fractal-server 2.14.5__py3-none-any.whl → 2.14.7__py3-none-any.whl

fractal_server/app/runner/v2/runner_functions.py

@@ -1,8 +1,7 @@
+from collections.abc import Callable
 from pathlib import Path
 from typing import Any
-from typing import Callable
 from typing import Literal
-from typing import Optional
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -129,7 +128,7 @@ def run_v2_task_non_parallel(
         [
             WorkflowTaskV2,
             Literal["non_parallel", "parallel"],
-            Optional[Path],
+            Path | None,
             int,
         ],
         Any,
@@ -251,7 +250,7 @@ def run_v2_task_parallel(
         [
             WorkflowTaskV2,
             Literal["non_parallel", "parallel"],
-            Optional[Path],
+            Path | None,
             int,
         ],
         Any,
@@ -382,7 +381,7 @@ def run_v2_task_compound(
         [
             WorkflowTaskV2,
             Literal["non_parallel", "parallel"],
-            Optional[Path],
+            Path | None,
             int,
         ],
         Any,

fractal_server/app/runner/v2/submit_workflow.py

@@ -8,7 +8,6 @@ the individual backends.
 import os
 import traceback
 from pathlib import Path
-from typing import Optional
 
 from sqlalchemy.orm import Session as DBSyncSession
 
@@ -69,10 +68,10 @@ def submit_workflow(
     job_id: int,
     user_id: int,
     user_settings: UserSettings,
-    worker_init: Optional[str] = None,
-    slurm_user: Optional[str] = None,
-    user_cache_dir: Optional[str] = None,
-    fractal_ssh: Optional[FractalSSH] = None,
+    worker_init: str | None = None,
+    slurm_user: str | None = None,
+    user_cache_dir: str | None = None,
+    fractal_ssh: FractalSSH | None = None,
 ) -> None:
     """
     Prepares a workflow and applies it to a dataset
@@ -109,11 +108,9 @@ def submit_workflow(
 
     with next(DB.get_sync_db()) as db_sync:
         try:
-            job: Optional[JobV2] = db_sync.get(JobV2, job_id)
-            dataset: Optional[DatasetV2] = db_sync.get(DatasetV2, dataset_id)
-            workflow: Optional[WorkflowV2] = db_sync.get(
-                WorkflowV2, workflow_id
-            )
+            job: JobV2 | None = db_sync.get(JobV2, job_id)
+            dataset: DatasetV2 | None = db_sync.get(DatasetV2, dataset_id)
+            workflow: WorkflowV2 | None = db_sync.get(WorkflowV2, workflow_id)
         except Exception as e:
             logger.error(
                 f"Error connecting to the database. Original error: {str(e)}"
@@ -239,6 +236,7 @@ def submit_workflow(
         elif FRACTAL_RUNNER_BACKEND == "slurm_ssh":
             logger.debug(f"ssh_user: {user_settings.ssh_username}")
             logger.debug(f"base dir: {user_settings.ssh_tasks_dir}")
+            logger.debug(f"slurm_account: {job.slurm_account}")
             logger.debug(f"worker_init: {worker_init}")
         logger.debug(f"job.id: {job.id}")
         logger.debug(f"job.working_dir: {job.working_dir}")
@@ -260,7 +258,10 @@ def submit_workflow(
             )
         elif FRACTAL_RUNNER_BACKEND == "slurm_ssh":
             process_workflow = slurm_ssh_process_workflow
-            backend_specific_kwargs = dict(fractal_ssh=fractal_ssh)
+            backend_specific_kwargs = dict(
+                fractal_ssh=fractal_ssh,
+                slurm_account=job.slurm_account,
+            )
         else:
             raise RuntimeError(
                 f"Invalid runner backend {FRACTAL_RUNNER_BACKEND=}"

fractal_server/app/runner/v2/task_interface.py

@@ -1,5 +1,4 @@
 from typing import Any
-from typing import Optional
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -57,7 +56,7 @@ class InitTaskOutput(BaseModel):
 
 def _cast_and_validate_TaskOutput(
     task_output: dict[str, Any]
-) -> Optional[TaskOutput]:
+) -> TaskOutput | None:
     try:
         validated_task_output = TaskOutput(**task_output)
         return validated_task_output
@@ -71,7 +70,7 @@ def _cast_and_validate_TaskOutput(
 
 def _cast_and_validate_InitTaskOutput(
     init_task_output: dict[str, Any],
-) -> Optional[InitTaskOutput]:
+) -> InitTaskOutput | None:
     try:
         validated_init_task_output = InitTaskOutput(**init_task_output)
         return validated_init_task_output

fractal_server/app/runner/versions.py

@@ -1,11 +1,10 @@
 import json
 import sys
-from typing import Union
 
 import fractal_server
 
 
-def get_versions() -> dict[str, Union[list[int], str]]:
+def get_versions() -> dict[str, list[int] | str]:
     """
     Extract versions of Python and fractal-server.
     """

fractal_server/app/schemas/user.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi_users import schemas
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -41,8 +39,8 @@ class UserRead(schemas.BaseUser[int]):
         username:
     """
 
-    username: Optional[str] = None
-    group_ids_names: Optional[list[tuple[int, str]]] = None
+    username: str | None = None
+    group_ids_names: list[tuple[int, str]] | None = None
     oauth_accounts: list[OAuthAccountRead]
 
 

fractal_server/app/schemas/user_group.py

@@ -1,5 +1,4 @@
 from datetime import datetime
-from typing import Optional
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -33,7 +32,7 @@ class UserGroupRead(BaseModel):
     id: int
     name: str
     timestamp_created: AwareDatetime
-    user_ids: Optional[list[int]] = None
+    user_ids: list[int] | None = None
     viewer_paths: list[str]
 
     @field_serializer("timestamp_created")

fractal_server/app/schemas/user_settings.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from pydantic import BaseModel
 from pydantic import ConfigDict
 from pydantic import field_validator
@@ -23,21 +21,21 @@ class UserSettingsRead(BaseModel):
     """
 
     id: int
-    ssh_host: Optional[str] = None
-    ssh_username: Optional[str] = None
-    ssh_private_key_path: Optional[str] = None
-    ssh_tasks_dir: Optional[str] = None
-    ssh_jobs_dir: Optional[str] = None
-    slurm_user: Optional[str] = None
+    ssh_host: str | None = None
+    ssh_username: str | None = None
+    ssh_private_key_path: str | None = None
+    ssh_tasks_dir: str | None = None
+    ssh_jobs_dir: str | None = None
+    slurm_user: str | None = None
     slurm_accounts: list[str]
-    project_dir: Optional[str] = None
+    project_dir: str | None = None
 
 
 class UserSettingsReadStrict(BaseModel):
-    slurm_user: Optional[str] = None
+    slurm_user: str | None = None
     slurm_accounts: list[str]
-    ssh_username: Optional[str] = None
-    project_dir: Optional[str] = None
+    ssh_username: str | None = None
+    project_dir: str | None = None
 
 
 class UserSettingsUpdate(BaseModel):
@@ -47,14 +45,14 @@ class UserSettingsUpdate(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
 
-    ssh_host: Optional[NonEmptyStr] = None
-    ssh_username: Optional[NonEmptyStr] = None
-    ssh_private_key_path: Optional[AbsolutePathStr] = None
-    ssh_tasks_dir: Optional[AbsolutePathStr] = None
-    ssh_jobs_dir: Optional[AbsolutePathStr] = None
-    slurm_user: Optional[NonEmptyStr] = None
-    slurm_accounts: Optional[ListUniqueNonEmptyString] = None
-    project_dir: Optional[AbsolutePathStr] = None
+    ssh_host: NonEmptyStr | None = None
+    ssh_username: NonEmptyStr | None = None
+    ssh_private_key_path: AbsolutePathStr | None = None
+    ssh_tasks_dir: AbsolutePathStr | None = None
+    ssh_jobs_dir: AbsolutePathStr | None = None
+    slurm_user: NonEmptyStr | None = None
+    slurm_accounts: ListUniqueNonEmptyString | None = None
+    project_dir: AbsolutePathStr | None = None
 
     @field_validator("project_dir", mode="after")
     @classmethod
@@ -66,4 +64,4 @@ class UserSettingsUpdate(BaseModel):
 
 class UserSettingsUpdateStrict(BaseModel):
     model_config = ConfigDict(extra="forbid")
-    slurm_accounts: Optional[ListUniqueNonEmptyString] = None
+    slurm_accounts: ListUniqueNonEmptyString | None = None

fractal_server/app/schemas/v2/dataset.py

@@ -1,5 +1,4 @@
 from datetime import datetime
-from typing import Optional
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -19,7 +18,7 @@ class DatasetCreateV2(BaseModel):
 
     name: NonEmptyStr
 
-    zarr_dir: Optional[ZarrDirStr] = None
+    zarr_dir: ZarrDirStr | None = None
 
     attribute_filters: AttributeFilters = Field(default_factory=dict)
 
@@ -44,7 +43,7 @@ class DatasetUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None
-    zarr_dir: Optional[ZarrDirStr] = None
+    zarr_dir: ZarrDirStr | None = None
 
 
 class DatasetImportV2(BaseModel):

fractal_server/app/schemas/v2/dumps.py

@@ -7,8 +7,6 @@ These models are used in at least two situations:
 1. In the "*_dump" attributes of Job models;
 2. In the history items, to trim their size.
 """
-from typing import Optional
-
 from pydantic import BaseModel
 from pydantic import ConfigDict
 from pydantic import Field
@@ -29,10 +27,10 @@ class TaskDumpV2(BaseModel):
     name: str
     type: TaskTypeType
 
-    command_non_parallel: Optional[str] = None
-    command_parallel: Optional[str] = None
-    source: Optional[str] = None
-    version: Optional[str] = None
+    command_non_parallel: str | None = None
+    command_parallel: str | None = None
+    source: str | None = None
+    version: str | None = None
 
     input_types: dict[str, bool]
     output_types: dict[str, bool]
@@ -47,12 +45,12 @@ class WorkflowTaskDumpV2(BaseModel):
 
     id: int
     workflow_id: int
-    order: Optional[int] = None
+    order: int | None = None
 
     type_filters: dict[str, bool]
 
-    task_id: Optional[int] = None
-    task: Optional[TaskDumpV2] = None
+    task_id: int | None = None
+    task: TaskDumpV2 | None = None
 
 
 class WorkflowDumpV2(BaseModel):
@@ -81,11 +79,11 @@ class TaskGroupDumpV2(BaseModel):
     id: int
     origin: TaskGroupV2OriginEnum
     pkg_name: str
-    version: Optional[str] = None
-    python_version: Optional[str] = None
-    pip_extras: Optional[str] = None
+    version: str | None = None
+    python_version: str | None = None
+    pip_extras: str | None = None
     pinned_package_versions: dict[str, str] = Field(default_factory=dict)
 
-    path: Optional[str] = None
-    venv_path: Optional[str] = None
-    wheel_path: Optional[str] = None
+    path: str | None = None
+    venv_path: str | None = None
+    wheel_path: str | None = None

fractal_server/app/schemas/v2/history.py

@@ -1,7 +1,6 @@
 from datetime import datetime
-from enum import Enum
+from enum import StrEnum
 from typing import Any
-from typing import Optional
 
 from pydantic import AwareDatetime
 from pydantic import BaseModel
@@ -10,7 +9,7 @@ from pydantic import field_serializer
 from ....images import SingleImage
 
 
-class HistoryUnitStatus(str, Enum):
+class HistoryUnitStatus(StrEnum):
     """
     Available status for images
 
@@ -25,7 +24,7 @@ class HistoryUnitStatus(str, Enum):
     FAILED = "failed"
 
 
-class HistoryUnitStatusQuery(str, Enum):
+class HistoryUnitStatusQuery(StrEnum):
 
     SUBMITTED = "submitted"
     DONE = "done"
@@ -36,7 +35,7 @@ class HistoryUnitStatusQuery(str, Enum):
 
 class HistoryUnitRead(BaseModel):
     id: int
-    logfile: Optional[str] = None
+    logfile: str | None = None
     status: HistoryUnitStatus
     zarr_urls: list[str]
 
@@ -44,7 +43,7 @@ class HistoryUnitRead(BaseModel):
 class HistoryRunRead(BaseModel):
     id: int
     dataset_id: int
-    workflowtask_id: Optional[int] = None
+    workflowtask_id: int | None = None
     job_id: int
     workflowtask_dump: dict[str, Any]
     task_group_dump: dict[str, Any]
@@ -77,4 +76,4 @@ class ImageLogsRequest(BaseModel):
 
 
 class SingleImageWithStatus(SingleImage):
-    status: Optional[HistoryUnitStatus] = None
+    status: HistoryUnitStatus | None = None

fractal_server/app/schemas/v2/job.py

@@ -1,6 +1,5 @@
 from datetime import datetime
-from enum import Enum
-from typing import Optional
+from enum import StrEnum
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -19,7 +18,7 @@ from fractal_server.types import NonEmptyStr
 from fractal_server.types import TypeFilters
 
 
-class JobStatusTypeV2(str, Enum):
+class JobStatusTypeV2(StrEnum):
     """
     Define the available job statuses
 
@@ -43,9 +42,9 @@ class JobStatusTypeV2(str, Enum):
 class JobCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
-    first_task_index: Optional[NonNegativeInt] = None
-    last_task_index: Optional[NonNegativeInt] = None
-    slurm_account: Optional[StrictStr] = None
+    first_task_index: NonNegativeInt | None = None
+    last_task_index: NonNegativeInt | None = None
+    slurm_account: StrictStr | None = None
     worker_init: NonEmptyStr = None
 
     attribute_filters: AttributeFilters = Field(default_factory=dict)
@@ -68,23 +67,23 @@ class JobCreateV2(BaseModel):
 
 class JobReadV2(BaseModel):
     id: int
-    project_id: Optional[int] = None
+    project_id: int | None = None
     project_dump: ProjectDumpV2
     user_email: str
-    slurm_account: Optional[str] = None
-    workflow_id: Optional[int] = None
+    slurm_account: str | None = None
+    workflow_id: int | None = None
     workflow_dump: WorkflowDumpV2
-    dataset_id: Optional[int] = None
+    dataset_id: int | None = None
     dataset_dump: DatasetDumpV2
     start_timestamp: AwareDatetime
-    end_timestamp: Optional[AwareDatetime] = None
+    end_timestamp: AwareDatetime | None = None
     status: str
-    log: Optional[str] = None
-    working_dir: Optional[str] = None
-    working_dir_user: Optional[str] = None
-    first_task_index: Optional[int] = None
-    last_task_index: Optional[int] = None
-    worker_init: Optional[str] = None
+    log: str | None = None
+    working_dir: str | None = None
+    working_dir_user: str | None = None
+    first_task_index: int | None = None
+    last_task_index: int | None = None
+    worker_init: str | None = None
     attribute_filters: AttributeFilters
     type_filters: dict[str, bool]
 
@@ -93,7 +92,7 @@ class JobReadV2(BaseModel):
         return v.isoformat()
 
     @field_serializer("end_timestamp")
-    def serialize_datetime_end(v: Optional[datetime]) -> Optional[str]:
+    def serialize_datetime_end(v: datetime | None) -> str | None:
         if v is None:
             return None
         else:

fractal_server/app/schemas/v2/manifest.py

@@ -1,5 +1,4 @@
 from typing import Literal
-from typing import Optional
 
 from pydantic import BaseModel
 from pydantic import Field
@@ -41,22 +40,22 @@ class TaskManifestV2(BaseModel):
     """
 
     name: str
-    executable_non_parallel: Optional[str] = None
-    executable_parallel: Optional[str] = None
+    executable_non_parallel: str | None = None
+    executable_parallel: str | None = None
     input_types: dict[str, bool] = Field(default_factory=dict)
     output_types: dict[str, bool] = Field(default_factory=dict)
     meta_non_parallel: DictStrAny = Field(default_factory=dict)
     meta_parallel: DictStrAny = Field(default_factory=dict)
-    args_schema_non_parallel: Optional[DictStrAny] = None
-    args_schema_parallel: Optional[DictStrAny] = None
-    docs_info: Optional[str] = None
-    docs_link: Optional[HttpUrlStr] = None
+    args_schema_non_parallel: DictStrAny | None = None
+    args_schema_parallel: DictStrAny | None = None
+    docs_info: str | None = None
+    docs_link: HttpUrlStr | None = None
 
-    category: Optional[str] = None
-    modality: Optional[str] = None
+    category: str | None = None
+    modality: str | None = None
     tags: list[str] = Field(default_factory=list)
 
-    type: Optional[
+    type: None | (
         Literal[
             "compound",
             "converter_compound",
@@ -64,7 +63,7 @@ class TaskManifestV2(BaseModel):
             "converter_non_parallel",
             "parallel",
         ]
-    ] = None
+    ) = None
 
     @model_validator(mode="after")
     def validate_executable_args_meta(self):
@@ -140,8 +139,8 @@ class ManifestV2(BaseModel):
     manifest_version: Literal["2"]
     task_list: list[TaskManifestV2]
     has_args_schemas: bool = False
-    args_schema_version: Optional[str] = None
-    authors: Optional[NonEmptyStr] = None
+    args_schema_version: str | None = None
+    authors: NonEmptyStr | None = None
 
     @model_validator(mode="after")
     def _check_args_schemas_are_present(self):

fractal_server/app/schemas/v2/status_legacy.py

@@ -1,10 +1,10 @@
-from enum import Enum
+from enum import StrEnum
 
 from pydantic import BaseModel
 from pydantic import Field
 
 
-class WorkflowTaskStatusTypeV2(str, Enum):
+class WorkflowTaskStatusTypeV2(StrEnum):
     """
     Define the available values for the status of a `WorkflowTask`.
 

fractal_server/app/schemas/v2/task.py

@@ -1,6 +1,5 @@
 from typing import Any
 from typing import Literal
-from typing import Optional
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -35,24 +34,24 @@ class TaskCreateV2(BaseModel):
     command_non_parallel: NonEmptyStr = None
     command_parallel: NonEmptyStr = None
 
-    meta_non_parallel: Optional[DictStrAny] = None
-    meta_parallel: Optional[DictStrAny] = None
+    meta_non_parallel: DictStrAny | None = None
+    meta_parallel: DictStrAny | None = None
     version: NonEmptyStr = None
-    args_schema_non_parallel: Optional[DictStrAny] = None
-    args_schema_parallel: Optional[DictStrAny] = None
+    args_schema_non_parallel: DictStrAny | None = None
+    args_schema_parallel: DictStrAny | None = None
     args_schema_version: NonEmptyStr = None
-    docs_info: Optional[str] = None
-    docs_link: Optional[HttpUrlStr] = None
+    docs_info: str | None = None
+    docs_link: HttpUrlStr | None = None
 
     input_types: TypeFilters = Field(default={})
     output_types: TypeFilters = Field(default={})
 
-    category: Optional[NonEmptyStr] = None
-    modality: Optional[NonEmptyStr] = None
+    category: NonEmptyStr | None = None
+    modality: NonEmptyStr | None = None
     tags: ListUniqueNonEmptyString = Field(default_factory=list)
-    authors: Optional[NonEmptyStr] = None
+    authors: NonEmptyStr | None = None
 
-    type: Optional[TaskTypeType] = None
+    type: TaskTypeType | None = None
 
     @model_validator(mode="after")
     def validate_commands(self):
@@ -92,26 +91,26 @@ class TaskReadV2(BaseModel):
     id: int
     name: str
     type: TaskTypeType
-    source: Optional[str] = None
-    version: Optional[str] = None
+    source: str | None = None
+    version: str | None = None
 
-    command_non_parallel: Optional[str] = None
-    command_parallel: Optional[str] = None
+    command_non_parallel: str | None = None
+    command_parallel: str | None = None
     meta_parallel: dict[str, Any]
     meta_non_parallel: dict[str, Any]
-    args_schema_non_parallel: Optional[dict[str, Any]] = None
-    args_schema_parallel: Optional[dict[str, Any]] = None
-    args_schema_version: Optional[str] = None
-    docs_info: Optional[str] = None
-    docs_link: Optional[str] = None
+    args_schema_non_parallel: dict[str, Any] | None = None
+    args_schema_parallel: dict[str, Any] | None = None
+    args_schema_version: str | None = None
+    docs_info: str | None = None
+    docs_link: str | None = None
     input_types: dict[str, bool]
     output_types: dict[str, bool]
 
-    taskgroupv2_id: Optional[int] = None
+    taskgroupv2_id: int | None = None
 
-    category: Optional[str] = None
-    modality: Optional[str] = None
-    authors: Optional[str] = None
+    category: str | None = None
+    modality: str | None = None
+    authors: str | None = None
     tags: list[str]
 
 
@@ -123,17 +122,17 @@ class TaskUpdateV2(BaseModel):
     input_types: TypeFilters = None
     output_types: TypeFilters = None
 
-    category: Optional[NonEmptyStr] = None
-    modality: Optional[NonEmptyStr] = None
-    authors: Optional[NonEmptyStr] = None
-    tags: Optional[ListUniqueNonEmptyString] = None
+    category: NonEmptyStr | None = None
+    modality: NonEmptyStr | None = None
+    authors: NonEmptyStr | None = None
+    tags: ListUniqueNonEmptyString | None = None
 
 
 class TaskImportV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     pkg_name: NonEmptyStr
-    version: Optional[NonEmptyStr] = None
+    version: NonEmptyStr | None = None
     name: NonEmptyStr
 
 
@@ -143,5 +142,5 @@ class TaskImportV2Legacy(BaseModel):
 
 class TaskExportV2(BaseModel):
     pkg_name: NonEmptyStr
-    version: Optional[NonEmptyStr] = None
+    version: NonEmptyStr | None = None
     name: NonEmptyStr

fractal_server/app/schemas/v2/task_collection.py

@@ -1,5 +1,4 @@
 from typing import Literal
-from typing import Optional
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -47,11 +46,11 @@ class TaskCollectPipV2(BaseModel):
     """
 
     model_config = ConfigDict(extra="forbid")
-    package: Optional[NonEmptyStr] = None
-    package_version: Optional[NonEmptyStr] = None
-    package_extras: Optional[NonEmptyStr] = None
-    python_version: Optional[Literal["3.9", "3.10", "3.11", "3.12"]] = None
-    pinned_package_versions: Optional[DictStrStr] = None
+    package: NonEmptyStr | None = None
+    package_version: NonEmptyStr | None = None
+    package_extras: NonEmptyStr | None = None
+    python_version: Literal["3.9", "3.10", "3.11", "3.12"] | None = None
+    pinned_package_versions: DictStrStr | None = None
 
     @field_validator(
         "package", "package_version", "package_extras", mode="after"
@@ -94,9 +93,9 @@ class TaskCollectCustomV2(BaseModel):
     manifest: ManifestV2
     python_interpreter: AbsolutePathStr
     label: NonEmptyStr
-    package_root: Optional[AbsolutePathStr] = None
-    package_name: Optional[NonEmptyStr] = None
-    version: Optional[NonEmptyStr] = None
+    package_root: AbsolutePathStr | None = None
+    package_name: NonEmptyStr | None = None
+    version: NonEmptyStr | None = None
 
     @field_validator("package_name", mode="after")
     @classmethod