fractal-server 2.17.1a1__py3-none-any.whl → 2.18.0__py3-none-any.whl

fractal_server/app/schemas/v2/__init__.py

@@ -1,25 +1,25 @@
 from .accounting import AccountingRecordRead  # noqa F401
-from .dataset import DatasetCreateV2  # noqa F401
-from .dataset import DatasetExportV2  # noqa F401
-from .dataset import DatasetImportV2  # noqa F401
-from .dataset import DatasetReadV2  # noqa F401
-from .dataset import DatasetUpdateV2  # noqa F401
-from .dumps import DatasetDumpV2  # noqa F401
-from .dumps import ProjectDumpV2  # noqa F401
-from .dumps import TaskDumpV2  # noqa F401
-from .dumps import TaskGroupDumpV2  # noqa F401
-from .dumps import WorkflowDumpV2  # noqa F401
-from .dumps import WorkflowTaskDumpV2  # noqa F401
+from .dataset import DatasetCreate  # noqa F401
+from .dataset import DatasetExport  # noqa F401
+from .dataset import DatasetImport  # noqa F401
+from .dataset import DatasetRead  # noqa F401
+from .dataset import DatasetUpdate  # noqa F401
+from .dumps import DatasetDump  # noqa F401
+from .dumps import ProjectDump  # noqa F401
+from .dumps import TaskDump  # noqa F401
+from .dumps import TaskGroupDump  # noqa F401
+from .dumps import WorkflowDump  # noqa F401
+from .dumps import WorkflowTaskDump  # noqa F401
 from .history import HistoryRunRead  # noqa F401
 from .history import HistoryRunReadAggregated  # noqa F401
 from .history import HistoryUnitRead  # noqa F401
 from .history import HistoryUnitStatus  # noqa F401
 from .history import HistoryUnitStatusWithUnset  # noqa F401
 from .history import ImageLogsRequest  # noqa F401
-from .job import JobCreateV2  # noqa F401
-from .job import JobReadV2  # noqa F401
-from .job import JobStatusTypeV2  # noqa F401
-from .job import JobUpdateV2  # noqa F401
+from .job import JobCreate  # noqa F401
+from .job import JobRead  # noqa F401
+from .job import JobStatusType  # noqa F401
+from .job import JobUpdate  # noqa F401
 from .manifest import ManifestV2  # noqa F401
 from .manifest import TaskManifestV2  # noqa F401
 from .profile import ProfileCreate  # noqa F401
@@ -27,45 +27,52 @@ from .profile import ProfileRead  # noqa F401
 from .profile import ValidProfileLocal  # noqa F401
 from .profile import ValidProfileSlurmSSH  # noqa F401
 from .profile import ValidProfileSlurmSudo  # noqa F401
-from .project import ProjectCreateV2  # noqa F401
-from .project import ProjectReadV2  # noqa F401
-from .project import ProjectUpdateV2  # noqa F401
+from .project import ProjectCreate  # noqa F401
+from .project import ProjectRead  # noqa F401
+from .project import ProjectUpdate  # noqa F401
+from .sharing import ProjectPermissions  # noqa F401
+from .sharing import ProjectGuestCreate  # noqa F401
+from .sharing import ProjectAccessRead  # noqa F401
+from .sharing import ProjectInvitationRead  # noqa F401
+from .sharing import ProjectGuestRead  # noqa F401
+from .sharing import ProjectGuestUpdate  # noqa F401
+from .sharing import LinkUserProjectRead  # noqa F401
 from .resource import ResourceCreate  # noqa F401
 from .resource import ResourceRead  # noqa F401
 from .resource import ResourceType  # noqa F401
 from .resource import ValidResourceLocal  # noqa F401
 from .resource import ValidResourceSlurmSSH  # noqa F401
 from .resource import ValidResourceSlurmSudo  # noqa F401
-from .status_legacy import WorkflowTaskStatusTypeV2  # noqa F401
-from .task import TaskCreateV2  # noqa F401
-from .task import TaskExportV2  # noqa F401
-from .task import TaskImportV2  # noqa F401
-from .task import TaskImportV2Legacy  # noqa F401
-from .task import TaskReadV2  # noqa F401
+from .status_legacy import WorkflowTaskStatusType  # noqa F401
+from .task import TaskCreate  # noqa F401
+from .task import TaskExport  # noqa F401
+from .task import TaskImport  # noqa F401
+from .task import TaskImportLegacy  # noqa F401
+from .task import TaskRead  # noqa F401
 from .task import TaskType  # noqa F401
-from .task import TaskUpdateV2  # noqa F401
+from .task import TaskUpdate  # noqa F401
 from .task_collection import FractalUploadedFile  # noqa F401
-from .task_collection import TaskCollectCustomV2  # noqa F401
-from .task_collection import TaskCollectPipV2  # noqa F401
-from .task_group import TaskGroupActivityActionV2  # noqa F401
-from .task_group import TaskGroupActivityStatusV2  # noqa F401
-from .task_group import TaskGroupActivityV2Read  # noqa F401
-from .task_group import TaskGroupCreateV2  # noqa F401
-from .task_group import TaskGroupCreateV2Strict  # noqa F401
+from .task_collection import TaskCollectCustom  # noqa F401
+from .task_collection import TaskCollectPip  # noqa F401
+from .task_group import TaskGroupActivityAction  # noqa F401
+from .task_group import TaskGroupActivityStatus  # noqa F401
+from .task_group import TaskGroupActivityRead  # noqa F401
+from .task_group import TaskGroupCreate  # noqa F401
+from .task_group import TaskGroupCreateStrict  # noqa F401
 from .task_group import TaskGroupReadSuperuser  # noqa F401
-from .task_group import TaskGroupReadV2  # noqa F401
-from .task_group import TaskGroupUpdateV2  # noqa F401
-from .task_group import TaskGroupV2OriginEnum  # noqa F401
-from .workflow import WorkflowCreateV2  # noqa F401
-from .workflow import WorkflowExportV2  # noqa F401
-from .workflow import WorkflowImportV2  # noqa F401
-from .workflow import WorkflowReadV2  # noqa F401
-from .workflow import WorkflowReadV2WithWarnings  # noqa F401
-from .workflow import WorkflowUpdateV2  # noqa F401
-from .workflowtask import WorkflowTaskCreateV2  # noqa F401
-from .workflowtask import WorkflowTaskExportV2  # noqa F401
-from .workflowtask import WorkflowTaskImportV2  # noqa F401
-from .workflowtask import WorkflowTaskReadV2  # noqa F401
-from .workflowtask import WorkflowTaskReadV2WithWarning  # noqa F401
-from .workflowtask import WorkflowTaskReplaceV2  # noqa F401
-from .workflowtask import WorkflowTaskUpdateV2  # noqa F401
+from .task_group import TaskGroupRead  # noqa F401
+from .task_group import TaskGroupUpdate  # noqa F401
+from .task_group import TaskGroupOriginEnum  # noqa F401
+from .workflow import WorkflowCreate  # noqa F401
+from .workflow import WorkflowExport  # noqa F401
+from .workflow import WorkflowImport  # noqa F401
+from .workflow import WorkflowRead  # noqa F401
+from .workflow import WorkflowReadWithWarnings  # noqa F401
+from .workflow import WorkflowUpdate  # noqa F401
+from .workflowtask import WorkflowTaskCreate  # noqa F401
+from .workflowtask import WorkflowTaskExport  # noqa F401
+from .workflowtask import WorkflowTaskImport  # noqa F401
+from .workflowtask import WorkflowTaskRead  # noqa F401
+from .workflowtask import WorkflowTaskReadWithWarning  # noqa F401
+from .workflowtask import WorkflowTaskReplace  # noqa F401
+from .workflowtask import WorkflowTaskUpdate  # noqa F401

fractal_server/app/schemas/v2/accounting.py

@@ -6,6 +6,17 @@ from pydantic.types import AwareDatetime
 
 
 class AccountingRecordRead(BaseModel):
+    """
+    AccountingRecordRead
+
+    Attributes:
+        id:
+        user_id:
+        timestamp:
+        num_tasks:
+        num_new_images:
+    """
+
     id: int
     user_id: int
     timestamp: AwareDatetime

fractal_server/app/schemas/v2/dataset.py

@@ -1,34 +1,64 @@
 from datetime import datetime
+from pathlib import Path
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
 from pydantic import Field
 from pydantic import field_serializer
+from pydantic import model_validator
 from pydantic.types import AwareDatetime
 
-from fractal_server.app.schemas.v2.project import ProjectReadV2
+from fractal_server.app.schemas.v2.project import ProjectRead
 from fractal_server.images import SingleImage
-from fractal_server.types import AttributeFilters
+from fractal_server.types import AbsolutePathStr
 from fractal_server.types import NonEmptyStr
+from fractal_server.types import RelativePathStr
 from fractal_server.types import ZarrDirStr
 
 
-class DatasetCreateV2(BaseModel):
+class DatasetCreate(BaseModel):
+    """
+    DatasetCreate
+
+    Attributes:
+        name:
+        project_dir:
+        zarr_subfolder:
+    """
+
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
+    project_dir: AbsolutePathStr | None = None
+    zarr_subfolder: RelativePathStr | None = None
+
+    @model_validator(mode="after")
+    def validate_zarr_dir(self):
+        if (self.project_dir is None) and (self.zarr_subfolder is not None):
+            raise ValueError(
+                "Cannot provide `zarr_subfolder` without `project_dir`"
+            )
+        return self
 
-    zarr_dir: ZarrDirStr | None = None
 
-    attribute_filters: AttributeFilters = Field(default_factory=dict)
+class DatasetRead(BaseModel):
+    """
+    DatasetRead
 
+    Attributes:
+        id:
+        name:
+        project_id:
+        project:
+        timestamp_created:
+        zarr_dir:
+    """
 
-class DatasetReadV2(BaseModel):
     id: int
     name: str
 
     project_id: int
-    project: ProjectReadV2
+    project: ProjectRead
 
     timestamp_created: AwareDatetime
 
@@ -39,14 +69,21 @@ class DatasetReadV2(BaseModel):
         return v.isoformat()
 
 
-class DatasetUpdateV2(BaseModel):
+class DatasetUpdate(BaseModel):
+    """
+    DatasetUpdate
+
+    Attributes:
+        name:
+        zarr_dir:
+    """
+
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None
-    zarr_dir: ZarrDirStr | None = None
 
 
-class DatasetImportV2(BaseModel):
+class DatasetImport(BaseModel):
     """
     Class for `Dataset` import.
 
@@ -64,8 +101,17 @@ class DatasetImportV2(BaseModel):
     zarr_dir: ZarrDirStr
     images: list[SingleImage] = Field(default_factory=list)
 
+    @model_validator(mode="after")
+    def validate_image_zarr_url(self):
+        for image in self.images:
+            if not Path(image.zarr_url).is_relative_to(self.zarr_dir):
+                raise ValueError(
+                    f"{image.zarr_url=} is not relative to {self.zarr_dir=}."
+                )
+        return self
+
 
-class DatasetExportV2(BaseModel):
+class DatasetExport(BaseModel):
     """
     Class for `Dataset` export.
 

fractal_server/app/schemas/v2/dumps.py

@@ -7,22 +7,23 @@ 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 pydantic import BaseModel
 from pydantic import ConfigDict
 from pydantic import Field
 
 from .task import TaskType
-from .task_group import TaskGroupV2OriginEnum
+from .task_group import TaskGroupOriginEnum
 
 
-class ProjectDumpV2(BaseModel):
+class ProjectDump(BaseModel):
     model_config = ConfigDict(extra="forbid")
     id: int
     name: str
     timestamp_created: str
 
 
-class TaskDumpV2(BaseModel):
+class TaskDump(BaseModel):
     id: int
     name: str
     type: TaskType
@@ -36,7 +37,7 @@ class TaskDumpV2(BaseModel):
     output_types: dict[str, bool]
 
 
-class WorkflowTaskDumpV2(BaseModel):
+class WorkflowTaskDump(BaseModel):
     """
     We do not include 'model_config = ConfigDict(extra="forbid")'
     because legacy data may include 'input_filters' field and we want to avoid
@@ -50,10 +51,10 @@ class WorkflowTaskDumpV2(BaseModel):
     type_filters: dict[str, bool]
 
     task_id: int | None = None
-    task: TaskDumpV2 | None = None
+    task: TaskDump | None = None
 
 
-class WorkflowDumpV2(BaseModel):
+class WorkflowDump(BaseModel):
     model_config = ConfigDict(extra="forbid")
     id: int
     name: str
@@ -61,7 +62,7 @@ class WorkflowDumpV2(BaseModel):
     timestamp_created: str
 
 
-class DatasetDumpV2(BaseModel):
+class DatasetDump(BaseModel):
     """
     We do not include 'model_config = ConfigDict(extra="forbid")' because
     legacy data may include 'type_filters' or 'attribute_filters' and we
@@ -75,9 +76,9 @@ class DatasetDumpV2(BaseModel):
     zarr_dir: str
 
 
-class TaskGroupDumpV2(BaseModel):
+class TaskGroupDump(BaseModel):
     id: int
-    origin: TaskGroupV2OriginEnum
+    origin: TaskGroupOriginEnum
     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 DatasetDumpV2
-from fractal_server.app.schemas.v2.dumps import ProjectDumpV2
-from fractal_server.app.schemas.v2.dumps import WorkflowDumpV2
+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.types import AttributeFilters
 from fractal_server.types import NonEmptyStr
 from fractal_server.types import TypeFilters
 
 
-class JobStatusTypeV2(StrEnum):
+class JobStatusType(StrEnum):
     """
     Define the available job statuses
 
@@ -39,7 +39,7 @@ class JobStatusTypeV2(StrEnum):
     FAILED = "failed"
 
 
-class JobCreateV2(BaseModel):
+class JobCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     first_task_index: NonNegativeInt | None = None
@@ -65,16 +65,16 @@ class JobCreateV2(BaseModel):
         return values
 
 
-class JobReadV2(BaseModel):
+class JobRead(BaseModel):
     id: int
     project_id: int | None = None
-    project_dump: ProjectDumpV2
+    project_dump: ProjectDump
     user_email: str
     slurm_account: str | None = None
     workflow_id: int | None = None
-    workflow_dump: WorkflowDumpV2
+    workflow_dump: WorkflowDump
     dataset_id: int | None = None
-    dataset_dump: DatasetDumpV2
+    dataset_dump: DatasetDump
     start_timestamp: AwareDatetime
     end_timestamp: AwareDatetime | None = None
     status: str
@@ -100,7 +100,7 @@ class JobReadV2(BaseModel):
             return v.isoformat()
 
 
-class JobUpdateV2(BaseModel):
+class JobUpdate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
-    status: JobStatusTypeV2
+    status: JobStatusType

fractal_server/app/schemas/v2/manifest.py

@@ -4,11 +4,12 @@ from pydantic import BaseModel
 from pydantic import Field
 from pydantic import model_validator
 
-from .task import TaskType
 from fractal_server.types import DictStrAny
 from fractal_server.types import HttpUrlStr
 from fractal_server.types import NonEmptyStr
 
+from .task import TaskType
+
 
 class TaskManifestV2(BaseModel):
     """
@@ -119,9 +120,9 @@ class ManifestV2(BaseModel):
             manifests as the schema evolves. This is for instance used by
             Fractal to determine which subclass of the present base class needs
             be used to read and validate the input.
-        task_list : list[TaskManifestType]
+        task_list:
             The list of tasks, represented as specified by subclasses of the
-            _TaskManifestBase (a.k.a. TaskManifestType)
+            `_TaskManifestBase` (a.k.a. `TaskManifestType`)
         has_args_schemas:
             `True` if the manifest includes JSON Schemas for the arguments of
             each task.

fractal_server/app/schemas/v2/profile.py

@@ -6,12 +6,21 @@ from pydantic import Discriminator
 from pydantic import Tag
 from pydantic import validate_call
 
-from .resource import ResourceType
 from fractal_server.types import AbsolutePathStr
 from fractal_server.types import NonEmptyStr
 
+from .resource import ResourceType
+
 
 class ValidProfileLocal(BaseModel):
+    """
+    Valid local profile.
+
+    Attributes:
+        name: Profile name.
+        resource_type: Type of the corresponding resource.
+    """
+
     name: NonEmptyStr
     resource_type: ResourceType
     username: None = None
@@ -21,6 +30,17 @@ class ValidProfileLocal(BaseModel):
 
 
 class ValidProfileSlurmSudo(BaseModel):
+    """
+    Valid SLURM/sudo profile.
+
+    Attributes:
+        name: Profile name.
+        resource_type: Type of the corresponding resource.
+        username:
+            SLURM user to impersonate (e.g. as in
+            `sudo -u username sbatch /some/script.sh`).
+    """
+
     name: NonEmptyStr
     resource_type: ResourceType
     username: NonEmptyStr
@@ -30,6 +50,23 @@ class ValidProfileSlurmSudo(BaseModel):
 
 
 class ValidProfileSlurmSSH(BaseModel):
+    """
+    Valid SLURM/sudo profile.
+
+    Attributes:
+        name: Profile name.
+        resource_type: Type of the corresponding resource.
+        username:
+            SLURM user to impersonate (e.g. as in
+            `ssh username@cluster sbatch /some/script.sh`).
+        ssh_key_path:
+            Local path of SSH private key for user `username`.
+        tasks_remote_dir:
+            Base folder for task environments on the remote SLURM cluster.
+        jobs_remote_dir:
+            Base folder for job directories on the remote SLURM cluster.
+    """
+
     name: NonEmptyStr
     resource_type: ResourceType
     username: NonEmptyStr
@@ -54,6 +91,20 @@ ProfileCreate = Annotated[
 
 
 class ProfileRead(BaseModel):
+    """
+    Profile schema for GET endpoints.
+
+    Attributes:
+        id:
+        name:
+        resource_id:
+        resource_type:
+        username:
+        ssh_key_path:
+        jobs_remote_dir:
+        tasks_remote_dir:
+    """
+
     id: int
     name: str
     resource_id: int
@@ -69,7 +120,7 @@ def cast_serialize_profile(_data: ProfileCreate) -> dict[str, Any]:
     """
     Cast/serialize round-trip for `Profile` data.
 
-    We use `@validate_call` because `ProfileeCreate` is a `Union` type and it
+    We use `@validate_call` because `ProfileCreate` is a `Union` type and it
     cannot be instantiated directly.
 
     Return:

fractal_server/app/schemas/v2/project.py

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