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

fractal_server/app/schemas/user.py

@@ -8,12 +8,18 @@ from pydantic import EmailStr
 from pydantic import Field
 
 from fractal_server.string_tools import validate_cmd
-from fractal_server.types import AbsolutePathStr
+from fractal_server.types import ListUniqueAbsolutePathStr
 from fractal_server.types import ListUniqueNonEmptyString
 from fractal_server.types import ListUniqueNonNegativeInt
 from fractal_server.types import NonEmptyStr
 
 
+def _validate_cmd_list(value: list[str]) -> list[str]:
+    for v in value:
+        validate_cmd(v)
+    return value
+
+
 class OAuthAccountRead(BaseModel):
     """
     Schema for storing essential `OAuthAccount` information within
@@ -38,20 +44,17 @@ class UserRead(schemas.BaseUser[int]):
         group_ids_names:
         oauth_accounts:
         profile_id:
+        project_dirs:
+        slurm_accounts:
     """
 
     group_ids_names: list[tuple[int, str]] | None = None
     oauth_accounts: list[OAuthAccountRead]
     profile_id: int | None = None
-    project_dir: str
+    project_dirs: list[str]
     slurm_accounts: list[str]
 
 
-def _validate_cmd(value: str) -> str:
-    validate_cmd(value)
-    return value
-
-
 class UserUpdate(schemas.BaseUserUpdate):
     """
     Schema for `User` update.
@@ -63,7 +66,7 @@ class UserUpdate(schemas.BaseUserUpdate):
         is_superuser:
         is_verified:
         profile_id:
-        project_dir:
+        project_dirs:
         slurm_accounts:
     """
 
@@ -74,9 +77,9 @@ class UserUpdate(schemas.BaseUserUpdate):
     is_superuser: bool = None
     is_verified: bool = None
     profile_id: int | None = None
-    project_dir: Annotated[AbsolutePathStr, AfterValidator(_validate_cmd)] = (
-        None
-    )
+    project_dirs: Annotated[
+        ListUniqueAbsolutePathStr, AfterValidator(_validate_cmd_list)
+    ] = Field(default=None, min_length=1)
     slurm_accounts: ListUniqueNonEmptyString = None
 
 
@@ -98,10 +101,14 @@ class UserCreate(schemas.BaseUserCreate):
 
     Attributes:
         profile_id:
+        project_dirs:
+        slurm_accounts:
     """
 
     profile_id: int | None = None
-    project_dir: Annotated[AbsolutePathStr, AfterValidator(_validate_cmd)]
+    project_dirs: Annotated[
+        ListUniqueAbsolutePathStr, AfterValidator(_validate_cmd_list)
+    ] = Field(min_length=1)
     slurm_accounts: list[str] = Field(default_factory=list)
 
 
@@ -109,6 +116,8 @@ class UserUpdateGroups(BaseModel):
     """
     Schema for `POST /auth/users/{user_id}/set-groups/`
 
+    Attributes:
+        group_ids:
     """
 
     model_config = ConfigDict(extra="forbid")
@@ -117,6 +126,14 @@ class UserUpdateGroups(BaseModel):
 
 
 class UserProfileInfo(BaseModel):
+    """
+    Attributes:
+        has_profile:
+        resource_name:
+        profile_name:
+        username:
+    """
+
     has_profile: bool
     resource_name: str | None = None
     profile_name: str | None = None

fractal_server/app/schemas/user_group.py

@@ -2,16 +2,13 @@ from datetime import datetime
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
-from pydantic import Field
 from pydantic import field_serializer
 from pydantic.types import AwareDatetime
 
-from fractal_server.types import ListUniqueAbsolutePathStr
 from fractal_server.types import NonEmptyStr
 
 __all__ = (
     "UserGroupRead",
-    "UserGroupUpdate",
     "UserGroupCreate",
 )
 
@@ -34,7 +31,6 @@ class UserGroupRead(BaseModel):
     name: str
     timestamp_created: AwareDatetime
     user_ids: list[int] | None = None
-    viewer_paths: list[str]
 
     @field_serializer("timestamp_created")
     def serialize_datetime(v: datetime) -> str:
@@ -52,14 +48,3 @@ class UserGroupCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
-    viewer_paths: ListUniqueAbsolutePathStr = Field(default_factory=list)
-
-
-class UserGroupUpdate(BaseModel):
-    """
-    Schema for `UserGroup` update
-    """
-
-    model_config = ConfigDict(extra="forbid")
-
-    viewer_paths: ListUniqueAbsolutePathStr = None

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/dataset.py

@@ -1,35 +1,49 @@
 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 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):
     """
-    DatasetCreateV2
+    DatasetCreate
 
     Attributes:
         name:
-        zarr_dir:
+        project_dir:
+        zarr_subfolder:
     """
 
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
-    zarr_dir: ZarrDirStr | None = None
+    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
 
 
-class DatasetReadV2(BaseModel):
+class DatasetRead(BaseModel):
     """
-    DatasetReadV2
+    DatasetRead
 
     Attributes:
         id:
@@ -44,7 +58,7 @@ class DatasetReadV2(BaseModel):
     name: str
 
     project_id: int
-    project: ProjectReadV2
+    project: ProjectRead
 
     timestamp_created: AwareDatetime
 
@@ -55,9 +69,9 @@ class DatasetReadV2(BaseModel):
         return v.isoformat()
 
 
-class DatasetUpdateV2(BaseModel):
+class DatasetUpdate(BaseModel):
     """
-    DatasetUpdateV2
+    DatasetUpdate
 
     Attributes:
         name:
@@ -67,10 +81,9 @@ class DatasetUpdateV2(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None
-    zarr_dir: ZarrDirStr | None = None
 
 
-class DatasetImportV2(BaseModel):
+class DatasetImport(BaseModel):
     """
     Class for `Dataset` import.
 
@@ -88,8 +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

@@ -13,17 +13,17 @@ 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
@@ -37,7 +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
@@ -51,10 +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
@@ -62,7 +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
@@ -76,9 +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/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

fractal_server/app/schemas/v2/resource.py

@@ -77,6 +77,8 @@ 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 (
@@ -95,6 +97,9 @@ 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:
@@ -105,7 +110,6 @@ class ValidResourceLocal(ValidResourceBase):
             Local base folder for job folders.
         jobs_runner_config:
             Runner configuration.
-
     """
 
     type: Literal[ResourceType.LOCAL]
@@ -121,6 +125,9 @@ 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:
@@ -150,6 +157,9 @@ 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:
@@ -198,10 +208,9 @@ class ResourceRead(BaseModel):
     """
 
     id: int
-
-    type: str
-
     name: str
+    type: str
+    prevent_new_submissions: bool
     timestamp_created: AwareDatetime
 
     host: str | None

fractal_server/app/schemas/v2/sharing.py

@@ -0,0 +1,99 @@
+from enum import StrEnum
+
+from pydantic import BaseModel
+
+
+class ProjectPermissions(StrEnum):
+    """
+    Available permissions for accessing Project
+    Attributes:
+        READ:
+        WRITE:
+        EXECUTE:
+    """
+
+    READ = "r"
+    WRITE = "rw"
+    EXECUTE = "rwx"
+
+
+class ProjectGuestCreate(BaseModel):
+    """
+    Request body for project-sharing invitation.
+
+    Attributes:
+        permissions:
+    """
+
+    permissions: ProjectPermissions
+
+
+class ProjectGuestRead(BaseModel):
+    """
+    Information about a guest.
+
+    Attributes:
+        email: Guest email.
+        is_verified: Project/guest verification status.
+        permissions: Guest permissions for project.
+    """
+
+    email: str
+    is_verified: bool
+    permissions: str
+
+
+class ProjectGuestUpdate(BaseModel):
+    """
+    Request body for updating permissions of an existing guest.
+
+    Attributes:
+        permissions: New permissions for guest.
+    """
+
+    permissions: ProjectPermissions
+
+
+class ProjectAccessRead(BaseModel):
+    """
+    Project-access information for current user.
+
+    Attributes:
+        is_owner: Whether current user is owner.
+        permissions: Current user permissions.
+        owner_email: Email of project owner
+    """
+
+    is_owner: bool
+    permissions: str
+    owner_email: str
+
+
+class ProjectInvitationRead(BaseModel):
+    """
+    Info about a pending invitation.
+
+    Attributes:
+        project_id:
+        project_name:
+        owner_email:
+        guest_permissions:
+    """
+
+    project_id: int
+    project_name: str
+    owner_email: str
+    guest_permissions: str
+
+
+class LinkUserProjectRead(BaseModel):
+    # User info
+    user_id: int
+    user_email: str
+    # Project info
+    project_id: int
+    project_name: str
+    # Permissions
+    is_verified: bool
+    is_owner: bool
+    permissions: str