fractal-server 2.13.1__py3-none-any.whl → 2.14.0__py3-none-any.whl

fractal_server/app/schemas/v2/task.py

@@ -9,38 +9,64 @@ from pydantic import field_validator
 from pydantic import HttpUrl
 from pydantic import model_validator
 
+from .._validators import cant_set_none
+from fractal_server.app.schemas._validators import NonEmptyString
 from fractal_server.app.schemas._validators import val_unique_list
 from fractal_server.app.schemas._validators import valdict_keys
-from fractal_server.app.schemas._validators import valstr
+from fractal_server.logger import set_logger
 from fractal_server.string_tools import validate_cmd
 
+TaskTypeType = Literal[
+    "compound",
+    "converter_compound",
+    "non_parallel",
+    "converter_non_parallel",
+    "parallel",
+]
+
+
+logger = set_logger(__name__)
+
 
 class TaskCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
-    name: str
+    name: NonEmptyString
 
-    command_non_parallel: Optional[str] = None
-    command_parallel: Optional[str] = None
+    command_non_parallel: Optional[NonEmptyString] = None
+    command_parallel: Optional[NonEmptyString] = None
 
     meta_non_parallel: Optional[dict[str, Any]] = None
     meta_parallel: Optional[dict[str, Any]] = None
-    version: Optional[str] = None
+    version: Optional[NonEmptyString] = None
     args_schema_non_parallel: Optional[dict[str, Any]] = None
     args_schema_parallel: Optional[dict[str, Any]] = None
-    args_schema_version: Optional[str] = None
+    args_schema_version: Optional[NonEmptyString] = None
     docs_info: Optional[str] = None
     docs_link: Optional[str] = None
 
     input_types: dict[str, bool] = Field(default={})
     output_types: dict[str, bool] = Field(default={})
 
-    category: Optional[str] = None
-    modality: Optional[str] = None
-    tags: list[str] = Field(default_factory=list)
-    authors: Optional[str] = None
+    category: Optional[NonEmptyString] = None
+    modality: Optional[NonEmptyString] = None
+    tags: list[NonEmptyString] = Field(default_factory=list)
+    authors: Optional[NonEmptyString] = None
+
+    type: Optional[TaskTypeType] = None
 
     # Validators
+
+    @field_validator(
+        "command_non_parallel",
+        "command_parallel",
+        "version",
+        "args_schema_version",
+    )
+    @classmethod
+    def _cant_set_none(cls, v):
+        return cant_set_none(v)
+
     @model_validator(mode="after")
     def validate_commands(self):
         command_parallel = self.command_parallel
@@ -57,14 +83,22 @@ class TaskCreateV2(BaseModel):
 
         return self
 
-    _name = field_validator("name")(classmethod(valstr("name")))
-    _command_non_parallel = field_validator("command_non_parallel")(
-        classmethod(valstr("command_non_parallel"))
-    )
-    _command_parallel = field_validator("command_parallel")(
-        classmethod(valstr("command_parallel"))
-    )
-    _version = field_validator("version")(classmethod(valstr("version")))
+    @model_validator(mode="after")
+    def set_task_type(self):
+        if self.type is None:
+            logger.warning(
+                f"Task type is not set for task '{self.name}', "
+                "which will be deprecated in a future version. "
+                "Please move to `fractal-task-tools`."
+            )
+            if self.command_non_parallel is None:
+                self.type = "parallel"
+            elif self.command_parallel is None:
+                self.type = "non_parallel"
+            else:
+                self.type = "compound"
+
+        return self
 
     _meta_non_parallel = field_validator("meta_non_parallel")(
         classmethod(valdict_keys("meta_non_parallel"))
@@ -78,9 +112,6 @@ class TaskCreateV2(BaseModel):
     _args_schema_parallel = field_validator("args_schema_parallel")(
         classmethod(valdict_keys("args_schema_parallel"))
     )
-    _args_schema_version = field_validator("args_schema_version")(
-        classmethod(valstr("args_schema_version"))
-    )
     _input_types = field_validator("input_types")(
         classmethod(valdict_keys("input_types"))
     )
@@ -88,21 +119,9 @@ class TaskCreateV2(BaseModel):
         classmethod(valdict_keys("output_types"))
     )
 
-    _category = field_validator("category")(
-        classmethod(valstr("category", accept_none=True))
-    )
-    _modality = field_validator("modality")(
-        classmethod(valstr("modality", accept_none=True))
-    )
-    _authors = field_validator("authors")(
-        classmethod(valstr("authors", accept_none=True))
-    )
-
     @field_validator("tags")
     @classmethod
     def validate_list_of_strings(cls, value):
-        for i, tag in enumerate(value):
-            value[i] = valstr(f"tags[{i}]")(cls, tag)
         return val_unique_list("tags")(cls, value)
 
     @field_validator("docs_link", mode="after")
@@ -116,7 +135,7 @@ class TaskCreateV2(BaseModel):
 class TaskReadV2(BaseModel):
     id: int
     name: str
-    type: Literal["parallel", "non_parallel", "compound"]
+    type: TaskTypeType
     source: Optional[str] = None
     version: Optional[str] = None
 
@@ -143,17 +162,23 @@ class TaskReadV2(BaseModel):
 class TaskUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
-    command_parallel: Optional[str] = None
-    command_non_parallel: Optional[str] = None
+    command_parallel: Optional[NonEmptyString] = None
+    command_non_parallel: Optional[NonEmptyString] = None
     input_types: Optional[dict[str, bool]] = None
     output_types: Optional[dict[str, bool]] = None
 
-    category: Optional[str] = None
-    modality: Optional[str] = None
-    authors: Optional[str] = None
-    tags: Optional[list[str]] = None
+    category: Optional[NonEmptyString] = None
+    modality: Optional[NonEmptyString] = None
+    authors: Optional[NonEmptyString] = None
+    tags: Optional[list[NonEmptyString]] = None
 
     # Validators
+
+    @field_validator("command_parallel", "command_non_parallel")
+    @classmethod
+    def _cant_set_none(cls, v):
+        return cant_set_none(v)
+
     @field_validator("input_types", "output_types")
     @classmethod
     def val_is_dict(cls, v):
@@ -161,12 +186,6 @@ class TaskUpdateV2(BaseModel):
             raise ValueError
         return v
 
-    _command_parallel = field_validator("command_parallel")(
-        classmethod(valstr("command_parallel"))
-    )
-    _command_non_parallel = field_validator("command_non_parallel")(
-        classmethod(valstr("command_non_parallel"))
-    )
     _input_types = field_validator("input_types")(
         classmethod(valdict_keys("input_types"))
     )
@@ -174,49 +193,25 @@ class TaskUpdateV2(BaseModel):
         classmethod(valdict_keys("output_types"))
     )
 
-    _category = field_validator("category")(
-        classmethod(valstr("category", accept_none=True))
-    )
-    _modality = field_validator("modality")(
-        classmethod(valstr("modality", accept_none=True))
-    )
-    _authors = field_validator("authors")(
-        classmethod(valstr("authors", accept_none=True))
-    )
-
     @field_validator("tags")
     @classmethod
     def validate_tags(cls, value):
-        for i, tag in enumerate(value):
-            value[i] = valstr(f"tags[{i}]")(cls, tag)
         return val_unique_list("tags")(cls, value)
 
 
 class TaskImportV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
-    pkg_name: str
-    version: Optional[str] = None
-    name: str
-    _pkg_name = field_validator("pkg_name")(classmethod(valstr("pkg_name")))
-    _version = field_validator("version")(
-        classmethod(valstr("version", accept_none=True))
-    )
-    _name = field_validator("name")(classmethod(valstr("name")))
+    pkg_name: NonEmptyString
+    version: Optional[NonEmptyString] = None
+    name: NonEmptyString
 
 
 class TaskImportV2Legacy(BaseModel):
-    source: str
-    _source = field_validator("source")(classmethod(valstr("source")))
+    source: NonEmptyString
 
 
 class TaskExportV2(BaseModel):
-    pkg_name: str
-    version: Optional[str] = None
-    name: str
-
-    _pkg_name = field_validator("pkg_name")(classmethod(valstr("pkg_name")))
-    _version = field_validator("version")(
-        classmethod(valstr("version", accept_none=True))
-    )
-    _name = field_validator("name")(classmethod(valstr("name")))
+    pkg_name: NonEmptyString
+    version: Optional[NonEmptyString] = None
+    name: NonEmptyString

fractal_server/app/schemas/v2/task_collection.py

@@ -7,7 +7,7 @@ from pydantic import ConfigDict
 from pydantic import field_validator
 from pydantic import model_validator
 
-from .._validators import valstr
+from .._validators import NonEmptyString
 from fractal_server.app.schemas.v2 import ManifestV2
 from fractal_server.string_tools import validate_cmd
 
@@ -46,9 +46,9 @@ class TaskCollectPipV2(BaseModel):
     """
 
     model_config = ConfigDict(extra="forbid")
-    package: Optional[str] = None
-    package_version: Optional[str] = None
-    package_extras: Optional[str] = None
+    package: Optional[NonEmptyString] = None
+    package_version: Optional[NonEmptyString] = None
+    package_extras: Optional[NonEmptyString] = None
     python_version: Optional[Literal["3.9", "3.10", "3.11", "3.12"]] = None
     pinned_package_versions: Optional[dict[str, str]] = None
 
@@ -57,7 +57,6 @@ class TaskCollectPipV2(BaseModel):
     def package_validator(cls, value: Optional[str]) -> Optional[str]:
         if value is None:
             return value
-        value = valstr("package")(cls, value)
         validate_cmd(value, attribute_name="package")
         return value
 
@@ -66,7 +65,6 @@ class TaskCollectPipV2(BaseModel):
     def package_version_validator(cls, value: Optional[str]) -> Optional[str]:
         if value is None:
             return value
-        value = valstr("package_version")(cls, value)
         validate_cmd(value, attribute_name="package_version")
         return value
 
@@ -75,11 +73,11 @@ class TaskCollectPipV2(BaseModel):
     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}]")(cls, key)
-            for key in old_keys
-        ]
+        new_keys = [key.strip() for key in old_keys]
+        if any(k == "" for k in new_keys):
+            raise ValueError(f"Empty string in {new_keys}.")
         if len(new_keys) != len(set(new_keys)):
             raise ValueError(
                 f"Dictionary contains multiple identical keys: {value}."
@@ -87,6 +85,7 @@ class TaskCollectPipV2(BaseModel):
         for old_key, new_key in zip(old_keys, new_keys):
             if new_key != old_key:
                 value[new_key] = value.pop(old_key)
+
         for pkg, version in value.items():
             validate_cmd(pkg)
             validate_cmd(version)
@@ -97,7 +96,6 @@ class TaskCollectPipV2(BaseModel):
     def package_extras_validator(cls, value: Optional[str]) -> Optional[str]:
         if value is None:
             return value
-        value = valstr("package_extras")(cls, value)
         validate_cmd(value, attribute_name="package_extras")
         return value
 
@@ -122,26 +120,11 @@ class TaskCollectCustomV2(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
     manifest: ManifestV2
-    python_interpreter: str
-    label: str
-    package_root: Optional[str] = None
-    package_name: Optional[str] = None
-    version: Optional[str] = None
-
-    # Valstr
-    _python_interpreter = field_validator("python_interpreter")(
-        classmethod(valstr("python_interpreter"))
-    )
-    _label = field_validator("label")(classmethod(valstr("label")))
-    _package_root = field_validator("package_root")(
-        classmethod(valstr("package_root", accept_none=True))
-    )
-    _package_name = field_validator("package_name")(
-        classmethod(valstr("package_name", accept_none=True))
-    )
-    _version = field_validator("version")(
-        classmethod(valstr("version", accept_none=True))
-    )
+    python_interpreter: NonEmptyString
+    label: NonEmptyString
+    package_root: Optional[NonEmptyString] = None
+    package_name: Optional[NonEmptyString] = None
+    version: Optional[NonEmptyString] = None
 
     @model_validator(mode="before")
     @classmethod
@@ -165,7 +148,6 @@ class TaskCollectCustomV2(BaseModel):
         """
         if value is not None:
             validate_cmd(value)
-            value = valstr("package_name")(cls, value)
             value = value.replace(" ", "")
         return value
 

fractal_server/app/schemas/v2/task_group.py

@@ -9,9 +9,10 @@ from pydantic import field_serializer
 from pydantic import field_validator
 from pydantic.types import AwareDatetime
 
+from .._validators import cant_set_none
+from .._validators import NonEmptyString
 from .._validators import val_absolute_path
 from .._validators import valdict_keys
-from .._validators import valstr
 from .task import TaskReadV2
 
 
@@ -42,15 +43,21 @@ class TaskGroupCreateV2(BaseModel):
     origin: TaskGroupV2OriginEnum
     pkg_name: str
     version: Optional[str] = None
-    python_version: Optional[str] = None
+    python_version: Optional[NonEmptyString] = None
     path: Optional[str] = None
     venv_path: Optional[str] = None
     wheel_path: Optional[str] = None
-    pip_extras: Optional[str] = None
+    pip_extras: Optional[NonEmptyString] = None
     pip_freeze: Optional[str] = None
     pinned_package_versions: dict[str, str] = Field(default_factory=dict)
 
     # Validators
+
+    @field_validator("python_version", "pip_extras")
+    @classmethod
+    def _cant_set_none(cls, v):
+        return cant_set_none(v)
+
     _path = field_validator("path")(classmethod(val_absolute_path("path")))
     _venv_path = field_validator("venv_path")(
         classmethod(val_absolute_path("venv_path"))
@@ -61,12 +68,6 @@ class TaskGroupCreateV2(BaseModel):
     _pinned_package_versions = field_validator("pinned_package_versions")(
         valdict_keys("pinned_package_versions")
     )
-    _pip_extras = field_validator("pip_extras")(
-        classmethod(valstr("pip_extras"))
-    )
-    _python_version = field_validator("python_version")(
-        classmethod(valstr("python_version"))
-    )
 
 
 class TaskGroupCreateV2Strict(TaskGroupCreateV2):

fractal_server/app/schemas/v2/workflow.py

@@ -7,7 +7,8 @@ from pydantic import field_serializer
 from pydantic import field_validator
 from pydantic.types import AwareDatetime
 
-from .._validators import valstr
+from .._validators import cant_set_none
+from .._validators import NonEmptyString
 from .project import ProjectReadV2
 from .workflowtask import WorkflowTaskExportV2
 from .workflowtask import WorkflowTaskImportV2
@@ -19,10 +20,7 @@ class WorkflowCreateV2(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
 
-    name: str
-
-    # Validators
-    _name = field_validator("name")(classmethod(valstr("name")))
+    name: NonEmptyString
 
 
 class WorkflowReadV2(BaseModel):
@@ -47,11 +45,15 @@ class WorkflowUpdateV2(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
 
-    name: Optional[str] = None
+    name: Optional[NonEmptyString] = None
     reordered_workflowtask_ids: Optional[list[int]] = None
 
     # Validators
-    _name = field_validator("name")(classmethod(valstr("name")))
+
+    @field_validator("name")
+    @classmethod
+    def _cant_set_none(cls, v):
+        return cant_set_none(v)
 
     @field_validator("reordered_workflowtask_ids")
     @classmethod
@@ -72,12 +74,9 @@ class WorkflowImportV2(BaseModel):
     """
 
     model_config = ConfigDict(extra="forbid")
-    name: str
+    name: NonEmptyString
     task_list: list[WorkflowTaskImportV2]
 
-    # Validators
-    _name = field_validator("name")(classmethod(valstr("name")))
-
 
 class WorkflowExportV2(BaseModel):
     """

fractal_server/app/schemas/v2/workflowtask.py

@@ -1,4 +1,3 @@
-from enum import Enum
 from typing import Any
 from typing import Optional
 from typing import Union
@@ -16,29 +15,11 @@ from .task import TaskExportV2
 from .task import TaskImportV2
 from .task import TaskImportV2Legacy
 from .task import TaskReadV2
+from .task import TaskTypeType
 
 RESERVED_ARGUMENTS = {"zarr_dir", "zarr_url", "zarr_urls", "init_args"}
 
 
-class WorkflowTaskStatusTypeV2(str, Enum):
-    """
-    Define the available values for the status of a `WorkflowTask`.
-
-    This model is used within the `Dataset.history` attribute, which is
-    constructed in the runner and then used in the API (e.g. in the
-    `api/v2/project/{project_id}/dataset/{dataset_id}/status` endpoint).
-
-    Attributes:
-        SUBMITTED: The `WorkflowTask` is part of a running job.
-        DONE: The most-recent execution of this `WorkflowTask` was successful.
-        FAILED: The most-recent execution of this `WorkflowTask` failed.
-    """
-
-    SUBMITTED = "submitted"
-    DONE = "done"
-    FAILED = "failed"
-
-
 class WorkflowTaskCreateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
@@ -113,7 +94,7 @@ class WorkflowTaskReadV2(BaseModel):
 
     type_filters: dict[str, bool]
 
-    task_type: str
+    task_type: TaskTypeType
     task_id: int
     task: TaskReadV2
 

fractal_server/app/security/__init__.py

@@ -24,7 +24,7 @@ FastAPIUsers with Barer Token and cookie transports and register local routes.
 Then, for each OAuth client defined in the Fractal Settings configuration, it
 registers the client and the relative routes.
 
-All routes are registerd under the `auth/` prefix.
+All routes are registered under the `auth/` prefix.
 """
 import contextlib
 from typing import Any
@@ -296,7 +296,7 @@ async def _create_first_user(
     Private method to create the first fractal-server user
 
     Create a user with the given default arguments and return a message with
-    the relevant informations. If the user alredy exists, for example after a
+    the relevant information. If the user already exists, for example after a
     restart, it returns a message to inform that user already exists.
 
     **WARNING**: This function is only meant to create the first user, and then
@@ -312,7 +312,7 @@ async def _create_first_user(
         email: New user's email
         password: New user's password
         is_superuser: `True` if the new user is a superuser
-        is_verified: `True` if the new user is verifie
+        is_verified: `True` if the new user is verified
         username:
     """
     function_logger = set_logger("fractal_server.create_first_user")

fractal_server/app/security/signup_email.py

@@ -36,8 +36,8 @@ def mail_new_oauth_signup(msg: str, email_settings: MailSettings):
             server.ehlo()
         if email_settings.use_login:
             password = (
-                Fernet(email_settings.encryption_key)
-                .decrypt(email_settings.encrypted_password)
+                Fernet(email_settings.encryption_key.get_secret_value())
+                .decrypt(email_settings.encrypted_password.get_secret_value())
                 .decode("utf-8")
             )
             server.login(user=email_settings.sender, password=password)