fractal-server 2.18.0__py3-none-any.whl → 2.18.0a1__py3-none-any.whl

fractal_server/app/schemas/v2/dumps.py

@@ -13,17 +13,17 @@ from pydantic import ConfigDict
 from pydantic import Field
 
 from .task import TaskType
-from .task_group import TaskGroupOriginEnum
+from .task_group import TaskGroupV2OriginEnum
 
 
-class ProjectDump(BaseModel):
+class ProjectDumpV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
     id: int
     name: str
     timestamp_created: str
 
 
-class TaskDump(BaseModel):
+class TaskDumpV2(BaseModel):
     id: int
     name: str
     type: TaskType
@@ -37,7 +37,7 @@ class TaskDump(BaseModel):
     output_types: dict[str, bool]
 
 
-class WorkflowTaskDump(BaseModel):
+class WorkflowTaskDumpV2(BaseModel):
     """
     We do not include 'model_config = ConfigDict(extra="forbid")'
     because legacy data may include 'input_filters' field and we want to avoid
@@ -51,10 +51,10 @@ class WorkflowTaskDump(BaseModel):
     type_filters: dict[str, bool]
 
     task_id: int | None = None
-    task: TaskDump | None = None
+    task: TaskDumpV2 | None = None
 
 
-class WorkflowDump(BaseModel):
+class WorkflowDumpV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
     id: int
     name: str
@@ -62,7 +62,7 @@ class WorkflowDump(BaseModel):
     timestamp_created: str
 
 
-class DatasetDump(BaseModel):
+class DatasetDumpV2(BaseModel):
     """
     We do not include 'model_config = ConfigDict(extra="forbid")' because
     legacy data may include 'type_filters' or 'attribute_filters' and we
@@ -76,9 +76,9 @@ class DatasetDump(BaseModel):
     zarr_dir: str
 
 
-class TaskGroupDump(BaseModel):
+class TaskGroupDumpV2(BaseModel):
     id: int
-    origin: TaskGroupOriginEnum
+    origin: TaskGroupV2OriginEnum
     pkg_name: str
     version: str | None = None
     python_version: str | None = None

fractal_server/app/schemas/v2/job.py

@@ -10,15 +10,15 @@ from pydantic.types import AwareDatetime
 from pydantic.types import NonNegativeInt
 from pydantic.types import StrictStr
 
-from fractal_server.app.schemas.v2.dumps import DatasetDump
-from fractal_server.app.schemas.v2.dumps import ProjectDump
-from fractal_server.app.schemas.v2.dumps import WorkflowDump
+from fractal_server.app.schemas.v2.dumps import DatasetDumpV2
+from fractal_server.app.schemas.v2.dumps import ProjectDumpV2
+from fractal_server.app.schemas.v2.dumps import WorkflowDumpV2
 from fractal_server.types import AttributeFilters
 from fractal_server.types import NonEmptyStr
 from fractal_server.types import TypeFilters
 
 
-class JobStatusType(StrEnum):
+class JobStatusTypeV2(StrEnum):
     """
     Define the available job statuses
 
@@ -39,7 +39,7 @@ class JobStatusType(StrEnum):
     FAILED = "failed"
 
 
-class JobCreate(BaseModel):
+class JobCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     first_task_index: NonNegativeInt | None = None
@@ -65,16 +65,16 @@ class JobCreate(BaseModel):
         return values
 
 
-class JobRead(BaseModel):
+class JobReadV2(BaseModel):
     id: int
     project_id: int | None = None
-    project_dump: ProjectDump
+    project_dump: ProjectDumpV2
     user_email: str
     slurm_account: str | None = None
     workflow_id: int | None = None
-    workflow_dump: WorkflowDump
+    workflow_dump: WorkflowDumpV2
     dataset_id: int | None = None
-    dataset_dump: DatasetDump
+    dataset_dump: DatasetDumpV2
     start_timestamp: AwareDatetime
     end_timestamp: AwareDatetime | None = None
     status: str
@@ -100,7 +100,7 @@ class JobRead(BaseModel):
             return v.isoformat()
 
 
-class JobUpdate(BaseModel):
+class JobUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
-    status: JobStatusType
+    status: JobStatusTypeV2

fractal_server/app/schemas/v2/project.py

@@ -8,13 +8,13 @@ from pydantic.types import AwareDatetime
 from fractal_server.types import NonEmptyStr
 
 
-class ProjectCreate(BaseModel):
+class ProjectCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
-class ProjectRead(BaseModel):
+class ProjectReadV2(BaseModel):
     id: int
     name: str
     timestamp_created: AwareDatetime
@@ -24,7 +24,7 @@ class ProjectRead(BaseModel):
         return v.isoformat()
 
 
-class ProjectUpdate(BaseModel):
+class ProjectUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None

fractal_server/app/schemas/v2/resource.py

@@ -77,8 +77,6 @@ class ValidResourceBase(BaseModel):
     jobs_runner_config: dict[NonEmptyStr, Any]
     jobs_poll_interval: int = 5
 
-    prevent_new_submissions: bool = False
-
     @model_validator(mode="after")
     def _pixi_slurm_config(self) -> Self:
         if (
@@ -97,9 +95,6 @@ class ValidResourceLocal(ValidResourceBase):
     Attributes:
         name: Resource name.
         type: Resource type.
-        prevent_new_submissions:
-            When set to true: Prevent new job submissions and stop execution of
-            ongoing jobs as soon as the current task is complete.
         tasks_python_config:
             Configuration of Python interpreters used for task collection.
         tasks_pixi_config:
@@ -110,6 +105,7 @@ class ValidResourceLocal(ValidResourceBase):
             Local base folder for job folders.
         jobs_runner_config:
             Runner configuration.
+
     """
 
     type: Literal[ResourceType.LOCAL]
@@ -125,9 +121,6 @@ class ValidResourceSlurmSudo(ValidResourceBase):
     Attributes:
         name: Resource name.
         type: Resource type.
-        prevent_new_submissions:
-            When set to true: Prevent new job submissions and stop execution of
-            ongoing jobs as soon as the current task is complete.
         tasks_python_config:
             Configuration of Python interpreters used for task collection.
         tasks_pixi_config:
@@ -157,9 +150,6 @@ class ValidResourceSlurmSSH(ValidResourceBase):
     Attributes:
         name: Resource name
         type: Resource type.
-        prevent_new_submissions:
-            When set to true: Prevent new job submissions and stop execution of
-            ongoing jobs as soon as the current task is complete.
         tasks_python_config:
             Configuration of Python interpreters used for task collection.
         tasks_pixi_config:
@@ -208,9 +198,10 @@ class ResourceRead(BaseModel):
     """
 
     id: int
-    name: str
+
     type: str
-    prevent_new_submissions: bool
+
+    name: str
     timestamp_created: AwareDatetime
 
     host: str | None

fractal_server/app/schemas/v2/status_legacy.py

@@ -4,7 +4,7 @@ from pydantic import BaseModel
 from pydantic import Field
 
 
-class WorkflowTaskStatusType(StrEnum):
+class WorkflowTaskStatusTypeV2(StrEnum):
     """
     Define the available values for the status of a `WorkflowTask`.
 
@@ -23,7 +23,7 @@ class WorkflowTaskStatusType(StrEnum):
     FAILED = "failed"
 
 
-class LegacyStatusRead(BaseModel):
+class LegacyStatusReadV2(BaseModel):
     """
     Response type for the
     `/project/{project_id}/status/` endpoint
@@ -31,5 +31,5 @@ class LegacyStatusRead(BaseModel):
 
     status: dict[
         str,
-        WorkflowTaskStatusType,
+        WorkflowTaskStatusTypeV2,
     ] = Field(default_factory=dict)

fractal_server/app/schemas/v2/task.py

@@ -29,7 +29,7 @@ class TaskType(StrEnum):
     PARALLEL = "parallel"
 
 
-class TaskCreate(BaseModel):
+class TaskCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
@@ -90,7 +90,7 @@ class TaskCreate(BaseModel):
         return self
 
 
-class TaskRead(BaseModel):
+class TaskReadV2(BaseModel):
     id: int
     name: str
     type: TaskType
@@ -117,7 +117,7 @@ class TaskRead(BaseModel):
     tags: list[str]
 
 
-class TaskUpdate(BaseModel):
+class TaskUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     command_parallel: NonEmptyStr = None
@@ -131,7 +131,7 @@ class TaskUpdate(BaseModel):
     tags: ListUniqueNonEmptyString | None = None
 
 
-class TaskImport(BaseModel):
+class TaskImportV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     pkg_name: NonEmptyStr
@@ -139,11 +139,11 @@ class TaskImport(BaseModel):
     name: NonEmptyStr
 
 
-class TaskImportLegacy(BaseModel):
+class TaskImportV2Legacy(BaseModel):
     source: NonEmptyStr
 
 
-class TaskExport(BaseModel):
+class TaskExportV2(BaseModel):
     pkg_name: NonEmptyStr
     version: NonEmptyStr | None = None
     name: NonEmptyStr

fractal_server/app/schemas/v2/task_collection.py

@@ -21,9 +21,9 @@ class FractalUploadedFile(BaseModel):
     contents: bytes
 
 
-class TaskCollectPip(BaseModel):
+class TaskCollectPipV2(BaseModel):
     """
-    TaskCollectPip class
+    TaskCollectPipV2 class
 
     This class only encodes the attributes required to trigger a
     task-collection operation. Other attributes (that are assigned *during*
@@ -91,7 +91,7 @@ class TaskCollectPip(BaseModel):
         return value
 
 
-class TaskCollectCustom(BaseModel):
+class TaskCollectCustomV2(BaseModel):
     """
     Attributes:
         manifest: Manifest of a Fractal task package (this is typically the
@@ -99,7 +99,7 @@ class TaskCollectCustom(BaseModel):
         python_interpreter: Absolute path to the Python interpreter to be used
             for running tasks.
         name: A name identifying this package, that will fill the
-            `TaskGroup.pkg_name` column.
+            `TaskGroupV2.pkg_name` column.
         package_root: The folder where the package is installed.
             If not provided, it will be extracted via `pip show`
             (requires `package_name` to be set).

fractal_server/app/schemas/v2/task_group.py

@@ -7,40 +7,40 @@ from pydantic import Field
 from pydantic import field_serializer
 from pydantic.types import AwareDatetime
 
-from fractal_server.app.schemas.v2.task import TaskRead
+from fractal_server.app.schemas.v2.task import TaskReadV2
 from fractal_server.types import AbsolutePathStr
 from fractal_server.types import DictStrStr
 from fractal_server.types import NonEmptyStr
 
 
-class TaskGroupOriginEnum(StrEnum):
+class TaskGroupV2OriginEnum(StrEnum):
     PYPI = "pypi"
     WHEELFILE = "wheel-file"
     PIXI = "pixi"
     OTHER = "other"
 
 
-class TaskGroupActivityStatus(StrEnum):
+class TaskGroupActivityStatusV2(StrEnum):
     PENDING = "pending"
     ONGOING = "ongoing"
     FAILED = "failed"
     OK = "OK"
 
 
-class TaskGroupActivityAction(StrEnum):
+class TaskGroupActivityActionV2(StrEnum):
     COLLECT = "collect"
     DEACTIVATE = "deactivate"
     REACTIVATE = "reactivate"
     DELETE = "delete"
 
 
-class TaskGroupCreate(BaseModel):
+class TaskGroupCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
     user_id: int
     resource_id: int
     user_group_id: int | None = None
     active: bool = True
-    origin: TaskGroupOriginEnum
+    origin: TaskGroupV2OriginEnum
     pkg_name: str
     version: str | None = None
     python_version: NonEmptyStr = None
@@ -54,9 +54,9 @@ class TaskGroupCreate(BaseModel):
     pinned_package_versions_post: DictStrStr = Field(default_factory=dict)
 
 
-class TaskGroupCreateStrict(TaskGroupCreate):
+class TaskGroupCreateV2Strict(TaskGroupCreateV2):
     """
-    A strict version of TaskGroupCreate, to be used for task collection.
+    A strict version of TaskGroupCreateV2, to be used for task collection.
     """
 
     path: AbsolutePathStr
@@ -65,14 +65,14 @@ class TaskGroupCreateStrict(TaskGroupCreate):
     python_version: NonEmptyStr
 
 
-class TaskGroupRead(BaseModel):
+class TaskGroupReadV2(BaseModel):
     id: int
-    task_list: list[TaskRead]
+    task_list: list[TaskReadV2]
 
     user_id: int
     user_group_id: int | None = None
 
-    origin: TaskGroupOriginEnum
+    origin: TaskGroupV2OriginEnum
     pkg_name: str
     version: str | None = None
     python_version: str | None = None
@@ -96,16 +96,16 @@ class TaskGroupRead(BaseModel):
         return v.isoformat()
 
 
-class TaskGroupReadSuperuser(TaskGroupRead):
+class TaskGroupReadSuperuser(TaskGroupReadV2):
     resource_id: int
 
 
-class TaskGroupUpdate(BaseModel):
+class TaskGroupUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
     user_group_id: int | None = None
 
 
-class TaskGroupActivityRead(BaseModel):
+class TaskGroupActivityV2Read(BaseModel):
     id: int
     user_id: int
     taskgroupv2_id: int | None = None
@@ -113,8 +113,8 @@ class TaskGroupActivityRead(BaseModel):
     timestamp_ended: AwareDatetime | None = None
     pkg_name: str
     version: str
-    status: TaskGroupActivityStatus
-    action: TaskGroupActivityAction
+    status: TaskGroupActivityStatusV2
+    action: TaskGroupActivityActionV2
     log: str | None = None
 
     @field_serializer("timestamp_started")

fractal_server/app/schemas/v2/workflow.py

@@ -5,29 +5,29 @@ from pydantic import ConfigDict
 from pydantic import field_serializer
 from pydantic.types import AwareDatetime
 
-from fractal_server.app.schemas.v2.project import ProjectRead
-from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskExport
-from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskImport
-from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskRead
+from fractal_server.app.schemas.v2.project import ProjectReadV2
+from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskExportV2
+from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskImportV2
+from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskReadV2
 from fractal_server.app.schemas.v2.workflowtask import (
-    WorkflowTaskReadWithWarning,
+    WorkflowTaskReadV2WithWarning,
 )
 from fractal_server.types import ListUniqueNonNegativeInt
 from fractal_server.types import NonEmptyStr
 
 
-class WorkflowCreate(BaseModel):
+class WorkflowCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
-class WorkflowRead(BaseModel):
+class WorkflowReadV2(BaseModel):
     id: int
     name: str
     project_id: int
-    task_list: list[WorkflowTaskRead]
-    project: ProjectRead
+    task_list: list[WorkflowTaskReadV2]
+    project: ProjectReadV2
     timestamp_created: AwareDatetime
 
     @field_serializer("timestamp_created")
@@ -35,18 +35,18 @@ class WorkflowRead(BaseModel):
         return v.isoformat()
 
 
-class WorkflowReadWithWarnings(WorkflowRead):
-    task_list: list[WorkflowTaskReadWithWarning]
+class WorkflowReadV2WithWarnings(WorkflowReadV2):
+    task_list: list[WorkflowTaskReadV2WithWarning]
 
 
-class WorkflowUpdate(BaseModel):
+class WorkflowUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None
     reordered_workflowtask_ids: ListUniqueNonNegativeInt | None = None
 
 
-class WorkflowImport(BaseModel):
+class WorkflowImportV2(BaseModel):
     """
     Class for `Workflow` import.
 
@@ -56,10 +56,10 @@ class WorkflowImport(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
     name: NonEmptyStr
-    task_list: list[WorkflowTaskImport]
+    task_list: list[WorkflowTaskImportV2]
 
 
-class WorkflowExport(BaseModel):
+class WorkflowExportV2(BaseModel):
     """
     Class for `Workflow` export.
 
@@ -68,4 +68,4 @@ class WorkflowExport(BaseModel):
     """
 
     name: str
-    task_list: list[WorkflowTaskExport]
+    task_list: list[WorkflowTaskExportV2]

fractal_server/app/schemas/v2/workflowtask.py

@@ -9,14 +9,14 @@ from fractal_server.types import DictStrAny
 from fractal_server.types import TypeFilters
 from fractal_server.types import WorkflowTaskArgument
 
-from .task import TaskExport
-from .task import TaskImport
-from .task import TaskImportLegacy
-from .task import TaskRead
+from .task import TaskExportV2
+from .task import TaskImportV2
+from .task import TaskImportV2Legacy
+from .task import TaskReadV2
 from .task import TaskType
 
 
-class WorkflowTaskCreate(BaseModel):
+class WorkflowTaskCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     meta_non_parallel: DictStrAny | None = None
@@ -26,14 +26,14 @@ class WorkflowTaskCreate(BaseModel):
     type_filters: TypeFilters = Field(default_factory=dict)
 
 
-class WorkflowTaskReplace(BaseModel):
+class WorkflowTaskReplaceV2(BaseModel):
     """Used by 'replace-task' endpoint"""
 
     args_non_parallel: dict[str, Any] | None = None
     args_parallel: dict[str, Any] | None = None
 
 
-class WorkflowTaskRead(BaseModel):
+class WorkflowTaskReadV2(BaseModel):
     id: int
 
     workflow_id: int
@@ -48,14 +48,14 @@ class WorkflowTaskRead(BaseModel):
 
     task_type: TaskType
     task_id: int
-    task: TaskRead
+    task: TaskReadV2
 
 
-class WorkflowTaskReadWithWarning(WorkflowTaskRead):
+class WorkflowTaskReadV2WithWarning(WorkflowTaskReadV2):
     warning: str | None = None
 
 
-class WorkflowTaskUpdate(BaseModel):
+class WorkflowTaskUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     meta_non_parallel: DictStrAny | None = None
@@ -65,7 +65,7 @@ class WorkflowTaskUpdate(BaseModel):
     type_filters: TypeFilters = None
 
 
-class WorkflowTaskImport(BaseModel):
+class WorkflowTaskImportV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     meta_non_parallel: DictStrAny | None = None
@@ -75,7 +75,7 @@ class WorkflowTaskImport(BaseModel):
     type_filters: TypeFilters | None = None
     input_filters: dict[str, Any] | None = None
 
-    task: TaskImport | TaskImportLegacy
+    task: TaskImportV2 | TaskImportV2Legacy
 
     @model_validator(mode="before")
     @classmethod
@@ -106,11 +106,11 @@ class WorkflowTaskImport(BaseModel):
         return values
 
 
-class WorkflowTaskExport(BaseModel):
+class WorkflowTaskExportV2(BaseModel):
     meta_non_parallel: dict[str, Any] | None = None
     meta_parallel: dict[str, Any] | None = None
     args_non_parallel: dict[str, Any] | None = None
     args_parallel: dict[str, Any] | None = None
     type_filters: dict[str, bool] = Field(default_factory=dict)
 
-    task: TaskExport
+    task: TaskExportV2

fractal_server/app/security/__init__.py

@@ -425,7 +425,7 @@ async def _create_first_user(
                     kwargs = dict(
                         email=email,
                         password=password,
-                        project_dirs=[project_dir],
+                        project_dir=project_dir,
                         profile_id=profile_id,
                         is_superuser=is_superuser,
                         is_verified=is_verified,

fractal_server/app/shutdown.py

@@ -4,26 +4,26 @@ from sqlmodel import select
 
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models.v2 import JobV2
-from fractal_server.app.models.v2.job import JobStatusType
+from fractal_server.app.models.v2.job import JobStatusTypeV2
 from fractal_server.app.routes.aux._job import _write_shutdown_file
 from fractal_server.config import get_settings
 from fractal_server.logger import get_logger
 from fractal_server.syringe import Inject
 
 
-async def cleanup_after_shutdown(*, jobs: list[int], logger_name: str):
+async def cleanup_after_shutdown(*, jobsV2: list[int], logger_name: str):
     settings = Inject(get_settings)
     logger = get_logger(logger_name)
     logger.info("Cleanup function after shutdown")
     stm_objects = (
         select(JobV2)
-        .where(JobV2.id.in_(jobs))
-        .where(JobV2.status == JobStatusType.SUBMITTED)
+        .where(JobV2.id.in_(jobsV2))
+        .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
     )
     stm_ids = (
         select(JobV2.id)
-        .where(JobV2.id.in_(jobs))
-        .where(JobV2.status == JobStatusType.SUBMITTED)
+        .where(JobV2.id.in_(jobsV2))
+        .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
     )
 
     async for session in get_async_db():

fractal_server/config/__init__.py

@@ -1,3 +1,5 @@
+from ._data import DataAuthScheme  # noqa F401
+from ._data import DataSettings
 from ._database import DatabaseSettings
 from ._email import EmailSettings
 from ._email import PublicEmailSettings  # noqa F401
@@ -19,3 +21,7 @@ def get_email_settings(email_settings=EmailSettings()) -> EmailSettings:
 
 def get_oauth_settings(oauth_settings=OAuthSettings()) -> OAuthSettings:
     return oauth_settings
+
+
+def get_data_settings(data_settings=DataSettings()) -> DataSettings:
+    return data_settings