fractal-server 2.12.1__py3-none-any.whl → 2.13.0__py3-none-any.whl

fractal_server/app/schemas/v2/task_collection.py

@@ -3,9 +3,9 @@ from typing import Literal
 from typing import Optional
 
 from pydantic import BaseModel
-from pydantic import Extra
-from pydantic import root_validator
-from pydantic import validator
+from pydantic import ConfigDict
+from pydantic import field_validator
+from pydantic import model_validator
 
 from .._validators import valstr
 from fractal_server.app.schemas.v2 import ManifestV2
@@ -21,7 +21,7 @@ class WheelFile(BaseModel):
     contents: bytes
 
 
-class TaskCollectPipV2(BaseModel, extra=Extra.forbid):
+class TaskCollectPipV2(BaseModel):
     """
     TaskCollectPipV2 class
 
@@ -45,35 +45,40 @@ class TaskCollectPipV2(BaseModel, extra=Extra.forbid):
 
     """
 
+    model_config = ConfigDict(extra="forbid")
     package: Optional[str] = None
     package_version: Optional[str] = None
     package_extras: Optional[str] = None
     python_version: Optional[Literal["3.9", "3.10", "3.11", "3.12"]] = None
     pinned_package_versions: Optional[dict[str, str]] = None
 
-    @validator("package")
+    @field_validator("package")
+    @classmethod
     def package_validator(cls, value: Optional[str]) -> Optional[str]:
         if value is None:
             return value
-        value = valstr("package")(value)
+        value = valstr("package")(cls, value)
         validate_cmd(value, attribute_name="package")
         return value
 
-    @validator("package_version")
+    @field_validator("package_version")
+    @classmethod
     def package_version_validator(cls, value: Optional[str]) -> Optional[str]:
         if value is None:
             return value
-        value = valstr("package_version")(value)
+        value = valstr("package_version")(cls, value)
         validate_cmd(value, attribute_name="package_version")
         return value
 
-    @validator("pinned_package_versions")
+    @field_validator("pinned_package_versions")
+    @classmethod
     def pinned_package_versions_validator(cls, value):
         if value is None:
             return value
         old_keys = list(value.keys())
         new_keys = [
-            valstr(f"pinned_package_versions[{key}]")(key) for key in old_keys
+            valstr(f"pinned_package_versions[{key}]")(cls, key)
+            for key in old_keys
         ]
         if len(new_keys) != len(set(new_keys)):
             raise ValueError(
@@ -87,16 +92,17 @@ class TaskCollectPipV2(BaseModel, extra=Extra.forbid):
             validate_cmd(version)
         return value
 
-    @validator("package_extras")
+    @field_validator("package_extras")
+    @classmethod
     def package_extras_validator(cls, value: Optional[str]) -> Optional[str]:
         if value is None:
             return value
-        value = valstr("package_extras")(value)
+        value = valstr("package_extras")(cls, value)
         validate_cmd(value, attribute_name="package_extras")
         return value
 
 
-class TaskCollectCustomV2(BaseModel, extra=Extra.forbid):
+class TaskCollectCustomV2(BaseModel):
     """
     Attributes:
         manifest: Manifest of a Fractal task package (this is typically the
@@ -114,29 +120,31 @@ class TaskCollectCustomV2(BaseModel, extra=Extra.forbid):
         version: Optional version of tasks to be collected.
     """
 
+    model_config = ConfigDict(extra="forbid")
     manifest: ManifestV2
     python_interpreter: str
     label: str
-    package_root: Optional[str]
-    package_name: Optional[str]
-    version: Optional[str]
+    package_root: Optional[str] = None
+    package_name: Optional[str] = None
+    version: Optional[str] = None
 
     # Valstr
-    _python_interpreter = validator("python_interpreter", allow_reuse=True)(
-        valstr("python_interpreter")
+    _python_interpreter = field_validator("python_interpreter")(
+        classmethod(valstr("python_interpreter"))
     )
-    _label = validator("label", allow_reuse=True)(valstr("label"))
-    _package_root = validator("package_root", allow_reuse=True)(
-        valstr("package_root", accept_none=True)
+    _label = field_validator("label")(classmethod(valstr("label")))
+    _package_root = field_validator("package_root")(
+        classmethod(valstr("package_root", accept_none=True))
     )
-    _package_name = validator("package_name", allow_reuse=True)(
-        valstr("package_name", accept_none=True)
+    _package_name = field_validator("package_name")(
+        classmethod(valstr("package_name", accept_none=True))
     )
-    _version = validator("version", allow_reuse=True)(
-        valstr("version", accept_none=True)
+    _version = field_validator("version")(
+        classmethod(valstr("version", accept_none=True))
     )
 
-    @root_validator(pre=True)
+    @model_validator(mode="before")
+    @classmethod
     def one_of_package_root_or_name(cls, values):
         package_root = values.get("package_root")
         package_name = values.get("package_name")
@@ -149,18 +157,20 @@ class TaskCollectCustomV2(BaseModel, extra=Extra.forbid):
             )
         return values
 
-    @validator("package_name")
+    @field_validator("package_name")
+    @classmethod
     def package_name_validator(cls, value: str):
         """
         Remove all whitespace characters, then check for invalid code.
         """
         if value is not None:
             validate_cmd(value)
-            value = valstr("package_name")(value)
+            value = valstr("package_name")(cls, value)
             value = value.replace(" ", "")
         return value
 
-    @validator("package_root")
+    @field_validator("package_root")
+    @classmethod
     def package_root_validator(cls, value):
         if (value is not None) and (not Path(value).is_absolute()):
             raise ValueError(
@@ -168,7 +178,8 @@ class TaskCollectCustomV2(BaseModel, extra=Extra.forbid):
             )
         return value
 
-    @validator("python_interpreter")
+    @field_validator("python_interpreter")
+    @classmethod
     def python_interpreter_validator(cls, value):
         if not Path(value).is_absolute():
             raise ValueError(

fractal_server/app/schemas/v2/task_group.py

@@ -3,9 +3,11 @@ from enum import Enum
 from typing import Optional
 
 from pydantic import BaseModel
-from pydantic import Extra
+from pydantic import ConfigDict
 from pydantic import Field
-from pydantic import validator
+from pydantic import field_serializer
+from pydantic import field_validator
+from pydantic.types import AwareDatetime
 
 from .._validators import val_absolute_path
 from .._validators import valdict_keys
@@ -32,7 +34,8 @@ class TaskGroupActivityActionV2(str, Enum):
     REACTIVATE = "reactivate"
 
 
-class TaskGroupCreateV2(BaseModel, extra=Extra.forbid):
+class TaskGroupCreateV2(BaseModel):
+    model_config = ConfigDict(extra="forbid")
     user_id: int
     user_group_id: Optional[int] = None
     active: bool = True
@@ -48,21 +51,21 @@ class TaskGroupCreateV2(BaseModel, extra=Extra.forbid):
     pinned_package_versions: dict[str, str] = Field(default_factory=dict)
 
     # Validators
-    _path = validator("path", allow_reuse=True)(val_absolute_path("path"))
-    _venv_path = validator("venv_path", allow_reuse=True)(
-        val_absolute_path("venv_path")
+    _path = field_validator("path")(classmethod(val_absolute_path("path")))
+    _venv_path = field_validator("venv_path")(
+        classmethod(val_absolute_path("venv_path"))
     )
-    _wheel_path = validator("wheel_path", allow_reuse=True)(
-        val_absolute_path("wheel_path")
+    _wheel_path = field_validator("wheel_path")(
+        classmethod(val_absolute_path("wheel_path"))
     )
-    _pinned_package_versions = validator(
-        "pinned_package_versions", allow_reuse=True
-    )(valdict_keys("pinned_package_versions"))
-    _pip_extras = validator("pip_extras", allow_reuse=True)(
-        valstr("pip_extras")
+    _pinned_package_versions = field_validator("pinned_package_versions")(
+        valdict_keys("pinned_package_versions")
     )
-    _python_version = validator("python_version", allow_reuse=True)(
-        valstr("python_version")
+    _pip_extras = field_validator("pip_extras")(
+        classmethod(valstr("pip_extras"))
+    )
+    _python_version = field_validator("python_version")(
+        classmethod(valstr("python_version"))
     )
 
 
@@ -99,11 +102,16 @@ class TaskGroupReadV2(BaseModel):
     venv_file_number: Optional[int] = None
 
     active: bool
-    timestamp_created: datetime
-    timestamp_last_used: datetime
+    timestamp_created: AwareDatetime
+    timestamp_last_used: AwareDatetime
+
+    @field_serializer("timestamp_created", "timestamp_last_used")
+    def serialize_datetime(v: datetime) -> str:
+        return v.isoformat()
 
 
-class TaskGroupUpdateV2(BaseModel, extra=Extra.forbid):
+class TaskGroupUpdateV2(BaseModel):
+    model_config = ConfigDict(extra="forbid")
     user_group_id: Optional[int] = None
 
 
@@ -111,10 +119,21 @@ class TaskGroupActivityV2Read(BaseModel):
     id: int
     user_id: int
     taskgroupv2_id: Optional[int] = None
-    timestamp_started: datetime
-    timestamp_ended: Optional[datetime] = None
+    timestamp_started: AwareDatetime
+    timestamp_ended: Optional[AwareDatetime] = None
     pkg_name: str
     version: str
     status: TaskGroupActivityStatusV2
     action: TaskGroupActivityActionV2
     log: Optional[str] = None
+
+    @field_serializer("timestamp_started")
+    def serialize_datetime_start(v: datetime) -> str:
+        return v.isoformat()
+
+    @field_serializer("timestamp_ended")
+    def serialize_datetime_end(v: Optional[datetime]) -> Optional[str]:
+        if v is None:
+            return None
+        else:
+            return v.isoformat()

fractal_server/app/schemas/v2/workflow.py

@@ -2,8 +2,10 @@ from datetime import datetime
 from typing import Optional
 
 from pydantic import BaseModel
-from pydantic import Extra
-from pydantic import validator
+from pydantic import ConfigDict
+from pydantic import field_serializer
+from pydantic import field_validator
+from pydantic.types import AwareDatetime
 
 from .._validators import valstr
 from .project import ProjectReadV2
@@ -13,12 +15,14 @@ from .workflowtask import WorkflowTaskReadV2
 from .workflowtask import WorkflowTaskReadV2WithWarning
 
 
-class WorkflowCreateV2(BaseModel, extra=Extra.forbid):
+class WorkflowCreateV2(BaseModel):
+
+    model_config = ConfigDict(extra="forbid")
 
     name: str
 
     # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
+    _name = field_validator("name")(classmethod(valstr("name")))
 
 
 class WorkflowReadV2(BaseModel):
@@ -28,22 +32,29 @@ class WorkflowReadV2(BaseModel):
     project_id: int
     task_list: list[WorkflowTaskReadV2]
     project: ProjectReadV2
-    timestamp_created: datetime
+    timestamp_created: AwareDatetime
+
+    @field_serializer("timestamp_created")
+    def serialize_datetime(v: datetime) -> str:
+        return v.isoformat()
 
 
 class WorkflowReadV2WithWarnings(WorkflowReadV2):
     task_list: list[WorkflowTaskReadV2WithWarning]
 
 
-class WorkflowUpdateV2(BaseModel, extra=Extra.forbid):
+class WorkflowUpdateV2(BaseModel):
+
+    model_config = ConfigDict(extra="forbid")
 
-    name: Optional[str]
-    reordered_workflowtask_ids: Optional[list[int]]
+    name: Optional[str] = None
+    reordered_workflowtask_ids: Optional[list[int]] = None
 
     # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
+    _name = field_validator("name")(classmethod(valstr("name")))
 
-    @validator("reordered_workflowtask_ids")
+    @field_validator("reordered_workflowtask_ids")
+    @classmethod
     def check_positive_and_unique(cls, value):
         if any(i < 0 for i in value):
             raise ValueError("Negative `id` in `reordered_workflowtask_ids`")
@@ -52,7 +63,7 @@ class WorkflowUpdateV2(BaseModel, extra=Extra.forbid):
         return value
 
 
-class WorkflowImportV2(BaseModel, extra=Extra.forbid):
+class WorkflowImportV2(BaseModel):
     """
     Class for `Workflow` import.
 
@@ -60,11 +71,12 @@ class WorkflowImportV2(BaseModel, extra=Extra.forbid):
         task_list:
     """
 
+    model_config = ConfigDict(extra="forbid")
     name: str
     task_list: list[WorkflowTaskImportV2]
 
     # Validators
-    _name = validator("name", allow_reuse=True)(valstr("name"))
+    _name = field_validator("name")(classmethod(valstr("name")))
 
 
 class WorkflowExportV2(BaseModel):

fractal_server/app/schemas/v2/workflowtask.py

@@ -4,10 +4,10 @@ from typing import Optional
 from typing import Union
 
 from pydantic import BaseModel
-from pydantic import Extra
+from pydantic import ConfigDict
 from pydantic import Field
-from pydantic import root_validator
-from pydantic import validator
+from pydantic import field_validator
+from pydantic import model_validator
 
 from .._filter_validators import validate_type_filters
 from .._validators import root_validate_dict_keys
@@ -39,34 +39,35 @@ class WorkflowTaskStatusTypeV2(str, Enum):
     FAILED = "failed"
 
 
-class WorkflowTaskCreateV2(BaseModel, extra=Extra.forbid):
+class WorkflowTaskCreateV2(BaseModel):
+    model_config = ConfigDict(extra="forbid")
 
-    meta_non_parallel: Optional[dict[str, Any]]
-    meta_parallel: Optional[dict[str, Any]]
-    args_non_parallel: Optional[dict[str, Any]]
-    args_parallel: Optional[dict[str, Any]]
+    meta_non_parallel: Optional[dict[str, Any]] = None
+    meta_parallel: Optional[dict[str, Any]] = None
+    args_non_parallel: Optional[dict[str, Any]] = None
+    args_parallel: Optional[dict[str, Any]] = None
     type_filters: dict[str, bool] = Field(default_factory=dict)
 
     # Validators
-    _dict_keys = root_validator(pre=True, allow_reuse=True)(
-        root_validate_dict_keys
+    _dict_keys = model_validator(mode="before")(
+        classmethod(root_validate_dict_keys)
     )
-    _type_filters = validator("type_filters", allow_reuse=True)(
-        validate_type_filters
+    _type_filters = field_validator("type_filters")(
+        classmethod(validate_type_filters)
     )
-
-    _meta_non_parallel = validator("meta_non_parallel", allow_reuse=True)(
-        valdict_keys("meta_non_parallel")
+    _meta_non_parallel = field_validator("meta_non_parallel")(
+        classmethod(valdict_keys("meta_non_parallel"))
     )
-    _meta_parallel = validator("meta_parallel", allow_reuse=True)(
-        valdict_keys("meta_parallel")
+    _meta_parallel = field_validator("meta_parallel")(
+        classmethod(valdict_keys("meta_parallel"))
     )
 
-    @validator("args_non_parallel")
+    @field_validator("args_non_parallel")
+    @classmethod
     def validate_args_non_parallel(cls, value):
         if value is None:
             return
-        valdict_keys("args_non_parallel")(value)
+        valdict_keys("args_non_parallel")(cls, value)
         args_keys = set(value.keys())
         intersect_keys = RESERVED_ARGUMENTS.intersection(args_keys)
         if intersect_keys:
@@ -76,11 +77,12 @@ class WorkflowTaskCreateV2(BaseModel, extra=Extra.forbid):
             )
         return value
 
-    @validator("args_parallel")
+    @field_validator("args_parallel")
+    @classmethod
     def validate_args_parallel(cls, value):
         if value is None:
             return
-        valdict_keys("args_parallel")(value)
+        valdict_keys("args_parallel")(cls, value)
         args_keys = set(value.keys())
         intersect_keys = RESERVED_ARGUMENTS.intersection(args_keys)
         if intersect_keys:
@@ -99,16 +101,15 @@ class WorkflowTaskReplaceV2(BaseModel):
 
 
 class WorkflowTaskReadV2(BaseModel):
-
     id: int
 
     workflow_id: int
-    order: Optional[int]
-    meta_non_parallel: Optional[dict[str, Any]]
-    meta_parallel: Optional[dict[str, Any]]
+    order: Optional[int] = None
+    meta_non_parallel: Optional[dict[str, Any]] = None
+    meta_parallel: Optional[dict[str, Any]] = None
 
-    args_non_parallel: Optional[dict[str, Any]]
-    args_parallel: Optional[dict[str, Any]]
+    args_non_parallel: Optional[dict[str, Any]] = None
+    args_parallel: Optional[dict[str, Any]] = None
 
     type_filters: dict[str, bool]
 
@@ -121,34 +122,35 @@ class WorkflowTaskReadV2WithWarning(WorkflowTaskReadV2):
     warning: Optional[str] = None
 
 
-class WorkflowTaskUpdateV2(BaseModel, extra=Extra.forbid):
+class WorkflowTaskUpdateV2(BaseModel):
+    model_config = ConfigDict(extra="forbid")
 
-    meta_non_parallel: Optional[dict[str, Any]]
-    meta_parallel: Optional[dict[str, Any]]
-    args_non_parallel: Optional[dict[str, Any]]
-    args_parallel: Optional[dict[str, Any]]
-    type_filters: Optional[dict[str, bool]]
+    meta_non_parallel: Optional[dict[str, Any]] = None
+    meta_parallel: Optional[dict[str, Any]] = None
+    args_non_parallel: Optional[dict[str, Any]] = None
+    args_parallel: Optional[dict[str, Any]] = None
+    type_filters: Optional[dict[str, bool]] = None
 
     # Validators
-    _dict_keys = root_validator(pre=True, allow_reuse=True)(
-        root_validate_dict_keys
+    _dict_keys = model_validator(mode="before")(
+        classmethod(root_validate_dict_keys)
     )
-    _type_filters = validator("type_filters", allow_reuse=True)(
-        validate_type_filters
+    _type_filters = field_validator("type_filters")(
+        classmethod(validate_type_filters)
     )
-
-    _meta_non_parallel = validator("meta_non_parallel", allow_reuse=True)(
-        valdict_keys("meta_non_parallel")
+    _meta_non_parallel = field_validator("meta_non_parallel")(
+        classmethod(valdict_keys("meta_non_parallel"))
     )
-    _meta_parallel = validator("meta_parallel", allow_reuse=True)(
-        valdict_keys("meta_parallel")
+    _meta_parallel = field_validator("meta_parallel")(
+        classmethod(valdict_keys("meta_parallel"))
     )
 
-    @validator("args_non_parallel")
+    @field_validator("args_non_parallel")
+    @classmethod
     def validate_args_non_parallel(cls, value):
         if value is None:
             return
-        valdict_keys("args_non_parallel")(value)
+        valdict_keys("args_non_parallel")(cls, value)
         args_keys = set(value.keys())
         intersect_keys = RESERVED_ARGUMENTS.intersection(args_keys)
         if intersect_keys:
@@ -158,11 +160,12 @@ class WorkflowTaskUpdateV2(BaseModel, extra=Extra.forbid):
             )
         return value
 
-    @validator("args_parallel")
+    @field_validator("args_parallel")
+    @classmethod
     def validate_args_parallel(cls, value):
         if value is None:
             return
-        valdict_keys("args_parallel")(value)
+        valdict_keys("args_parallel")(cls, value)
         args_keys = set(value.keys())
         intersect_keys = RESERVED_ARGUMENTS.intersection(args_keys)
         if intersect_keys:
@@ -173,7 +176,8 @@ class WorkflowTaskUpdateV2(BaseModel, extra=Extra.forbid):
         return value
 
 
-class WorkflowTaskImportV2(BaseModel, extra=Extra.forbid):
+class WorkflowTaskImportV2(BaseModel):
+    model_config = ConfigDict(extra="forbid")
 
     meta_non_parallel: Optional[dict[str, Any]] = None
     meta_parallel: Optional[dict[str, Any]] = None
@@ -185,7 +189,8 @@ class WorkflowTaskImportV2(BaseModel, extra=Extra.forbid):
     task: Union[TaskImportV2, TaskImportV2Legacy]
 
     # Validators
-    @root_validator(pre=True)
+    @model_validator(mode="before")
+    @classmethod
     def update_legacy_filters(cls, values: dict):
         """
         Transform legacy filters (created with fractal-server<2.11.0)
@@ -197,7 +202,6 @@ class WorkflowTaskImportV2(BaseModel, extra=Extra.forbid):
                     "Cannot set filters both through the legacy field "
                     "('filters') and the new one ('type_filters')."
                 )
-
             else:
                 # As of 2.11.0, WorkflowTask do not have attribute filters
                 # any more.
@@ -213,26 +217,24 @@ class WorkflowTaskImportV2(BaseModel, extra=Extra.forbid):
 
         return values
 
-    _type_filters = validator("type_filters", allow_reuse=True)(
-        validate_type_filters
+    _type_filters = field_validator("type_filters")(
+        classmethod(validate_type_filters)
     )
-
-    _meta_non_parallel = validator("meta_non_parallel", allow_reuse=True)(
-        valdict_keys("meta_non_parallel")
+    _meta_non_parallel = field_validator("meta_non_parallel")(
+        classmethod(valdict_keys("meta_non_parallel"))
     )
-    _meta_parallel = validator("meta_parallel", allow_reuse=True)(
-        valdict_keys("meta_parallel")
+    _meta_parallel = field_validator("meta_parallel")(
+        classmethod(valdict_keys("meta_parallel"))
     )
-    _args_non_parallel = validator("args_non_parallel", allow_reuse=True)(
-        valdict_keys("args_non_parallel")
+    _args_non_parallel = field_validator("args_non_parallel")(
+        classmethod(valdict_keys("args_non_parallel"))
     )
-    _args_parallel = validator("args_parallel", allow_reuse=True)(
-        valdict_keys("args_parallel")
+    _args_parallel = field_validator("args_parallel")(
+        classmethod(valdict_keys("args_parallel"))
     )
 
 
 class WorkflowTaskExportV2(BaseModel):
-
     meta_non_parallel: Optional[dict[str, Any]] = None
     meta_parallel: Optional[dict[str, Any]] = None
     args_non_parallel: Optional[dict[str, Any]] = None

fractal_server/app/security/__init__.py

@@ -83,7 +83,7 @@ class SQLModelUserDatabaseAsync(Generic[UP, ID], BaseUserDatabase[UP, ID]):
 
     session: AsyncSession
     user_model: Type[UP]
-    oauth_account_model: Optional[Type[OAuthAccount]]
+    oauth_account_model: Optional[Type[OAuthAccount]] = None
 
     def __init__(
         self,