fractal-server 2.17.2__py3-none-any.whl → 2.18.0__py3-none-any.whl

fractal_server/app/schemas/v2/status_legacy.py

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

fractal_server/app/schemas/v2/task.py

@@ -29,7 +29,7 @@ class TaskType(StrEnum):
     PARALLEL = "parallel"
 
 
-class TaskCreateV2(BaseModel):
+class TaskCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
@@ -90,7 +90,7 @@ class TaskCreateV2(BaseModel):
         return self
 
 
-class TaskReadV2(BaseModel):
+class TaskRead(BaseModel):
     id: int
     name: str
     type: TaskType
@@ -117,7 +117,7 @@ class TaskReadV2(BaseModel):
     tags: list[str]
 
 
-class TaskUpdateV2(BaseModel):
+class TaskUpdate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     command_parallel: NonEmptyStr = None
@@ -131,7 +131,7 @@ class TaskUpdateV2(BaseModel):
     tags: ListUniqueNonEmptyString | None = None
 
 
-class TaskImportV2(BaseModel):
+class TaskImport(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     pkg_name: NonEmptyStr
@@ -139,11 +139,11 @@ class TaskImportV2(BaseModel):
     name: NonEmptyStr
 
 
-class TaskImportV2Legacy(BaseModel):
+class TaskImportLegacy(BaseModel):
     source: NonEmptyStr
 
 
-class TaskExportV2(BaseModel):
+class TaskExport(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 TaskCollectPipV2(BaseModel):
+class TaskCollectPip(BaseModel):
     """
-    TaskCollectPipV2 class
+    TaskCollectPip 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 TaskCollectPipV2(BaseModel):
         return value
 
 
-class TaskCollectCustomV2(BaseModel):
+class TaskCollectCustom(BaseModel):
     """
     Attributes:
         manifest: Manifest of a Fractal task package (this is typically the
@@ -99,7 +99,7 @@ class TaskCollectCustomV2(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
-            `TaskGroupV2.pkg_name` column.
+            `TaskGroup.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 TaskReadV2
+from fractal_server.app.schemas.v2.task import TaskRead
 from fractal_server.types import AbsolutePathStr
 from fractal_server.types import DictStrStr
 from fractal_server.types import NonEmptyStr
 
 
-class TaskGroupV2OriginEnum(StrEnum):
+class TaskGroupOriginEnum(StrEnum):
     PYPI = "pypi"
     WHEELFILE = "wheel-file"
     PIXI = "pixi"
     OTHER = "other"
 
 
-class TaskGroupActivityStatusV2(StrEnum):
+class TaskGroupActivityStatus(StrEnum):
     PENDING = "pending"
     ONGOING = "ongoing"
     FAILED = "failed"
     OK = "OK"
 
 
-class TaskGroupActivityActionV2(StrEnum):
+class TaskGroupActivityAction(StrEnum):
     COLLECT = "collect"
     DEACTIVATE = "deactivate"
     REACTIVATE = "reactivate"
     DELETE = "delete"
 
 
-class TaskGroupCreateV2(BaseModel):
+class TaskGroupCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
     user_id: int
     resource_id: int
     user_group_id: int | None = None
     active: bool = True
-    origin: TaskGroupV2OriginEnum
+    origin: TaskGroupOriginEnum
     pkg_name: str
     version: str | None = None
     python_version: NonEmptyStr = None
@@ -54,9 +54,9 @@ class TaskGroupCreateV2(BaseModel):
     pinned_package_versions_post: DictStrStr = Field(default_factory=dict)
 
 
-class TaskGroupCreateV2Strict(TaskGroupCreateV2):
+class TaskGroupCreateStrict(TaskGroupCreate):
     """
-    A strict version of TaskGroupCreateV2, to be used for task collection.
+    A strict version of TaskGroupCreate, to be used for task collection.
     """
 
     path: AbsolutePathStr
@@ -65,14 +65,14 @@ class TaskGroupCreateV2Strict(TaskGroupCreateV2):
     python_version: NonEmptyStr
 
 
-class TaskGroupReadV2(BaseModel):
+class TaskGroupRead(BaseModel):
     id: int
-    task_list: list[TaskReadV2]
+    task_list: list[TaskRead]
 
     user_id: int
     user_group_id: int | None = None
 
-    origin: TaskGroupV2OriginEnum
+    origin: TaskGroupOriginEnum
     pkg_name: str
     version: str | None = None
     python_version: str | None = None
@@ -96,16 +96,16 @@ class TaskGroupReadV2(BaseModel):
         return v.isoformat()
 
 
-class TaskGroupReadSuperuser(TaskGroupReadV2):
+class TaskGroupReadSuperuser(TaskGroupRead):
     resource_id: int
 
 
-class TaskGroupUpdateV2(BaseModel):
+class TaskGroupUpdate(BaseModel):
     model_config = ConfigDict(extra="forbid")
     user_group_id: int | None = None
 
 
-class TaskGroupActivityV2Read(BaseModel):
+class TaskGroupActivityRead(BaseModel):
     id: int
     user_id: int
     taskgroupv2_id: int | None = None
@@ -113,8 +113,8 @@ class TaskGroupActivityV2Read(BaseModel):
     timestamp_ended: AwareDatetime | None = None
     pkg_name: str
     version: str
-    status: TaskGroupActivityStatusV2
-    action: TaskGroupActivityActionV2
+    status: TaskGroupActivityStatus
+    action: TaskGroupActivityAction
     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 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.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.workflowtask import (
-    WorkflowTaskReadV2WithWarning,
+    WorkflowTaskReadWithWarning,
 )
 from fractal_server.types import ListUniqueNonNegativeInt
 from fractal_server.types import NonEmptyStr
 
 
-class WorkflowCreateV2(BaseModel):
+class WorkflowCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
-class WorkflowReadV2(BaseModel):
+class WorkflowRead(BaseModel):
     id: int
     name: str
     project_id: int
-    task_list: list[WorkflowTaskReadV2]
-    project: ProjectReadV2
+    task_list: list[WorkflowTaskRead]
+    project: ProjectRead
     timestamp_created: AwareDatetime
 
     @field_serializer("timestamp_created")
@@ -35,18 +35,18 @@ class WorkflowReadV2(BaseModel):
         return v.isoformat()
 
 
-class WorkflowReadV2WithWarnings(WorkflowReadV2):
-    task_list: list[WorkflowTaskReadV2WithWarning]
+class WorkflowReadWithWarnings(WorkflowRead):
+    task_list: list[WorkflowTaskReadWithWarning]
 
 
-class WorkflowUpdateV2(BaseModel):
+class WorkflowUpdate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None
     reordered_workflowtask_ids: ListUniqueNonNegativeInt | None = None
 
 
-class WorkflowImportV2(BaseModel):
+class WorkflowImport(BaseModel):
     """
     Class for `Workflow` import.
 
@@ -56,10 +56,10 @@ class WorkflowImportV2(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
     name: NonEmptyStr
-    task_list: list[WorkflowTaskImportV2]
+    task_list: list[WorkflowTaskImport]
 
 
-class WorkflowExportV2(BaseModel):
+class WorkflowExport(BaseModel):
     """
     Class for `Workflow` export.
 
@@ -68,4 +68,4 @@ class WorkflowExportV2(BaseModel):
     """
 
     name: str
-    task_list: list[WorkflowTaskExportV2]
+    task_list: list[WorkflowTaskExport]

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

fractal_server/app/security/__init__.py

@@ -425,7 +425,7 @@ async def _create_first_user(
                     kwargs = dict(
                         email=email,
                         password=password,
-                        project_dir=project_dir,
+                        project_dirs=[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 JobStatusTypeV2
+from fractal_server.app.models.v2.job import JobStatusType
 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(*, jobsV2: list[int], logger_name: str):
+async def cleanup_after_shutdown(*, jobs: 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_(jobsV2))
-        .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
+        .where(JobV2.id.in_(jobs))
+        .where(JobV2.status == JobStatusType.SUBMITTED)
     )
     stm_ids = (
         select(JobV2.id)
-        .where(JobV2.id.in_(jobsV2))
-        .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
+        .where(JobV2.id.in_(jobs))
+        .where(JobV2.status == JobStatusType.SUBMITTED)
     )
 
     async for session in get_async_db():

fractal_server/config/__init__.py

@@ -1,5 +1,3 @@
-from ._data import DataAuthScheme  # noqa F401
-from ._data import DataSettings
 from ._database import DatabaseSettings
 from ._email import EmailSettings
 from ._email import PublicEmailSettings  # noqa F401
@@ -21,7 +19,3 @@ 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

fractal_server/config/_data.py

@@ -1,79 +0,0 @@
-from enum import StrEnum
-from typing import Self
-
-from pydantic import model_validator
-from pydantic_settings import BaseSettings
-from pydantic_settings import SettingsConfigDict
-
-from fractal_server.types import AbsolutePathStr
-
-from ._settings_config import SETTINGS_CONFIG_DICT
-
-
-class DataAuthScheme(StrEnum):
-    VIEWER_PATHS = "viewer-paths"
-    USERS_FOLDERS = "users-folders"
-    NONE = "none"
-
-
-class DataSettings(BaseSettings):
-    """
-    Settings for the `fractal-data` integration.
-
-    See https://github.com/fractal-analytics-platform/fractal-data.
-
-    Attributes:
-        FRACTAL_DATA_AUTH_SCHEME:
-            Defines how the list of allowed viewer paths is built.
-
-            This variable affects the
-            `GET /auth/current-user/allowed-viewer-paths/` response, which is
-            then consumed by
-            [fractal-data](https://github.com/fractal-analytics-platform/fractal-data).
-
-            Options:
-                <ul>
-                <li> `"viewer-paths"`: The list of allowed viewer paths will
-                    include the user's `project_dir` along with any path
-                    defined in  UserGroups `viewer_paths` attributes.
-                </li>
-                <li> `"users-folders"`: The list will consist of the user's
-                    `project_dir` and a user-specific folder. The user folder
-                    is constructed by concatenating the base folder
-                    `FRACTAL_DATA_BASE_FOLDER` with the user's profile
-                    `username`.
-                </li>
-                <li> `"none"`: An empty list will be returned, indicating no
-                    access to viewer paths. Useful when vizarr viewer is not
-                    used.
-                </li>
-                </ul>
-        FRACTAL_DATA_BASE_FOLDER:
-            Base path to Zarr files that will be served by
-            fractal-vizarr-viewer.
-            This variable is required and used only when
-            `FRACTAL_DATA_AUTHORIZATION_SCHEME` is set to `"users-folders"`.
-    """
-
-    model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
-
-    FRACTAL_DATA_AUTH_SCHEME: DataAuthScheme = "none"
-
-    FRACTAL_DATA_BASE_FOLDER: AbsolutePathStr | None = None
-
-    @model_validator(mode="after")
-    def check(self: Self) -> Self:
-        """
-        `FRACTAL_DATA_BASE_FOLDER` is required when
-        `FRACTAL_DATA_AUTHORIZATION_SCHEME` is set to `"users-folders"`.
-        """
-        if (
-            self.FRACTAL_DATA_AUTH_SCHEME == DataAuthScheme.USERS_FOLDERS
-            and self.FRACTAL_DATA_BASE_FOLDER is None
-        ):
-            raise ValueError(
-                "FRACTAL_DATA_BASE_FOLDER is required when "
-                "FRACTAL_DATA_AUTH_SCHEME is set to "
-                "users-folders"
-            )
-        return self

fractal_server/config/_main.py

@@ -28,7 +28,7 @@ class Settings(BaseSettings):
             Only logs of with this level (or higher) will appear in the console
             logs.
         FRACTAL_API_MAX_JOB_LIST_LENGTH:
-            Number of ids that can be stored in the `jobsV2` attribute of
+            Number of ids that can be stored in the `jobs` attribute of
             `app.state`.
         FRACTAL_GRACEFUL_SHUTDOWN_TIME:
             Waiting time for the shutdown phase of executors, in seconds.
@@ -41,6 +41,10 @@ class Settings(BaseSettings):
             user group (e.g. it cannot be deleted, and new users are
             automatically added to it). If set to `None` (the default value),
             then user groups are all equivalent, independently on their name.
+        FRACTAL_LONG_REQUEST_TIME:
+            Time limit beyond which the execution of an API request is
+            considered *slow* and an appropriate warning is logged by the
+            middleware.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
@@ -57,3 +61,4 @@ class Settings(BaseSettings):
     FRACTAL_GRACEFUL_SHUTDOWN_TIME: float = 30.0
     FRACTAL_HELP_URL: HttpUrl | None = None
     FRACTAL_DEFAULT_GROUP_NAME: Literal["All"] | None = None
+    FRACTAL_LONG_REQUEST_TIME: float = 30.0

fractal_server/data_migrations/2_18_0.py

@@ -0,0 +1,30 @@
+import logging
+import sys
+from os.path import normpath
+
+from sqlalchemy.orm.attributes import flag_modified
+from sqlmodel import select
+
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models import UserOAuth
+
+logging.basicConfig(level=logging.INFO)
+
+
+def fix_db():
+    logging.info("START - fix db")
+
+    with next(get_sync_db()) as db:
+        res = db.execute(select(UserOAuth).order_by(UserOAuth.email))
+        user_list = res.scalars().unique().all()
+
+        for user in user_list:
+            logging.info(f"Now handling user {user.email}.")
+            if user.project_dirs != []:
+                sys.exit(f"Non empty `project_dirs` for User[{user.id}]")
+            user.project_dirs.append(normpath(user.project_dir))
+            flag_modified(user, "project_dirs")
+
+        db.commit()
+
+    logging.info("END - fix db")

fractal_server/images/models.py

@@ -5,7 +5,6 @@ from fractal_server.types import DictStrAny
 from fractal_server.types import ImageAttributes
 from fractal_server.types import ImageAttributesWithNone
 from fractal_server.types import ImageTypes
-from fractal_server.types import ZarrDirStr
 from fractal_server.types import ZarrUrlStr
 
 
@@ -21,7 +20,7 @@ class SingleImageBase(BaseModel):
     """
 
     zarr_url: ZarrUrlStr
-    origin: ZarrDirStr | None = None
+    origin: ZarrUrlStr | None = None
 
     attributes: DictStrAny = Field(default_factory=dict)
     types: ImageTypes = Field(default_factory=dict)