fractal-server 1.4.6__py3-none-any.whl → 2.0.0__py3-none-any.whl

fractal_server/app/schemas/_validators.py

@@ -1,6 +1,8 @@
 import os
 from datetime import datetime
 from datetime import timezone
+from typing import Any
+from typing import Optional
 
 
 def valstr(attribute: str, accept_none: bool = False):
@@ -11,7 +13,7 @@ def valstr(attribute: str, accept_none: bool = False):
     If `accept_none`, the validator also accepts `None`.
     """
 
-    def val(string: str):
+    def val(string: Optional[str]) -> Optional[str]:
         if string is None:
             if accept_none:
                 return string
@@ -27,13 +29,34 @@ def valstr(attribute: str, accept_none: bool = False):
     return val
 
 
+def valdictkeys(attribute: str):
+    def val(d: Optional[dict[str, Any]]) -> Optional[dict[str, Any]]:
+        """
+        Apply valstr to every key of the dictionary, and fail if there are
+        identical keys.
+        """
+        if d is not None:
+            old_keys = list(d.keys())
+            new_keys = [valstr(f"{attribute}[{key}]")(key) for key in old_keys]
+            if len(new_keys) != len(set(new_keys)):
+                raise ValueError(
+                    f"Dictionary contains multiple identical keys: {d}."
+                )
+            for old_key, new_key in zip(old_keys, new_keys):
+                if new_key != old_key:
+                    d[new_key] = d.pop(old_key)
+        return d
+
+    return val
+
+
 def valint(attribute: str, min_val: int = 1):
     """
     Check that an integer attribute (e.g. if it is meant to be the ID of a
     database entry) is greater or equal to min_val.
     """
 
-    def val(integer: int):
+    def val(integer: Optional[int]) -> Optional[int]:
         if integer is None:
             raise ValueError(f"Integer attribute '{attribute}' cannot be None")
         if integer < min_val:
@@ -51,7 +74,7 @@ def val_absolute_path(attribute: str):
     Check that a string attribute is an absolute path
     """
 
-    def val(string: str):
+    def val(string: Optional[str]) -> str:
         if string is None:
             raise ValueError(f"String attribute '{attribute}' cannot be None")
         s = string.strip()
@@ -68,7 +91,7 @@ def val_absolute_path(attribute: str):
 
 
 def val_unique_list(attribute: str):
-    def val(must_be_unique: list):
+    def val(must_be_unique: Optional[list]) -> Optional[list]:
         if must_be_unique is not None:
             if len(set(must_be_unique)) != len(must_be_unique):
                 raise ValueError(f"`{attribute}` list has repetitions")
@@ -78,7 +101,7 @@ def val_unique_list(attribute: str):
 
 
 def valutc(attribute: str):
-    def val(timestamp: datetime):
+    def val(timestamp: Optional[datetime]) -> Optional[datetime]:
         """
         Replacing `tzinfo` with `timezone.utc` is just required by SQLite data.
         If using Postgres, this function leaves the datetime exactly as it is.

fractal_server/app/schemas/v1/__init__.py

@@ -0,0 +1,36 @@
+"""
+Schemas for API request/response bodies
+"""
+from .applyworkflow import ApplyWorkflowCreateV1  # noqa: F401
+from .applyworkflow import ApplyWorkflowReadV1  # noqa: F401
+from .applyworkflow import ApplyWorkflowUpdateV1  # noqa: F401
+from .applyworkflow import JobStatusTypeV1  # noqa: F401
+from .dataset import DatasetCreateV1  # noqa: F401
+from .dataset import DatasetReadV1  # noqa: F401
+from .dataset import DatasetStatusReadV1  # noqa: F401
+from .dataset import DatasetUpdateV1  # noqa: F401
+from .dataset import ResourceCreateV1  # noqa: F401
+from .dataset import ResourceReadV1  # noqa: F401
+from .dataset import ResourceUpdateV1  # noqa: F401
+from .manifest import ManifestV1  # noqa: F401
+from .manifest import TaskManifestV1  # noqa: F401
+from .project import ProjectCreateV1  # noqa: F401
+from .project import ProjectReadV1  # noqa: F401
+from .project import ProjectUpdateV1  # noqa: F401
+from .task import TaskCreateV1  # noqa: F401
+from .task import TaskImportV1  # noqa: F401
+from .task import TaskReadV1  # noqa: F401
+from .task import TaskUpdateV1  # noqa: F401
+from .task_collection import TaskCollectPipV1  # noqa: F401
+from .task_collection import TaskCollectStatusV1  # noqa: F401
+from .workflow import WorkflowCreateV1  # noqa: F401
+from .workflow import WorkflowExportV1  # noqa: F401
+from .workflow import WorkflowImportV1  # noqa: F401
+from .workflow import WorkflowReadV1  # noqa: F401
+from .workflow import WorkflowTaskCreateV1  # noqa: F401
+from .workflow import WorkflowTaskExportV1  # noqa: F401
+from .workflow import WorkflowTaskImportV1  # noqa: F401
+from .workflow import WorkflowTaskReadV1  # noqa: F401
+from .workflow import WorkflowTaskStatusTypeV1  # noqa: F401
+from .workflow import WorkflowTaskUpdateV1  # noqa: F401
+from .workflow import WorkflowUpdateV1  # noqa: F401

fractal_server/app/schemas/{applyworkflow.py → v1/applyworkflow.py}

@@ -6,21 +6,21 @@ from pydantic import BaseModel
 from pydantic import validator
 from pydantic.types import StrictStr
 
-from ._validators import valstr
-from ._validators import valutc
-from .dumps import DatasetDump
-from .dumps import ProjectDump
-from .dumps import WorkflowDump
+from .._validators import valstr
+from .._validators import valutc
+from .dumps import DatasetDumpV1
+from .dumps import ProjectDumpV1
+from .dumps import WorkflowDumpV1
 
 
 __all__ = (
-    "_ApplyWorkflowBase",
-    "ApplyWorkflowCreate",
-    "ApplyWorkflowRead",
+    "_ApplyWorkflowBaseV1",
+    "ApplyWorkflowCreateV1",
+    "ApplyWorkflowReadV1",
 )
 
 
-class JobStatusType(str, Enum):
+class JobStatusTypeV1(str, Enum):
     """
     Define the available job statuses
 
@@ -41,7 +41,7 @@ class JobStatusType(str, Enum):
     FAILED = "failed"
 
 
-class _ApplyWorkflowBase(BaseModel):
+class _ApplyWorkflowBaseV1(BaseModel):
     """
     Base class for `ApplyWorkflow`.
 
@@ -52,7 +52,7 @@ class _ApplyWorkflowBase(BaseModel):
     worker_init: Optional[str]
 
 
-class ApplyWorkflowCreate(_ApplyWorkflowBase):
+class ApplyWorkflowCreateV1(_ApplyWorkflowBaseV1):
     """
     Class for `ApplyWorkflow` creation.
 
@@ -104,7 +104,7 @@ class ApplyWorkflowCreate(_ApplyWorkflowBase):
         return v
 
 
-class ApplyWorkflowRead(_ApplyWorkflowBase):
+class ApplyWorkflowReadV1(_ApplyWorkflowBaseV1):
     """
     Class for `ApplyWorkflow` read from database.
 
@@ -132,15 +132,15 @@ class ApplyWorkflowRead(_ApplyWorkflowBase):
 
     id: int
     project_id: Optional[int]
-    project_dump: ProjectDump
+    project_dump: ProjectDumpV1
     user_email: str
     slurm_account: Optional[str]
     workflow_id: Optional[int]
-    workflow_dump: WorkflowDump
+    workflow_dump: WorkflowDumpV1
     input_dataset_id: Optional[int]
-    input_dataset_dump: DatasetDump
+    input_dataset_dump: DatasetDumpV1
     output_dataset_id: Optional[int]
-    output_dataset_dump: DatasetDump
+    output_dataset_dump: DatasetDumpV1
     start_timestamp: datetime
     end_timestamp: Optional[datetime]
     status: str
@@ -158,7 +158,7 @@ class ApplyWorkflowRead(_ApplyWorkflowBase):
     )
 
 
-class ApplyWorkflowUpdate(BaseModel):
+class ApplyWorkflowUpdateV1(BaseModel):
     """
     Class for updating a job status.
 
@@ -166,4 +166,4 @@ class ApplyWorkflowUpdate(BaseModel):
         status: New job status.
     """
 
-    status: JobStatusType
+    status: JobStatusTypeV1

fractal_server/app/schemas/{dataset.py → v1/dataset.py}

@@ -6,25 +6,25 @@ from pydantic import BaseModel
 from pydantic import Field
 from pydantic import validator
 
-from ._validators import val_absolute_path
-from ._validators import valstr
-from ._validators import valutc
-from .dumps import WorkflowTaskDump
-from .project import ProjectRead
-from .workflow import WorkflowTaskStatusType
+from .._validators import val_absolute_path
+from .._validators import valstr
+from .._validators import valutc
+from .dumps import WorkflowTaskDumpV1
+from .project import ProjectReadV1
+from .workflow import WorkflowTaskStatusTypeV1
 
 __all__ = (
-    "DatasetUpdate",
-    "DatasetCreate",
-    "DatasetRead",
-    "ResourceCreate",
-    "ResourceRead",
-    "ResourceUpdate",
-    "DatasetStatusRead",
+    "DatasetUpdateV1",
+    "DatasetCreateV1",
+    "DatasetReadV1",
+    "ResourceCreateV1",
+    "ResourceReadV1",
+    "ResourceUpdateV1",
+    "DatasetStatusReadV1",
 )
 
 
-class _ResourceBase(BaseModel):
+class _ResourceBaseV1(BaseModel):
     """
     Base class for `Resource`.
 
@@ -35,7 +35,7 @@ class _ResourceBase(BaseModel):
     path: str
 
 
-class ResourceCreate(_ResourceBase):
+class ResourceCreateV1(_ResourceBaseV1):
     """
     Class for `Resource` creation.
     """
@@ -44,7 +44,7 @@ class ResourceCreate(_ResourceBase):
     _path = validator("path", allow_reuse=True)(val_absolute_path("path"))
 
 
-class ResourceUpdate(_ResourceBase):
+class ResourceUpdateV1(_ResourceBaseV1):
     """
     Class for `Resource` update.
     """
@@ -53,7 +53,7 @@ class ResourceUpdate(_ResourceBase):
     _path = validator("path", allow_reuse=True)(val_absolute_path("path"))
 
 
-class ResourceRead(_ResourceBase):
+class ResourceReadV1(_ResourceBaseV1):
     """
     Class for `Resource` read from database.
 
@@ -66,7 +66,7 @@ class ResourceRead(_ResourceBase):
     dataset_id: int
 
 
-class _DatasetHistoryItem(BaseModel):
+class _DatasetHistoryItemV1(BaseModel):
     """
     Class for an item of `Dataset.history`.
 
@@ -77,12 +77,12 @@ class _DatasetHistoryItem(BaseModel):
             and `component_list`.
     """
 
-    workflowtask: WorkflowTaskDump
-    status: WorkflowTaskStatusType
+    workflowtask: WorkflowTaskDumpV1
+    status: WorkflowTaskStatusTypeV1
     parallelization: Optional[dict]
 
 
-class _DatasetBase(BaseModel):
+class _DatasetBaseV1(BaseModel):
     """
     Base class for `Dataset`.
 
@@ -97,11 +97,11 @@ class _DatasetBase(BaseModel):
     name: str
     type: Optional[str]
     meta: dict[str, Any] = Field(default={})
-    history: list[_DatasetHistoryItem] = Field(default=[])
+    history: list[_DatasetHistoryItemV1] = Field(default=[])
     read_only: bool = False
 
 
-class DatasetUpdate(_DatasetBase):
+class DatasetUpdateV1(_DatasetBaseV1):
     """
     Class for `Dataset` update.
 
@@ -114,7 +114,7 @@ class DatasetUpdate(_DatasetBase):
 
     name: Optional[str]
     meta: Optional[dict[str, Any]] = None
-    history: Optional[list[_DatasetHistoryItem]] = None
+    history: Optional[list[_DatasetHistoryItemV1]] = None
     read_only: Optional[bool]
 
     # Validators
@@ -122,7 +122,7 @@ class DatasetUpdate(_DatasetBase):
     _type = validator("type", allow_reuse=True)(valstr("type"))
 
 
-class DatasetCreate(_DatasetBase):
+class DatasetCreateV1(_DatasetBaseV1):
     """
     Class for `Dataset` creation.
     """
@@ -132,7 +132,7 @@ class DatasetCreate(_DatasetBase):
     _type = validator("type", allow_reuse=True)(valstr("type"))
 
 
-class DatasetRead(_DatasetBase):
+class DatasetReadV1(_DatasetBaseV1):
     """
     Class for `Dataset` read from database.
 
@@ -145,10 +145,10 @@ class DatasetRead(_DatasetBase):
     """
 
     id: int
-    resource_list: list[ResourceRead]
+    resource_list: list[ResourceReadV1]
     project_id: int
     read_only: bool
-    project: ProjectRead
+    project: ProjectReadV1
     timestamp_created: datetime
 
     _timestamp_created = validator("timestamp_created", allow_reuse=True)(
@@ -156,7 +156,7 @@ class DatasetRead(_DatasetBase):
     )
 
 
-class DatasetStatusRead(BaseModel):
+class DatasetStatusReadV1(BaseModel):
     """
     Response type for the
     `/project/{project_id}/dataset/{dataset_id}/status/` endpoint
@@ -165,6 +165,6 @@ class DatasetStatusRead(BaseModel):
     status: Optional[
         dict[
             int,
-            WorkflowTaskStatusType,
+            WorkflowTaskStatusTypeV1,
         ]
     ] = None

fractal_server/app/schemas/{dumps.py → v1/dumps.py}

@@ -14,7 +14,7 @@ from pydantic import BaseModel
 from pydantic import Extra
 
 
-class ProjectDump(BaseModel, extra=Extra.forbid):
+class ProjectDumpV1(BaseModel, extra=Extra.forbid):
 
     id: int
     name: str
@@ -22,7 +22,7 @@ class ProjectDump(BaseModel, extra=Extra.forbid):
     timestamp_created: str
 
 
-class TaskDump(BaseModel):
+class TaskDumpV1(BaseModel):
     id: int
     source: str
     name: str
@@ -33,32 +33,32 @@ class TaskDump(BaseModel):
     version: Optional[str]
 
 
-class WorkflowTaskDump(BaseModel):
+class WorkflowTaskDumpV1(BaseModel):
     id: int
     order: Optional[int]
     workflow_id: int
     task_id: int
-    task: TaskDump
+    task: TaskDumpV1
 
 
-class WorkflowDump(BaseModel):
+class WorkflowDumpV1(BaseModel):
     id: int
     name: str
     project_id: int
     timestamp_created: str
 
 
-class ResourceDump(BaseModel):
+class ResourceDumpV1(BaseModel):
     id: int
     path: str
     dataset_id: int
 
 
-class DatasetDump(BaseModel):
+class DatasetDumpV1(BaseModel):
     id: int
     name: str
     type: Optional[str]
     read_only: bool
-    resource_list: list[ResourceDump]
+    resource_list: list[ResourceDumpV1]
     project_id: int
     timestamp_created: str

fractal_server/app/schemas/{manifest.py → v1/manifest.py}

@@ -12,7 +12,7 @@ from pydantic import validator
 __all__ = ("TaskManifestV1", "ManifestV1")
 
 
-class _TaskManifestBase(BaseModel):
+class _TaskManifestBaseV1(BaseModel):
     """
     Base class for `TaskManifestV1`.
 
@@ -54,10 +54,10 @@ class _TaskManifestBase(BaseModel):
     docs_link: Optional[HttpUrl]
 
 
-TaskManifestType = TypeVar("TaskManifestType", bound=_TaskManifestBase)
+TaskManifestType = TypeVar("TaskManifestType", bound=_TaskManifestBaseV1)
 
 
-class _ManifestBase(BaseModel):
+class _ManifestBaseV1(BaseModel):
     """
     Base class for `ManifestV1`.
 
@@ -102,7 +102,7 @@ class _ManifestBase(BaseModel):
         return values
 
 
-class TaskManifestV1(_TaskManifestBase):
+class TaskManifestV1(_TaskManifestBaseV1):
     """
     Task manifest schema version 1.
     """
@@ -110,7 +110,7 @@ class TaskManifestV1(_TaskManifestBase):
     pass
 
 
-class ManifestV1(_ManifestBase):
+class ManifestV1(_ManifestBaseV1):
     """
     Manifest schema version 1.
 

fractal_server/app/schemas/{project.py → v1/project.py}

@@ -4,18 +4,18 @@ from typing import Optional
 from pydantic import BaseModel
 from pydantic import validator
 
-from ._validators import valstr
-from ._validators import valutc
+from .._validators import valstr
+from .._validators import valutc
 
 
 __all__ = (
-    "ProjectCreate",
-    "ProjectRead",
-    "ProjectUpdate",
+    "ProjectCreateV1",
+    "ProjectReadV1",
+    "ProjectUpdateV1",
 )
 
 
-class _ProjectBase(BaseModel):
+class _ProjectBaseV1(BaseModel):
     """
     Base class for `Project`.
 
@@ -28,7 +28,7 @@ class _ProjectBase(BaseModel):
     read_only: bool = False
 
 
-class ProjectCreate(_ProjectBase):
+class ProjectCreateV1(_ProjectBaseV1):
     """
     Class for `Project` creation.
     """
@@ -37,7 +37,7 @@ class ProjectCreate(_ProjectBase):
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
 
-class ProjectRead(_ProjectBase):
+class ProjectReadV1(_ProjectBaseV1):
     """
     Class for `Project` read from database.
 
@@ -55,7 +55,7 @@ class ProjectRead(_ProjectBase):
     )
 
 
-class ProjectUpdate(_ProjectBase):
+class ProjectUpdateV1(_ProjectBaseV1):
     """
     Class for `Project` update.
 

fractal_server/app/schemas/{task.py → v1/task.py}

@@ -6,18 +6,18 @@ from pydantic import Field
 from pydantic import HttpUrl
 from pydantic import validator
 
-from ._validators import valstr
+from .._validators import valstr
 
 __all__ = (
-    "TaskCreate",
-    "TaskUpdate",
-    "TaskRead",
-    "TaskImport",
-    "TaskExport",
+    "TaskCreateV1",
+    "TaskUpdateV1",
+    "TaskReadV1",
+    "TaskImportV1",
+    "TaskExportV1",
 )
 
 
-class _TaskBase(BaseModel):
+class _TaskBaseV1(BaseModel):
     """
 
     Base class for `Task`.
@@ -32,7 +32,7 @@ class _TaskBase(BaseModel):
     _source = validator("source", allow_reuse=True)(valstr("source"))
 
 
-class TaskUpdate(_TaskBase):
+class TaskUpdateV1(_TaskBaseV1):
     """
     Class for `Task` update.
 
@@ -76,7 +76,7 @@ class TaskUpdate(_TaskBase):
     )
 
 
-class TaskImport(_TaskBase):
+class TaskImportV1(_TaskBaseV1):
     """
     Class for `Task` import.
     """
@@ -84,7 +84,7 @@ class TaskImport(_TaskBase):
     pass
 
 
-class TaskExport(_TaskBase):
+class TaskExportV1(_TaskBaseV1):
     """
     Class for `Task` export.
     """
@@ -92,7 +92,7 @@ class TaskExport(_TaskBase):
     pass
 
 
-class TaskRead(_TaskBase):
+class TaskReadV1(_TaskBaseV1):
     """
     Class for `Task` read from database.
 
@@ -124,7 +124,7 @@ class TaskRead(_TaskBase):
     docs_link: Optional[HttpUrl]
 
 
-class TaskCreate(_TaskBase):
+class TaskCreateV1(_TaskBaseV1):
     """
     Class for `Task` creation.
 

fractal_server/app/schemas/{task_collection.py → v1/task_collection.py}

@@ -6,16 +6,16 @@ from pydantic import BaseModel
 from pydantic import Field
 from pydantic import validator
 
-from ._validators import valstr
-from .task import TaskRead
+from .._validators import valstr
+from .task import TaskReadV1
 
 __all__ = (
-    "TaskCollectPip",
-    "TaskCollectStatus",
+    "TaskCollectPipV1",
+    "TaskCollectStatusV1",
 )
 
 
-class TaskCollectPip(BaseModel):
+class TaskCollectPipV1(BaseModel):
     """
     TaskCollectPip class
 
@@ -81,7 +81,7 @@ class TaskCollectPip(BaseModel):
         return v
 
 
-class TaskCollectStatus(BaseModel):
+class TaskCollectStatusV1(BaseModel):
     """
     TaskCollectStatus class
 
@@ -97,7 +97,7 @@ class TaskCollectStatus(BaseModel):
     status: Literal["pending", "installing", "collecting", "fail", "OK"]
     package: str
     venv_path: Path
-    task_list: Optional[list[TaskRead]] = Field(default=[])
+    task_list: Optional[list[TaskReadV1]] = Field(default=[])
     log: Optional[str]
     info: Optional[str]