )
+
         # Submit job via sbatch, and retrieve jobid
 
         # Write script content to a job.slurm_script

fractal_server/app/runner/extract_archive.py

@@ -1,7 +1,22 @@
+"""
+Wrap `tar` extraction command.
+
+This module is used both locally (in the environment where `fractal-server`
+is running) and remotely (as a standalon Python module, executed over SSH).
+
+This is a twin-module of `compress_folder.py`.
+
+The reason for using the `tar` command via `subprocess` rather than Python
+built-in `tarfile` library has to do with performance issues we observed
+when handling files which were just created within a SLURM job, and in the
+context of a CephFS filesystem.
+"""
 import sys
-import tarfile
 from pathlib import Path
 
+from .run_subprocess import run_subprocess
+from fractal_server.logger import set_logger
+
 
 def _remove_suffix(*, string: str, suffix: str) -> str:
     if string.endswith(suffix):
@@ -10,29 +25,61 @@ def _remove_suffix(*, string: str, suffix: str) -> str:
         raise ValueError(f"Cannot remove {suffix=} from {string=}.")
 
 
-if __name__ == "__main__":
+def extract_archive(archive_path: Path):
+    """
+    Extract e.g. `/path/archive.tar.gz` archive into `/path/archive` folder
+
+    Note that `/path/archive` may already exist. In this case, files with
+    the same name are overwritten and new files are added.
+
+    Arguments:
+        archive_path: Absolute path to the archive file.
+    """
+
+    logger_name = "extract_archive"
+    logger = set_logger(logger_name)
+
+    logger.debug("START")
+    logger.debug(f"{archive_path.as_posix()=}")
+
+    # Check archive_path is valid
+    if not archive_path.exists():
+        sys.exit(f"Missing file {archive_path.as_posix()}.")
+
+    # Prepare subfolder path
+    parent_dir = archive_path.parent
+    subfolder_name = _remove_suffix(string=archive_path.name, suffix=".tar.gz")
+    subfolder_path = parent_dir / subfolder_name
+    logger.debug(f"{subfolder_path.as_posix()=}")
+
+    # Create subfolder
+    subfolder_path.mkdir(exist_ok=True)
+
+    # Run tar command
+    cmd_tar = (
+        f"tar -xzvf {archive_path} "
+        f"--directory={subfolder_path.as_posix()} "
+        "."
+    )
+    logger.debug(f"{cmd_tar=}")
+    run_subprocess(cmd=cmd_tar, logger_name=logger_name)
+
+    logger.debug("END")
+
+
+def main(sys_argv: list[str]):
     help_msg = (
         "Expected use:\n"
         "python -m fractal_server.app.runner.extract_archive "
         "path/to/archive.tar.gz"
     )
 
-    if len(sys.argv[1:]) != 1:
-        raise ValueError(
-            f"Invalid argument.\n{help_msg}\nProvided: {sys.argv=}"
-        )
-    elif not sys.argv[1].endswith(".tar.gz"):
-        raise ValueError(
-            f"Invalid argument.\n{help_msg}\nProvided: {sys.argv=}"
-        )
-
-    tarfile_path = Path(sys.argv[1])
-
-    print(f"[extract_archive.py] {tarfile_path=}")
+    if len(sys_argv[1:]) != 1 or not sys_argv[1].endswith(".tar.gz"):
+        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
+    else:
+        tarfile_path = Path(sys_argv[1])
+        extract_archive(tarfile_path)
 
-    job_folder = tarfile_path.parent
-    subfolder_name = _remove_suffix(string=tarfile_path.name, suffix=".tar.gz")
-    with tarfile.open(tarfile_path) as tar:
-        tar.extractall(path=Path(job_folder, subfolder_name).as_posix())
 
-    print(f"[extract_archive.py] {tarfile_path=}")
+if __name__ == "__main__":
+    main(sys.argv)

fractal_server/app/runner/run_subprocess.py

@@ -0,0 +1,27 @@
+import shlex
+import subprocess  # nosec
+from typing import Optional
+
+from fractal_server.logger import get_logger
+
+
+def run_subprocess(
+    cmd: str, logger_name: Optional[str] = None
+) -> subprocess.CompletedProcess:
+    logger = get_logger(logger_name)
+    try:
+        res = subprocess.run(  # nosec
+            shlex.split(cmd), check=True, capture_output=True, encoding="utf-8"
+        )
+        return res
+    except subprocess.CalledProcessError as e:
+        logger.debug(
+            f"Command '{e.cmd}' returned non-zero exit status {e.returncode}."
+        )
+        logger.debug(f"stdout: {e.stdout}")
+        logger.debug(f"stderr: {e.stderr}")
+        raise e
+    except Exception as e:
+        logger.debug(f"An error occurred while running command: {cmd}")
+        logger.debug(str(e))
+        raise e

fractal_server/app/runner/v2/__init__.py

@@ -36,8 +36,8 @@ from ._local import process_workflow as local_process_workflow
 from ._local_experimental import (
     process_workflow as local_experimental_process_workflow,
 )
-from ._slurm import process_workflow as slurm_sudo_process_workflow
 from ._slurm_ssh import process_workflow as slurm_ssh_process_workflow
+from ._slurm_sudo import process_workflow as slurm_sudo_process_workflow
 from .handle_failed_job import assemble_filters_failed_job
 from .handle_failed_job import assemble_history_failed_job
 from .handle_failed_job import assemble_images_failed_job

fractal_server/app/runner/v2/{_slurm_ssh → _slurm_common}/get_slurm_config.py

@@ -18,8 +18,6 @@ from fractal_server.app.runner.executors.slurm._slurm_config import (
 
 def get_slurm_config(
     wftask: WorkflowTaskV2,
-    workflow_dir_local: Path,
-    workflow_dir_remote: Path,
     which_type: Literal["non_parallel", "parallel"],
     config_path: Optional[Path] = None,
 ) -> SlurmConfig:
@@ -43,13 +41,6 @@ def get_slurm_config(
         wftask:
             WorkflowTask for which the SLURM configuration is is to be
             prepared.
-        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.
         config_path:
             Path of a Fractal SLURM configuration file; if `None`, use
             `FRACTAL_SLURM_CONFIG_FILE` variable from settings.
@@ -99,13 +90,13 @@ def get_slurm_config(
     # 1. This block of definitions takes priority over other definitions from
     #    slurm_env which are not under the `needs_gpu` subgroup
     # 2. This block of definitions has lower priority than whatever comes next
-    #    (i.e. from WorkflowTask.meta).
+    #    (i.e. from WorkflowTask.meta_parallel).
     if wftask_meta is not None:
         needs_gpu = wftask_meta.get("needs_gpu", False)
     else:
         needs_gpu = False
     logger.debug(f"[get_slurm_config] {needs_gpu=}")
-    if needs_gpu and slurm_env.gpu_slurm_config is not None:  # FIXME
+    if needs_gpu:
         for key, value in slurm_env.gpu_slurm_config.dict(
             exclude_unset=True, exclude={"mem"}
         ).items():
@@ -143,9 +134,9 @@ def get_slurm_config(
             )
             logger.error(error_msg)
             raise SlurmConfigError(error_msg)
-        for key in ["time", "gres", "constraint"]:
+        for key in ["time", "gres", "gpus", "constraint"]:
             value = wftask_meta.get(key, None)
-            if value:
+            if value is not None:
                 slurm_dict[key] = value
     if wftask_meta is not None:
         extra_lines = wftask_meta.get("extra_lines", [])

fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py

@@ -17,8 +17,10 @@ from pathlib import Path
 from typing import Literal
 
 from ...task_files import get_task_file_paths
-from .get_slurm_config import get_slurm_config
 from fractal_server.app.models.v2 import WorkflowTaskV2
+from fractal_server.app.runner.v2._slurm_common.get_slurm_config import (
+    get_slurm_config,
+)
 
 
 def _slurm_submit_setup(
@@ -62,8 +64,6 @@ def _slurm_submit_setup(
     # Get SlurmConfig object
     slurm_config = get_slurm_config(
         wftask=wftask,
-        workflow_dir_local=workflow_dir_local,
-        workflow_dir_remote=workflow_dir_remote,
         which_type=which_type,
     )
 

fractal_server/app/runner/v2/{_slurm → _slurm_sudo}/_submit_setup.py

@@ -17,8 +17,10 @@ from pathlib import Path
 from typing import Literal
 
 from ...task_files import get_task_file_paths
-from .get_slurm_config import get_slurm_config
 from fractal_server.app.models.v2 import WorkflowTaskV2
+from fractal_server.app.runner.v2._slurm_common.get_slurm_config import (
+    get_slurm_config,
+)
 
 
 def _slurm_submit_setup(
@@ -62,8 +64,6 @@ def _slurm_submit_setup(
     # Get SlurmConfig object
     slurm_config = get_slurm_config(
         wftask=wftask,
-        workflow_dir_local=workflow_dir_local,
-        workflow_dir_remote=workflow_dir_remote,
         which_type=which_type,
     )
 

fractal_server/config.py

@@ -546,7 +546,9 @@ class Settings(BaseSettings):
     attribute in their input-arguments JSON file.
     """
 
-    FRACTAL_API_V1_MODE: Literal["include", "exclude"] = "include"
+    FRACTAL_API_V1_MODE: Literal[
+        "include", "include_without_submission", "exclude"
+    ] = "include"
     """
     Whether to include the v1 API.
     """
@@ -685,6 +687,25 @@ class Settings(BaseSettings):
         self.check_db()
         self.check_runner()
 
+    def get_sanitized(self) -> dict:
+        def _must_be_sanitized(string) -> bool:
+            if not string.upper().startswith("FRACTAL") or any(
+                s in string.upper()
+                for s in ["PASSWORD", "SECRET", "PWD", "TOKEN"]
+            ):
+                return True
+            else:
+                return False
+
+        sanitized_settings = {}
+        for k, v in self.dict().items():
+            if _must_be_sanitized(k):
+                sanitized_settings[k] = "***"
+            else:
+                sanitized_settings[k] = v
+
+        return sanitized_settings
+
 
 def get_settings(settings=Settings()) -> Settings:
     return settings

fractal_server/main.py

@@ -49,7 +49,7 @@ def collect_routers(app: FastAPI) -> None:
     settings = Inject(get_settings)
 
     app.include_router(router_api, prefix="/api")
-    if settings.FRACTAL_API_V1_MODE == "include":
+    if settings.FRACTAL_API_V1_MODE.startswith("include"):
         app.include_router(router_api_v1, prefix="/api/v1")
         app.include_router(
             router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]

fractal_server/ssh/_fabric.py

@@ -306,6 +306,28 @@ class FractalSSH(object):
             cmd = f"rm -r {folder}"
             self.run_command(cmd=cmd)
 
+    def write_remote_file(
+        self,
+        *,
+        path: str,
+        content: str,
+        lock_timeout: Optional[float] = None,
+    ) -> None:
+        """
+        Open a remote file via SFTP and write it.
+
+        Args:
+            path: Absolute path
+            contents: File contents
+            lock_timeout:
+        """
+        actual_lock_timeout = self.default_lock_timeout
+        if lock_timeout is not None:
+            actual_lock_timeout = lock_timeout
+        with self.acquire_timeout(timeout=actual_lock_timeout):
+            with self.sftp().open(filename=path, mode="w") as f:
+                f.write(content)
+
 
 def get_ssh_connection(
     *,

{fractal_server-2.3.3.dist-info → fractal_server-2.3.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.3
+Version: 2.3.5
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.3.3.dist-info → fractal_server-2.3.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=cbDFprg05SSdPI6GVzVSaFJyKMlLMr-cn7_vn5ISPN4,22
+fractal_server/__init__.py,sha256=RqyrrNV86fgXA3ZGY013Ddl0XCyYA-YaiOneKISOYXc,22
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -25,12 +25,12 @@ fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJW
 fractal_server/app/routes/admin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/v1.py,sha256=ShmsUFtfyRqP84QScqmRDVrJFpbR4p-8baLxAkI3n1U,13926
 fractal_server/app/routes/admin/v2.py,sha256=JuG1qqVeQIgVJgPyqrB1053il22mGPGpKBiJi6zVsqQ,13687
-fractal_server/app/routes/api/__init__.py,sha256=EVyZrEq3I_1643QGTPCC5lgCp4xH_auYbrFfogTm4pc,315
+fractal_server/app/routes/api/__init__.py,sha256=XlJUFd-0FossfyKyJti4dmwY6SMysQn1yiisMrNzgBE,615
 fractal_server/app/routes/api/v1/__init__.py,sha256=Y2HQdG197J0a7DyQEE2jn53IfxD0EHGhzK1I2JZuEck,958
 fractal_server/app/routes/api/v1/_aux_functions.py,sha256=CeaVrNVYs_lEbiJbu4uaTeeiajljeXfdq1iLkt5RoRo,12636
 fractal_server/app/routes/api/v1/dataset.py,sha256=HRE-8vPmVkeXf7WFYkI19mDtbY-iJZeJ7PmMiV0LMgY,16923
 fractal_server/app/routes/api/v1/job.py,sha256=217fGh7U37esib1JG8INpLhE0W88t9X0fFwCNVt2r_M,5313
-fractal_server/app/routes/api/v1/project.py,sha256=MxbJUc9H14ZZ8mmMbX3LXGTVR3sHdD26YSw4TKI7WtU,16108
+fractal_server/app/routes/api/v1/project.py,sha256=0DavnACBDr8-BHWGQ0YPfxVNJLsYmbuo-TeKJk1s3Hw,16436
 fractal_server/app/routes/api/v1/task.py,sha256=udbKnenzc-Q10elYCVB9JmOPWATraa9tZi0AaByvWo0,6129
 fractal_server/app/routes/api/v1/task_collection.py,sha256=82XBsJHlPiDPCbpLa-16ojKDpj2LYj9_jFSZt0t58bQ,8911
 fractal_server/app/routes/api/v1/workflow.py,sha256=7r9IoIevg_rvYCrerMOsIsUabSOQatxdPCfLdkP0dRs,10942
@@ -57,24 +57,25 @@ fractal_server/app/runner/.gitignore,sha256=ytzN_oyHWXrGU7iFAtoHSTUbM6Rn6kG0Zkdd
 fractal_server/app/runner/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/async_wrap.py,sha256=_O6f8jftKYXG_DozkmlrDBhoiK9QhE9MablOyECq2_M,829
 fractal_server/app/runner/components.py,sha256=ZF8ct_Ky5k8IAcrmpYOZ-bc6OBgdELEighYVqFDEbZg,119
-fractal_server/app/runner/compress_folder.py,sha256=6UD9qo-ssPp6OBAZpQuCypJNINamzN5JVkyvqB2b9jU,3717
+fractal_server/app/runner/compress_folder.py,sha256=zmxo2EFkSaO4h3GnMRi9DYaf62bxy4zznZZGfmq-n68,3975
 fractal_server/app/runner/exceptions.py,sha256=_qZ_t8O4umAdJ1ikockiF5rDJuxnEskrGrLjZcnQl7A,4159
 fractal_server/app/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm/_batching.py,sha256=3mfeFuYm3UA4EXh4VWuqZTF-dcINECZgTHoPOaOszDo,8840
-fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=KtLQ5l_wmWcrSPVrG9nugzgjRKmycmSOkVrkTR0I7Rs,15660
+fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=iyhtDi1qveqq7I4S1tycVKsp3VfyocvBgGugYDpOzAs,16069
 fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77JRK82g_2hx0iBKTiMghuIo,5852
 fractal_server/app/runner/executors/slurm/ssh/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py,sha256=jM4G-wiHynZhNERusVGLtDTepJDiYjCDloWZyflaMV0,3482
 fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py,sha256=rwlqZzoGo4SAb4nSlFjsQJdaCgfM1J6YGcjb8yYxlqc,4506
-fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=FMS0lvb9-pPk8mTkgfLDwljnKq2J_yDqpwth9GZmOOM,55475
+fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=rfLEO6mN3sZvZYHqs3lmYvPYFGLmXyMPWl1Bg0mq-6k,56109
 fractal_server/app/runner/executors/slurm/sudo/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/sudo/_check_jobs_status.py,sha256=wAgwpVcr6JIslKHOuS0FhRa_6T1KCManyRJqA-fifzw,1909
 fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py,sha256=z5LlhaiqAb8pHsF1WwdzXN39C5anQmwjo1rSQgtRAYE,4422
 fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py,sha256=uZgmxP0ZneGpzTVt-GT-6EgNKUh1sW2-QH7LFYc1tNI,5132
-fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=nu1mcg3veOEaDwqPLyrf9_pMUc34-uXhd8er3IsMQZw,48236
-fractal_server/app/runner/extract_archive.py,sha256=JDK6wtTFdE7Cf1kGaJajLxNoMmhzweP6YyxdPCm65fc,1095
+fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=74jfNauDgQOdcILHcCLJM4Awm_SThsZYgc0Vwx0hnB8,48460
+fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
+fractal_server/app/runner/run_subprocess.py,sha256=KTkJnWLrLQdR2WRJ3jGu0RBu4330L3mtCAE_B0wDx3M,818
 fractal_server/app/runner/set_start_and_last_task_index.py,sha256=-q4zVybAj8ek2XlbENKlfOAJ39hT_zoJoZkqzDqiAMY,1254
 fractal_server/app/runner/shutdown.py,sha256=I_o2iYKJwzku0L3E85ETjrve3QPECygR5xhhsAo5huM,2910
 fractal_server/app/runner/task_files.py,sha256=sd_MpJ01C8c9QTO8GzGMidFGdlq_hXX_ARDRhd_YMnI,3762
@@ -89,7 +90,7 @@ fractal_server/app/runner/v1/_slurm/_submit_setup.py,sha256=KO9c694d318adoPQh9UG
 fractal_server/app/runner/v1/_slurm/get_slurm_config.py,sha256=6pQNNx997bLIfLp0guF09t_O0ZYRXnbEGLktSAcKnic,5999
 fractal_server/app/runner/v1/common.py,sha256=_L-vjLnWato80VdlB_BFN4G8P4jSM07u-5cnl1T3S34,3294
 fractal_server/app/runner/v1/handle_failed_job.py,sha256=bHzScC_aIlU3q-bQxGW6rfWV4xbZ2tho_sktjsAs1no,4684
-fractal_server/app/runner/v2/__init__.py,sha256=AFX2TiHfu8vAugvILz484ps4ehZpVHmc3kXGtbhi2zE,16912
+fractal_server/app/runner/v2/__init__.py,sha256=nD4uFi-RGsN6JAmJNpV2dS603u8KqFuGwXZS8jIrf50,16917
 fractal_server/app/runner/v2/_local/__init__.py,sha256=KTj14K6jH8fXGUi5P7u5_RqEE1zF4aXtgPxCKzw46iw,5971
 fractal_server/app/runner/v2/_local/_local_config.py,sha256=9oi209Dlp35ANfxb_DISqmMKKc6DPaMsmYVWbZLseME,3630
 fractal_server/app/runner/v2/_local/_submit_setup.py,sha256=MucNOo8Er0F5ZIwH7CnTeXgnFMc6d3pKPkv563QNVi0,1630
@@ -98,12 +99,12 @@ fractal_server/app/runner/v2/_local_experimental/__init__.py,sha256=53yS8a-l0dMT
 fractal_server/app/runner/v2/_local_experimental/_local_config.py,sha256=QiS5ODe-iGmUQdIT8QgpbyMc7-ZpIRv1V_f2q3qfPQ8,3211
 fractal_server/app/runner/v2/_local_experimental/_submit_setup.py,sha256=we7r-sQf0CJ9gxbfbgHcYdC6pKjx8eXweljIjthxkv8,1212
 fractal_server/app/runner/v2/_local_experimental/executor.py,sha256=vcBKjireIIyF5WgIQLatD6ojlWEydbTwyIG0bcpIjys,5438
-fractal_server/app/runner/v2/_slurm/__init__.py,sha256=q2fwiKqtNpXtfs5wUFQjwJxdYqKPPTbCy1ieBhhi-Bw,4316
-fractal_server/app/runner/v2/_slurm/_submit_setup.py,sha256=rvhMOK1QkqsxVWUvekT62KbDDlqpw49nq9mzQXSY3H0,2883
-fractal_server/app/runner/v2/_slurm/get_slurm_config.py,sha256=btGmbZB0fO6bg2WujFxbGEV2iWzaMKbHgV1r2hm_4a0,6748
+fractal_server/app/runner/v2/_slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py,sha256=V47uckqA4Vp-7m5esDnTitekc-yabLhaZSlPj4jN_D8,6307
 fractal_server/app/runner/v2/_slurm_ssh/__init__.py,sha256=1p6d_ppXBqRNPXPGxM8cmIOffEsfkEPEfvDeT-_90dE,3990
-fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py,sha256=rvhMOK1QkqsxVWUvekT62KbDDlqpw49nq9mzQXSY3H0,2883
-fractal_server/app/runner/v2/_slurm_ssh/get_slurm_config.py,sha256=ZK_yvZhe-nzMAvg54JB6TcaCBplKD9vje92m5-cTxsI,6801
+fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py,sha256=a5_FDPH_yxYmrjAjMRLgh_Y4DSG3mRslCLQodGM3-t4,2838
+fractal_server/app/runner/v2/_slurm_sudo/__init__.py,sha256=q2fwiKqtNpXtfs5wUFQjwJxdYqKPPTbCy1ieBhhi-Bw,4316
+fractal_server/app/runner/v2/_slurm_sudo/_submit_setup.py,sha256=a5_FDPH_yxYmrjAjMRLgh_Y4DSG3mRslCLQodGM3-t4,2838
 fractal_server/app/runner/v2/deduplicate_list.py,sha256=-imwO7OB7ATADEnqVbTElUwoY0YIJCTf_SbWJNN9OZg,639
 fractal_server/app/runner/v2/handle_failed_job.py,sha256=M1r3dnrbUMo_AI2qjaVuGhieMAyLh5gcvB10YOBpjvI,5415
 fractal_server/app/runner/v2/merge_outputs.py,sha256=IHuHqbKmk97K35BFvTrKVBs60z3e_--OzXTnsvmA02c,1281
@@ -138,14 +139,14 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=8PG1bOqkfQqORMN0brWf6mHD
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=atVuVN4aXsVEOmSd-vyg-8_8OnPmqx-gT75rXcn_AlQ,6552
 fractal_server/app/security/__init__.py,sha256=2-QbwuR-nsuHM_uwKS_WzYvkhnuhO5jUv8UVROetyVk,11169
-fractal_server/config.py,sha256=LoN530DB9Xxey-riV2BNgUcKEDquMrH9ijuRrwl7TMk,24284
+fractal_server/config.py,sha256=KOa2jrsbx0H6zG2ItNZkLiKqbuOkV3aUYKFuIN3FIyE,24921
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/gunicorn_fractal.py,sha256=2AOkgxu-oQ-XB578_voT0VuhmAXFTmb0c-nYn1XLy_Q,1231
 fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
 fractal_server/images/models.py,sha256=9ipU5h4N6ogBChoB-2vHoqtL0TXOHCv6kRR-fER3mkM,4167
 fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLiY,2209
 fractal_server/logger.py,sha256=56wfka6fHaa3Rx5qO009nEs_y8gx5wZ2NUNZZ1I-uvc,5130
-fractal_server/main.py,sha256=CTWA_EJBaSO7hty6AdAenFQjbNE4Chr1U-sZ2qsPDmw,5289
+fractal_server/main.py,sha256=Kmty1C9jPfH101nP3b82u9H9QvT-5Z-8Dd60wf9S5h0,5298
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
 fractal_server/migrations/env.py,sha256=Bvg-FJzRJZIH_wqS_ZyZNXANIaathjo22_IY7c3fCjo,2636
 fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
@@ -167,7 +168,7 @@ fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
 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=4B6D0F2bWWho1V_xdDDBWYAHno9h_6Smp7_FP2n8jYo,10739
+fractal_server/ssh/_fabric.py,sha256=9xcsOEwbCgbJtupkIeG8OOtT8ct8c7_ruIehhNmD4wc,11379
 fractal_server/string_tools.py,sha256=KThgTLn_FHNSuEUGLabryJAP6DaFd7bpi-hF5FgkBjw,1268
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
@@ -192,8 +193,8 @@ fractal_server/tasks/v2/templates/_5_pip_show.sh,sha256=GrJ19uHYQxANEy9JaeNJZVTq
 fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kqXRM,1657
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.3.3.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.3.3.dist-info/METADATA,sha256=He-pPtJu3dHSdXV-YYSsjeHbCHIYgMGPohJ67v-qIBQ,4425
-fractal_server-2.3.3.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.3.3.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.3.3.dist-info/RECORD,,
+fractal_server-2.3.5.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.3.5.dist-info/METADATA,sha256=dElt7KKeyH2IIRToMdsTiVKeIEww0ZsbFzlQcCskrKE,4425
+fractal_server-2.3.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.3.5.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.3.5.dist-info/RECORD,,

fractal_server/app/runner/v2/_slurm/get_slurm_config.py

@@ -1,182 +0,0 @@
-from pathlib import Path
-from typing import Literal
-from typing import Optional
-
-from fractal_server.app.models.v2 import WorkflowTaskV2
-from fractal_server.app.runner.executors.slurm._slurm_config import (
-    _parse_mem_value,
-)
-from fractal_server.app.runner.executors.slurm._slurm_config import (
-    load_slurm_config_file,
-)
-from fractal_server.app.runner.executors.slurm._slurm_config import logger
-from fractal_server.app.runner.executors.slurm._slurm_config import SlurmConfig
-from fractal_server.app.runner.executors.slurm._slurm_config import (
-    SlurmConfigError,
-)
-
-
-def get_slurm_config(
-    wftask: WorkflowTaskV2,
-    workflow_dir_local: Path,
-    workflow_dir_remote: Path,
-    which_type: Literal["non_parallel", "parallel"],
-    config_path: Optional[Path] = None,
-) -> SlurmConfig:
-    """
-    Prepare a `SlurmConfig` configuration object
-
-    The argument `which_type` determines whether we use `wftask.meta_parallel`
-    or `wftask.meta_non_parallel`. In the following descritpion, let us assume
-    that `which_type="parallel"`.
-
-    The sources for `SlurmConfig` attributes, in increasing priority order, are
-
-    1. The general content of the Fractal SLURM configuration file.
-    2. The GPU-specific content of the Fractal SLURM configuration file, if
-        appropriate.
-    3. Properties in `wftask.meta_parallel` (which typically include those in
-       `wftask.task.meta_parallel`). Note that `wftask.meta_parallel` may be
-       `None`.
-
-    Arguments:
-        wftask:
-            WorkflowTask for which the SLURM configuration is is to be
-            prepared.
-        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.
-        config_path:
-            Path of a Fractal SLURM configuration file; if `None`, use
-            `FRACTAL_SLURM_CONFIG_FILE` variable from settings.
-        which_type:
-            Determines whether to use `meta_parallel` or `meta_non_parallel`.
-
-    Returns:
-        slurm_config:
-            The SlurmConfig object
-    """
-
-    if which_type == "non_parallel":
-        wftask_meta = wftask.meta_non_parallel
-    elif which_type == "parallel":
-        wftask_meta = wftask.meta_parallel
-    else:
-        raise ValueError(
-            f"get_slurm_config received invalid argument {which_type=}."
-        )
-
-    logger.debug(
-        "[get_slurm_config] WorkflowTask meta attribute: {wftask_meta=}"
-    )
-
-    # Incorporate slurm_env.default_slurm_config
-    slurm_env = load_slurm_config_file(config_path=config_path)
-    slurm_dict = slurm_env.default_slurm_config.dict(
-        exclude_unset=True, exclude={"mem"}
-    )
-    if slurm_env.default_slurm_config.mem:
-        slurm_dict["mem_per_task_MB"] = slurm_env.default_slurm_config.mem
-
-    # Incorporate slurm_env.batching_config
-    for key, value in slurm_env.batching_config.dict().items():
-        slurm_dict[key] = value
-
-    # Incorporate slurm_env.user_local_exports
-    slurm_dict["user_local_exports"] = slurm_env.user_local_exports
-
-    logger.debug(
-        "[get_slurm_config] Fractal SLURM configuration file: "
-        f"{slurm_env.dict()=}"
-    )
-
-    # GPU-related options
-    # Notes about priority:
-    # 1. This block of definitions takes priority over other definitions from
-    #    slurm_env which are not under the `needs_gpu` subgroup
-    # 2. This block of definitions has lower priority than whatever comes next
-    #    (i.e. from WorkflowTask.meta).
-    if wftask_meta is not None:
-        needs_gpu = wftask_meta.get("needs_gpu", False)
-    else:
-        needs_gpu = False
-    logger.debug(f"[get_slurm_config] {needs_gpu=}")
-    if needs_gpu:
-        for key, value in slurm_env.gpu_slurm_config.dict(
-            exclude_unset=True, exclude={"mem"}
-        ).items():
-            slurm_dict[key] = value
-        if slurm_env.gpu_slurm_config.mem:
-            slurm_dict["mem_per_task_MB"] = slurm_env.gpu_slurm_config.mem
-
-    # Number of CPUs per task, for multithreading
-    if wftask_meta is not None and "cpus_per_task" in wftask_meta:
-        cpus_per_task = int(wftask_meta["cpus_per_task"])
-        slurm_dict["cpus_per_task"] = cpus_per_task
-
-    # Required memory per task, in MB
-    if wftask_meta is not None and "mem" in wftask_meta:
-        raw_mem = wftask_meta["mem"]
-        mem_per_task_MB = _parse_mem_value(raw_mem)
-        slurm_dict["mem_per_task_MB"] = mem_per_task_MB
-
-    # Job name
-    if wftask.is_legacy_task:
-        job_name = wftask.task_legacy.name.replace(" ", "_")
-    else:
-        job_name = wftask.task.name.replace(" ", "_")
-    slurm_dict["job_name"] = job_name
-
-    # Optional SLURM arguments and extra lines
-    if wftask_meta is not None:
-        account = wftask_meta.get("account", None)
-        if account is not None:
-            error_msg = (
-                f"Invalid {account=} property in WorkflowTask `meta` "
-                "attribute.\n"
-                "SLURM account must be set in the request body of the "
-                "apply-workflow endpoint, or by modifying the user properties."
-            )
-            logger.error(error_msg)
-            raise SlurmConfigError(error_msg)
-        for key in ["time", "gres", "constraint"]:
-            value = wftask_meta.get(key, None)
-            if value:
-                slurm_dict[key] = value
-    if wftask_meta is not None:
-        extra_lines = wftask_meta.get("extra_lines", [])
-    else:
-        extra_lines = []
-    extra_lines = slurm_dict.get("extra_lines", []) + extra_lines
-    if len(set(extra_lines)) != len(extra_lines):
-        logger.debug(
-            "[get_slurm_config] Removing repeated elements "
-            f"from {extra_lines=}."
-        )
-        extra_lines = list(set(extra_lines))
-    slurm_dict["extra_lines"] = extra_lines
-
-    # Job-batching parameters (if None, they will be determined heuristically)
-    if wftask_meta is not None:
-        tasks_per_job = wftask_meta.get("tasks_per_job", None)
-        parallel_tasks_per_job = wftask_meta.get(
-            "parallel_tasks_per_job", None
-        )
-    else:
-        tasks_per_job = None
-        parallel_tasks_per_job = None
-    slurm_dict["tasks_per_job"] = tasks_per_job
-    slurm_dict["parallel_tasks_per_job"] = parallel_tasks_per_job
-
-    # Put everything together
-    logger.debug(
-        "[get_slurm_config] Now create a SlurmConfig object based "
-        f"on {slurm_dict=}"
-    )
-    slurm_config = SlurmConfig(**slurm_dict)
-
-    return slurm_config