fractal-server 2.9.0a11__py3-none-any.whl → 2.9.1__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.9.0a11"
+__VERSION__ = "2.9.1"

fractal_server/app/routes/auth/group.py

@@ -10,6 +10,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from sqlmodel import select
 
 from . import current_active_superuser
+from ._aux_auth import _get_default_usergroup_id
 from ._aux_auth import _get_single_usergroup_with_user_ids
 from ._aux_auth import _user_or_404
 from ._aux_auth import _usergroup_or_404
@@ -234,16 +235,35 @@ async def remove_user_from_group(
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
+
+    # Check that user and group exist
     await _usergroup_or_404(group_id, db)
     user = await _user_or_404(user_id, db)
+
+    # Check that group is not the default one
+    default_user_group_id = await _get_default_usergroup_id(db=db)
+    if default_user_group_id == group_id:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                f"Cannot remove user from '{FRACTAL_DEFAULT_GROUP_NAME}' "
+                "group.",
+            ),
+        )
+
     link = await db.get(LinkUserGroup, (group_id, user_id))
     if link is None:
+        # If user and group are not linked, fail
         raise HTTPException(
             status_code=422,
             detail=f"User '{user.email}' is not a member of group {group_id}.",
         )
     else:
+        # If user and group are linked, delete the link
         await db.delete(link)
         await db.commit()
+
+    # Enrich the response object with user_ids
     group = await _get_single_usergroup_with_user_ids(group_id=group_id, db=db)
+
     return group

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

@@ -456,20 +456,3 @@ def _parse_mem_value(raw_mem: Union[str, int]) -> int:
 
     logger.debug(f"{info}, return {mem_MB}")
     return mem_MB
-
-
-def get_default_slurm_config():
-    """
-    Return a default `SlurmConfig` configuration object
-    """
-    return SlurmConfig(
-        partition="main",
-        cpus_per_task=1,
-        mem_per_task_MB=100,
-        target_cpus_per_job=1,
-        max_cpus_per_job=2,
-        target_mem_per_job=100,
-        max_mem_per_job=500,
-        target_num_jobs=2,
-        max_num_jobs=4,
-    )

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

@@ -31,9 +31,11 @@ from ....filenames import SHUTDOWN_FILENAME
 from ....task_files import get_task_file_paths
 from ....task_files import TaskFiles
 from ....versions import get_versions
-from ...slurm._slurm_config import get_default_slurm_config
 from ...slurm._slurm_config import SlurmConfig
 from .._batching import heuristics
+from ..utils_executors import get_pickle_file_path
+from ..utils_executors import get_slurm_file_path
+from ..utils_executors import get_slurm_script_file_path
 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
@@ -223,132 +225,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         with self.jobs_lock:
             self.map_jobid_to_slurm_files_local.pop(jobid)
 
-    def get_input_pickle_file_path_local(
-        self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-
-        prefix = prefix or "cfut"
-        output = (
-            self.workflow_dir_local
-            / subfolder_name
-            / f"{prefix}_in_{arg}.pickle"
-        )
-        return output
-
-    def get_input_pickle_file_path_remote(
-        self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-
-        prefix = prefix or "cfut"
-        output = (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_in_{arg}.pickle"
-        )
-        return output
-
-    def get_output_pickle_file_path_local(
-        self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-        prefix = prefix or "cfut"
-        return (
-            self.workflow_dir_local
-            / subfolder_name
-            / f"{prefix}_out_{arg}.pickle"
-        )
-
-    def get_output_pickle_file_path_remote(
-        self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-        prefix = prefix or "cfut"
-        return (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_out_{arg}.pickle"
-        )
-
-    def get_slurm_script_file_path_local(
-        self, *, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-        prefix = prefix or "_temp"
-        return (
-            self.workflow_dir_local
-            / subfolder_name
-            / f"{prefix}_slurm_submit.sbatch"
-        )
-
-    def get_slurm_script_file_path_remote(
-        self, *, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-        prefix = prefix or "_temp"
-        return (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_slurm_submit.sbatch"
-        )
-
-    def get_slurm_stdout_file_path_local(
-        self,
-        *,
-        subfolder_name: str,
-        arg: str = "%j",
-        prefix: Optional[str] = None,
-    ) -> Path:
-        prefix = prefix or "slurmpy.stdout"
-        return (
-            self.workflow_dir_local
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.out"
-        )
-
-    def get_slurm_stdout_file_path_remote(
-        self,
-        *,
-        subfolder_name: str,
-        arg: str = "%j",
-        prefix: Optional[str] = None,
-    ) -> Path:
-        prefix = prefix or "slurmpy.stdout"
-        return (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.out"
-        )
-
-    def get_slurm_stderr_file_path_local(
-        self,
-        *,
-        subfolder_name: str,
-        arg: str = "%j",
-        prefix: Optional[str] = None,
-    ) -> Path:
-        prefix = prefix or "slurmpy.stderr"
-        return (
-            self.workflow_dir_local
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.err"
-        )
-
-    def get_slurm_stderr_file_path_remote(
-        self,
-        *,
-        subfolder_name: str,
-        arg: str = "%j",
-        prefix: Optional[str] = None,
-    ) -> Path:
-        prefix = prefix or "slurmpy.stderr"
-        return (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.err"
-        )
-
     def submit(
         self,
         fun: Callable[..., Any],
         *fun_args: Sequence[Any],
-        slurm_config: Optional[SlurmConfig] = None,
-        task_files: Optional[TaskFiles] = None,
+        slurm_config: SlurmConfig,
+        task_files: TaskFiles,
         **fun_kwargs: dict,
     ) -> Future:
         """
@@ -359,11 +241,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             fun_args: Function positional arguments
             fun_kwargs: Function keyword arguments
             slurm_config:
-                A `SlurmConfig` object; if `None`, use
-                `get_default_slurm_config()`.
+                A `SlurmConfig` object.
             task_files:
-                A `TaskFiles` object; if `None`, use
-                `self.get_default_task_files()`.
+                A `TaskFiles` object.
 
         Returns:
             Future representing the execution of the current SLURM job.
@@ -375,12 +255,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             logger.warning(error_msg)
             raise JobExecutionError(info=error_msg)
 
-        # Set defaults, if needed
-        if slurm_config is None:
-            slurm_config = get_default_slurm_config()
-        if task_files is None:
-            task_files = self.get_default_task_files()
-
         # Set slurm_file_prefix
         slurm_file_prefix = task_files.file_prefix
 
@@ -418,8 +292,8 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         fn: Callable[..., Any],
         iterable: list[Sequence[Any]],
         *,
-        slurm_config: Optional[SlurmConfig] = None,
-        task_files: Optional[TaskFiles] = None,
+        slurm_config: SlurmConfig,
+        task_files: TaskFiles,
     ):
         """
         Return an iterator with the results of several execution of a function
@@ -442,12 +316,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
                 An iterable such that each element is the list of arguments to
                 be passed to `fn`, as in `fn(*args)`.
             slurm_config:
-                A `SlurmConfig` object; if `None`, use
-                `get_default_slurm_config()`.
+                A `SlurmConfig` object.
             task_files:
-                A `TaskFiles` object; if `None`, use
-                `self.get_default_task_files()`.
-
+                A `TaskFiles` object.
         """
 
         # Do not continue if auxiliary thread was shut down
@@ -472,12 +343,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
                 # self._exception
                 del fut
 
-        # Set defaults, if needed
-        if not slurm_config:
-            slurm_config = get_default_slurm_config()
-        if task_files is None:
-            task_files = self.get_default_task_files()
-
         # Include common_script_lines in extra_lines
         logger.debug(
             f"Adding {self.common_script_lines=} to "
@@ -710,63 +575,80 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
                 f"Missing folder {subfolder_path.as_posix()}."
             )
 
-        # Define I/O pickle file local/remote paths
         job.input_pickle_files_local = tuple(
-            self.get_input_pickle_file_path_local(
+            get_pickle_file_path(
                 arg=job.workerids[ind],
+                workflow_dir=self.workflow_dir_local,
                 subfolder_name=job.wftask_subfolder_name,
+                in_or_out="in",
                 prefix=job.wftask_file_prefixes[ind],
             )
             for ind in range(job.num_tasks_tot)
         )
+
         job.input_pickle_files_remote = tuple(
-            self.get_input_pickle_file_path_remote(
+            get_pickle_file_path(
                 arg=job.workerids[ind],
+                workflow_dir=self.workflow_dir_remote,
                 subfolder_name=job.wftask_subfolder_name,
+                in_or_out="in",
                 prefix=job.wftask_file_prefixes[ind],
             )
             for ind in range(job.num_tasks_tot)
         )
         job.output_pickle_files_local = tuple(
-            self.get_output_pickle_file_path_local(
+            get_pickle_file_path(
                 arg=job.workerids[ind],
+                workflow_dir=self.workflow_dir_local,
                 subfolder_name=job.wftask_subfolder_name,
+                in_or_out="out",
                 prefix=job.wftask_file_prefixes[ind],
             )
             for ind in range(job.num_tasks_tot)
         )
         job.output_pickle_files_remote = tuple(
-            self.get_output_pickle_file_path_remote(
+            get_pickle_file_path(
                 arg=job.workerids[ind],
+                workflow_dir=self.workflow_dir_remote,
                 subfolder_name=job.wftask_subfolder_name,
+                in_or_out="out",
                 prefix=job.wftask_file_prefixes[ind],
             )
             for ind in range(job.num_tasks_tot)
         )
-
-        # Define SLURM-job file local/remote paths
-        job.slurm_script_local = self.get_slurm_script_file_path_local(
+        # define slurm-job file local/remote paths
+        job.slurm_script_local = get_slurm_script_file_path(
+            workflow_dir=self.workflow_dir_local,
             subfolder_name=job.wftask_subfolder_name,
             prefix=job.slurm_file_prefix,
         )
-        job.slurm_script_remote = self.get_slurm_script_file_path_remote(
+        job.slurm_script_remote = get_slurm_script_file_path(
+            workflow_dir=self.workflow_dir_remote,
             subfolder_name=job.wftask_subfolder_name,
             prefix=job.slurm_file_prefix,
         )
-        job.slurm_stdout_local = self.get_slurm_stdout_file_path_local(
+        job.slurm_stdout_local = get_slurm_file_path(
+            workflow_dir=self.workflow_dir_local,
             subfolder_name=job.wftask_subfolder_name,
+            out_or_err="out",
             prefix=job.slurm_file_prefix,
         )
-        job.slurm_stdout_remote = self.get_slurm_stdout_file_path_remote(
+        job.slurm_stdout_remote = get_slurm_file_path(
+            workflow_dir=self.workflow_dir_remote,
             subfolder_name=job.wftask_subfolder_name,
+            out_or_err="out",
             prefix=job.slurm_file_prefix,
         )
-        job.slurm_stderr_local = self.get_slurm_stderr_file_path_local(
+        job.slurm_stderr_local = get_slurm_file_path(
+            workflow_dir=self.workflow_dir_local,
             subfolder_name=job.wftask_subfolder_name,
+            out_or_err="err",
             prefix=job.slurm_file_prefix,
         )
-        job.slurm_stderr_remote = self.get_slurm_stderr_file_path_remote(
+        job.slurm_stderr_remote = get_slurm_file_path(
+            workflow_dir=self.workflow_dir_remote,
             subfolder_name=job.wftask_subfolder_name,
+            out_or_err="err",
             prefix=job.slurm_file_prefix,
         )
 
@@ -1294,7 +1176,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         slurm_err_path: str,
         slurm_config: SlurmConfig,
     ):
-
         num_tasks_max_running = slurm_config.parallel_tasks_per_job
         mem_per_task_MB = slurm_config.mem_per_task_MB
 
@@ -1346,19 +1227,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         script = "\n".join(script_lines)
         return script
 
-    def get_default_task_files(self) -> TaskFiles:
-        """
-        This will be called when self.submit or self.map are called from
-        outside fractal-server, and then lack some optional arguments.
-        """
-        task_files = TaskFiles(
-            workflow_dir_local=self.workflow_dir_local,
-            workflow_dir_remote=self.workflow_dir_remote,
-            task_order=None,
-            task_name="name",
-        )
-        return task_files
-
     def shutdown(self, wait=True, *, cancel_futures=False):
         """
         Clean up all executor variables. Note that this function is executed on

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

@@ -37,9 +37,11 @@ from ....exceptions import TaskExecutionError
 from ....filenames import SHUTDOWN_FILENAME
 from ....task_files import get_task_file_paths
 from ....task_files import TaskFiles
-from ...slurm._slurm_config import get_default_slurm_config
 from ...slurm._slurm_config import SlurmConfig
 from .._batching import heuristics
+from ..utils_executors import get_pickle_file_path
+from ..utils_executors import get_slurm_file_path
+from ..utils_executors import get_slurm_script_file_path
 from ._executor_wait_thread import FractalSlurmWaitThread
 from ._subprocess_run_as_user import _glob_as_user
 from ._subprocess_run_as_user import _glob_as_user_strict
@@ -305,72 +307,12 @@ class FractalSlurmExecutor(SlurmExecutor):
         with self.jobs_lock:
             self.map_jobid_to_slurm_files.pop(jobid)
 
-    def get_input_pickle_file_path(
-        self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-
-        prefix = prefix or "cfut"
-        output = (
-            self.workflow_dir_local
-            / subfolder_name
-            / f"{prefix}_in_{arg}.pickle"
-        )
-        return output
-
-    def get_output_pickle_file_path(
-        self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-        prefix = prefix or "cfut"
-        return (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_out_{arg}.pickle"
-        )
-
-    def get_slurm_script_file_path(
-        self, *, subfolder_name: str, prefix: Optional[str] = None
-    ) -> Path:
-        prefix = prefix or "_temp"
-        return (
-            self.workflow_dir_local
-            / subfolder_name
-            / f"{prefix}_slurm_submit.sbatch"
-        )
-
-    def get_slurm_stdout_file_path(
-        self,
-        *,
-        subfolder_name: str,
-        arg: str = "%j",
-        prefix: Optional[str] = None,
-    ) -> Path:
-        prefix = prefix or "slurmpy.stdout"
-        return (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.out"
-        )
-
-    def get_slurm_stderr_file_path(
-        self,
-        *,
-        subfolder_name: str,
-        arg: str = "%j",
-        prefix: Optional[str] = None,
-    ) -> Path:
-        prefix = prefix or "slurmpy.stderr"
-        return (
-            self.workflow_dir_remote
-            / subfolder_name
-            / f"{prefix}_slurm_{arg}.err"
-        )
-
     def submit(
         self,
         fun: Callable[..., Any],
         *fun_args: Sequence[Any],
-        slurm_config: Optional[SlurmConfig] = None,
-        task_files: Optional[TaskFiles] = None,
+        slurm_config: SlurmConfig,
+        task_files: TaskFiles,
         **fun_kwargs: dict,
     ) -> Future:
         """
@@ -381,22 +323,14 @@ class FractalSlurmExecutor(SlurmExecutor):
             fun_args: Function positional arguments
             fun_kwargs: Function keyword arguments
             slurm_config:
-                A `SlurmConfig` object; if `None`, use
-                `get_default_slurm_config()`.
+                A `SlurmConfig` object.
             task_files:
-                A `TaskFiles` object; if `None`, use
-                `self.get_default_task_files()`.
+                A `TaskFiles` object.
 
         Returns:
             Future representing the execution of the current SLURM job.
         """
 
-        # Set defaults, if needed
-        if slurm_config is None:
-            slurm_config = get_default_slurm_config()
-        if task_files is None:
-            task_files = self.get_default_task_files()
-
         # Set slurm_file_prefix
         slurm_file_prefix = task_files.file_prefix
 
@@ -431,8 +365,8 @@ class FractalSlurmExecutor(SlurmExecutor):
         fn: Callable[..., Any],
         iterable: list[Sequence[Any]],
         *,
-        slurm_config: Optional[SlurmConfig] = None,
-        task_files: Optional[TaskFiles] = None,
+        slurm_config: SlurmConfig,
+        task_files: TaskFiles,
     ):
         """
         Return an iterator with the results of several execution of a function
@@ -455,11 +389,9 @@ class FractalSlurmExecutor(SlurmExecutor):
                 An iterable such that each element is the list of arguments to
                 be passed to `fn`, as in `fn(*args)`.
             slurm_config:
-                A `SlurmConfig` object; if `None`, use
-                `get_default_slurm_config()`.
+                A `SlurmConfig` object.
             task_files:
-                A `TaskFiles` object; if `None`, use
-                `self.get_default_task_files()`.
+                A `TaskFiles` object.
 
         """
 
@@ -479,12 +411,6 @@ class FractalSlurmExecutor(SlurmExecutor):
                 # self._exception
                 del fut
 
-        # Set defaults, if needed
-        if not slurm_config:
-            slurm_config = get_default_slurm_config()
-        if task_files is None:
-            task_files = self.get_default_task_files()
-
         # Include common_script_lines in extra_lines
         logger.debug(
             f"Adding {self.common_script_lines=} to "
@@ -700,39 +626,46 @@ class FractalSlurmExecutor(SlurmExecutor):
                 f"Missing folder {subfolder_path.as_posix()}."
             )
 
-        # Define I/O pickle file names/paths
         job.input_pickle_files = tuple(
-            self.get_input_pickle_file_path(
+            get_pickle_file_path(
                 arg=job.workerids[ind],
+                workflow_dir=self.workflow_dir_local,
                 subfolder_name=job.wftask_subfolder_name,
+                in_or_out="in",
                 prefix=job.wftask_file_prefixes[ind],
             )
             for ind in range(job.num_tasks_tot)
         )
         job.output_pickle_files = tuple(
-            self.get_output_pickle_file_path(
+            get_pickle_file_path(
                 arg=job.workerids[ind],
+                workflow_dir=self.workflow_dir_remote,
                 subfolder_name=job.wftask_subfolder_name,
+                in_or_out="out",
                 prefix=job.wftask_file_prefixes[ind],
             )
             for ind in range(job.num_tasks_tot)
         )
-
         # Define SLURM-job file names/paths
-        job.slurm_script = self.get_slurm_script_file_path(
+        job.slurm_script = get_slurm_script_file_path(
+            workflow_dir=self.workflow_dir_local,
             subfolder_name=job.wftask_subfolder_name,
             prefix=job.slurm_file_prefix,
         )
-        job.slurm_stdout = self.get_slurm_stdout_file_path(
+        job.slurm_stdout = get_slurm_file_path(
+            workflow_dir=self.workflow_dir_remote,
             subfolder_name=job.wftask_subfolder_name,
+            out_or_err="out",
             prefix=job.slurm_file_prefix,
         )
-        job.slurm_stderr = self.get_slurm_stderr_file_path(
+        job.slurm_stderr = get_slurm_file_path(
+            workflow_dir=self.workflow_dir_remote,
             subfolder_name=job.wftask_subfolder_name,
+            out_or_err="err",
             prefix=job.slurm_file_prefix,
         )
 
-        # Dump serialized versions+function+args+kwargs to pickle file
+        # Dump serialized versions+function+args+kwargs to pickle
         versions = dict(
             python=sys.version_info[:3],
             cloudpickle=cloudpickle.__version__,
@@ -824,7 +757,6 @@ class FractalSlurmExecutor(SlurmExecutor):
         """
         # Handle all uncaught exceptions in this broad try/except block
         try:
-
             # Retrieve job
             with self.jobs_lock:
                 try:
@@ -1039,7 +971,6 @@ class FractalSlurmExecutor(SlurmExecutor):
         )
 
         for prefix in prefixes:
-
             if prefix == job.slurm_file_prefix:
                 files_to_copy = _glob_as_user(
                     folder=str(self.workflow_dir_remote / subfolder_name),
@@ -1177,7 +1108,6 @@ class FractalSlurmExecutor(SlurmExecutor):
         slurm_err_path: str,
         slurm_config: SlurmConfig,
     ):
-
         num_tasks_max_running = slurm_config.parallel_tasks_per_job
         mem_per_task_MB = slurm_config.mem_per_task_MB
 
@@ -1229,19 +1159,6 @@ class FractalSlurmExecutor(SlurmExecutor):
         script = "\n".join(script_lines)
         return script
 
-    def get_default_task_files(self) -> TaskFiles:
-        """
-        This will be called when self.submit or self.map are called from
-        outside fractal-server, and then lack some optional arguments.
-        """
-        task_files = TaskFiles(
-            workflow_dir_local=self.workflow_dir_local,
-            workflow_dir_remote=self.workflow_dir_remote,
-            task_order=None,
-            task_name="name",
-        )
-        return task_files
-
     def shutdown(self, wait=True, *, cancel_futures=False):
         """
         Clean up all executor variables. Note that this function is executed on

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

@@ -0,0 +1,58 @@
+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/security/__init__.py

@@ -43,6 +43,9 @@ from fastapi_users.exceptions import UserAlreadyExists
 from fastapi_users.models import ID
 from fastapi_users.models import OAP
 from fastapi_users.models import UP
+from fastapi_users.password import PasswordHelper
+from pwdlib import PasswordHash
+from pwdlib.hashers.bcrypt import BcryptHasher
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 from sqlmodel import func
@@ -177,7 +180,21 @@ async def get_user_db(
     yield SQLModelUserDatabaseAsync(session, UserOAuth, OAuthAccount)
 
 
+password_hash = PasswordHash(hashers=(BcryptHasher(),))
+password_helper = PasswordHelper(password_hash=password_hash)
+
+
 class UserManager(IntegerIDMixin, BaseUserManager[UserOAuth, int]):
+    def __init__(self, user_db):
+        """
+        Override `__init__` of `BaseUserManager` to define custom
+        `password_helper`.
+        """
+        super().__init__(
+            user_db=user_db,
+            password_helper=password_helper,
+        )
+
     async def validate_password(self, password: str, user: UserOAuth) -> None:
         # check password length
         min_length = 4

fractal_server/tasks/v2/ssh/collect.py

@@ -69,7 +69,6 @@ def collect_ssh(
         )
 
         with next(get_sync_db()) as db:
-
             # Get main objects from db
             activity = db.get(TaskGroupActivityV2, task_group_activity_id)
             task_group = db.get(TaskGroupV2, task_group_id)
@@ -117,6 +116,25 @@ def collect_ssh(
                 return
 
             try:
+                script_dir_remote = (
+                    Path(task_group.path) / SCRIPTS_SUBFOLDER
+                ).as_posix()
+                # Create remote `task_group.path` and `script_dir_remote`
+                # folders (note that because of `parents=True` we  are in
+                # the `no error if existing, make parent directories as
+                # needed` scenario for `mkdir`)
+                fractal_ssh.mkdir(folder=task_group.path, parents=True)
+                fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
+
+                # Copy wheel file into task group path
+                if task_group.wheel_path:
+                    new_wheel_path = _copy_wheel_file_ssh(
+                        task_group=task_group,
+                        fractal_ssh=fractal_ssh,
+                        logger_name=LOGGER_NAME,
+                    )
+                    task_group.wheel_path = new_wheel_path
+                    task_group = add_commit_refresh(obj=task_group, db=db)
 
                 # Prepare replacements for templates
                 replacements = get_collection_replacements(
@@ -127,9 +145,6 @@ def collect_ssh(
                 )
 
                 # Prepare common arguments for `_customize_and_run_template``
-                script_dir_remote = (
-                    Path(task_group.path) / SCRIPTS_SUBFOLDER
-                ).as_posix()
                 common_args = dict(
                     replacements=replacements,
                     script_dir_local=(
@@ -144,23 +159,6 @@ def collect_ssh(
                     logger_name=LOGGER_NAME,
                 )
 
-                # Create remote `task_group.path` and `script_dir_remote`
-                # folders (note that because of `parents=True` we  are in
-                # the `no error if existing, make parent directories as
-                # needed` scenario for `mkdir`)
-                fractal_ssh.mkdir(folder=task_group.path, parents=True)
-                fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
-
-                # Copy wheel file into task group path
-                if task_group.wheel_path:
-                    new_wheel_path = _copy_wheel_file_ssh(
-                        task_group=task_group,
-                        fractal_ssh=fractal_ssh,
-                        logger_name=LOGGER_NAME,
-                    )
-                    task_group.wheel_path = new_wheel_path
-                    task_group = add_commit_refresh(obj=task_group, db=db)
-
                 logger.debug("installing - START")
 
                 # Set status to ONGOING and refresh logs

{fractal_server-2.9.0a11.dist-info → fractal_server-2.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.9.0a11
+Version: 2.9.1
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -13,12 +13,11 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: bcrypt (==4.0.1)
 Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)
 Requires-Dist: clusterfutures (>=0.5,<0.6)
 Requires-Dist: fabric (>=3.2.2,<4.0.0)
 Requires-Dist: fastapi (>=0.115.0,<0.116.0)
-Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
+Requires-Dist: fastapi-users[oauth] (>=14,<15)
 Requires-Dist: gunicorn (>=21.2,<23.0)
 Requires-Dist: packaging (>=23.2,<24.0)
 Requires-Dist: psutil (>=5.9.8,<6.0.0)

{fractal_server-2.9.0a11.dist-info → fractal_server-2.9.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=awxUTr6llNkjH1-5c-_yED0mpNs4APblXMX5R7fA0Qs,25
+fractal_server/__init__.py,sha256=PV3pFNkPgVbTBTGekRDdEwLUrBsGNXOb1hGr6F9R4OE,22
 fractal_server/__main__.py,sha256=dEkCfzLLQrIlxsGC-HBfoR-RBMWnJDgNrxYTyzmE9c0,6146
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -63,7 +63,7 @@ fractal_server/app/routes/api/v2/workflowtask.py,sha256=ciHTwXXFiFnMF7ZpJ3Xs0q6Y
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
 fractal_server/app/routes/auth/_aux_auth.py,sha256=ifkNocTYatBSMYGwiR14qohmvR9SfMldceiEj6uJBrU,4783
 fractal_server/app/routes/auth/current_user.py,sha256=I3aVY5etWAJ_SH6t65Mj5TjvB2X8sAGuu1KG7FxLyPU,5883
-fractal_server/app/routes/auth/group.py,sha256=cS9I6pCIWGbOWc3gUBYmQq6yjFYzm6rVQDukWF_9L90,7721
+fractal_server/app/routes/auth/group.py,sha256=EBwR-eiTfHSZUbsbrhjKTWTiwPkGPLFYhuHi7ifDbfY,8358
 fractal_server/app/routes/auth/login.py,sha256=tSu6OBLOieoBtMZB4JkBAdEgH2Y8KqPGSbwy7NIypIo,566
 fractal_server/app/routes/auth/oauth.py,sha256=AnFHbjqL2AgBX3eksI931xD6RTtmbciHBEuGf9YJLjU,1895
 fractal_server/app/routes/auth/register.py,sha256=DlHq79iOvGd_gt2v9uwtsqIKeO6i_GKaW59VIkllPqY,587
@@ -82,17 +82,18 @@ fractal_server/app/runner/exceptions.py,sha256=_qZ_t8O4umAdJ1ikockiF5rDJuxnEskrG
 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=iyhtDi1qveqq7I4S1tycVKsp3VfyocvBgGugYDpOzAs,16069
+fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=RkFrp9bltfVxrp5Ei2KuCMEft6q3mBArTvSBvtHA2n4,15682
 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=bKo5Ja0IGxJWpPWyh9dN0AG-PwzTDZzD5LyaEHB3YU4,3742
 fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py,sha256=rwlqZzoGo4SAb4nSlFjsQJdaCgfM1J6YGcjb8yYxlqc,4506
-fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=rVKAMVV7zb0x5T8R7NQlyeJZUOWDs7FRQuXEwCJbeNo,57899
+fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=yRn5v0ZUX_dQdN1MN8gjRBMCXVWZ_PZgcI2wnWXIAO8,54070
 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=g8wqUjSicN17UZVXlfaMomYZ-xOIbBu1oE7HdJTzfvw,5218
-fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=mTqTSvoRukvocyMLvlGuGWMaL6hy3McYLx_7bUW1pEM,48918
+fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=CAIPFMmsjQLxmjN8Kdpq0OlZIX9PZIiRo0XO1quKWEM,46495
+fractal_server/app/runner/executors/slurm/utils_executors.py,sha256=naPyJI0I3lD-sYHbSXbMFGUBK4h_SggA5V91Z1Ch1Xg,1416
 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=c3JbYXq3hX2aaflQU19qJ5Xs6J6oXGNvnTEoAfv2bxc,959
@@ -160,7 +161,7 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=yHpCRxoj6tKqCiQfUjaTj8Sf
 fractal_server/app/schemas/v2/task_group.py,sha256=fSjdLbClrpmrPj5hFZMu9DoJW4Y33EnbOh0HjMBsGVc,3784
 fractal_server/app/schemas/v2/workflow.py,sha256=-KWvXnbHBFA3pj5n7mfSyLKJQSqkJmoziIEe7mpLl3M,1875
 fractal_server/app/schemas/v2/workflowtask.py,sha256=vDdMktYbHeYBgB5OuWSv6wRPRXWqvetkeqQ7IC5YtfA,5751
-fractal_server/app/security/__init__.py,sha256=8Xd4GxumZgvxEH1Vli3ULehwdesEPiaAbtffJvAEgNo,12509
+fractal_server/app/security/__init__.py,sha256=MlWVrLFPj9M2Gug-k8yATM-Cw066RugVU4KK6kMRbnQ,13019
 fractal_server/app/user_settings.py,sha256=aZgQ3i0JkHfgwLGW1ee6Gzr1ae3IioFfJKKSsSS8Svk,1312
 fractal_server/config.py,sha256=Bk6EFKnU07sjgThf2NVEqrFAx9F4s0BfCvDKtWHzJTc,23217
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
@@ -221,7 +222,7 @@ fractal_server/tasks/v2/local/deactivate.py,sha256=XR1nvJY3mKCRqwPwV79rVaQmtb3J8
 fractal_server/tasks/v2/local/reactivate.py,sha256=R3rArAzUpMGf6xa3dGVwwXHW9WVDi5ia28AFisZsqNc,6112
 fractal_server/tasks/v2/ssh/__init__.py,sha256=aSQbVi6Ummt9QzcSLWNmSqYjfdxrn9ROmqgH6bDpI7k,135
 fractal_server/tasks/v2/ssh/_utils.py,sha256=2E-F_862zM6FZA-im-E8t8kjptWRIhBj1IDHC6QD1H8,2818
-fractal_server/tasks/v2/ssh/collect.py,sha256=ZOpz-v2t2kOAbbpdlsH_P_XjNtEh2TaC1dIZ1bBHwxw,12941
+fractal_server/tasks/v2/ssh/collect.py,sha256=FkTfyhdwAp4qa4W_dqjT0CmuDMFuCBSOYjg_y1Kq2Bs,12939
 fractal_server/tasks/v2/ssh/deactivate.py,sha256=Ffk_UuQSBUBNBCiviuKNhEUGyZPQa4_erJKFdwgMcE8,10616
 fractal_server/tasks/v2/ssh/reactivate.py,sha256=jdO8iyzavzSVPcOpIZrYSEkGPYTvz5XJ5h_5-nz9yzA,7896
 fractal_server/tasks/v2/templates/1_create_venv.sh,sha256=PK0jdHKtQpda1zULebBaVPORt4t6V17wa4N1ohcj5ac,548
@@ -238,8 +239,8 @@ fractal_server/tasks/v2/utils_templates.py,sha256=C5WLuY3uGG2s53OEL-__H35-fmSlgu
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=utvmBx8K9I8hRWFquxna2pBaOqe0JifDL_NVPmihEJI,3525
 fractal_server/zip_tools.py,sha256=GjDgo_sf6V_DDg6wWeBlZu5zypIxycn_l257p_YVKGc,4876
-fractal_server-2.9.0a11.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.9.0a11.dist-info/METADATA,sha256=0SUdcGO7gPL9_VuNTLt10VitKNIgZTgQ5VL4FV2xjX8,4586
-fractal_server-2.9.0a11.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.9.0a11.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.9.0a11.dist-info/RECORD,,
+fractal_server-2.9.1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.9.1.dist-info/METADATA,sha256=2XOrXmdvOE1zcrKJoCr4VemPcRk3PpZJOUg_0yXxeDc,4543
+fractal_server-2.9.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.9.1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.9.1.dist-info/RECORD,,