fractal-server 2.0.0a4__tar.gz → 2.0.0a6__tar.gz

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.0a4
+Version: 2.0.0a6
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.0.0a6/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.0.0a6"

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/models/v2/dataset.py

@@ -28,7 +28,6 @@ class DatasetV2(SQLModel, table=True):
     history: list[dict[str, Any]] = Field(
         sa_column=Column(JSON, server_default="[]", nullable=False)
     )
-    read_only: bool = False
 
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/models/v2/project.py

@@ -16,7 +16,6 @@ class ProjectV2(SQLModel, table=True):
 
     id: Optional[int] = Field(default=None, primary_key=True)
     name: str
-    read_only: bool = False
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/routes/api/v1/task_collection.py

@@ -140,6 +140,16 @@ async def collect_tasks_pip(
                     f"Original error: {e}"
                 ),
             )
+        except ValidationError as e:
+            await db.close()
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                detail=(
+                    "Cannot collect package. Possible reason: an old version "
+                    "of the same package has already been collected. "
+                    f"Original error: {e}"
+                ),
+            )
         task_collect_status.info = "Already installed"
         state = State(data=task_collect_status.sanitised_dict())
         response.status_code == status.HTTP_200_OK

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/routes/api/v2/__init__.py

@@ -10,6 +10,7 @@ from .project import router as project_router_v2
 from .submit import router as submit_job_router_v2
 from .task import router as task_router_v2
 from .task_collection import router as task_collection_router_v2
+from .task_legacy import router as task_legacy_router_v2
 from .workflow import router as workflow_router_v2
 from .workflowtask import router as workflowtask_router_v2
 
@@ -20,9 +21,12 @@ router_api_v2.include_router(job_router_v2, tags=["V2 Job"])
 router_api_v2.include_router(images_routes_v2, tags=["V2 Images"])
 router_api_v2.include_router(project_router_v2, tags=["V2 Project"])
 router_api_v2.include_router(submit_job_router_v2, tags=["V2 Job"])
-router_api_v2.include_router(task_router_v2, prefix="/task", tags=["V2 Task"])
 router_api_v2.include_router(
     task_collection_router_v2, prefix="/task", tags=["V2 Task Collection"]
 )
+router_api_v2.include_router(task_router_v2, prefix="/task", tags=["V2 Task"])
+router_api_v2.include_router(
+    task_legacy_router_v2, prefix="/task-legacy", tags=["V2 Task Legacy"]
+)
 router_api_v2.include_router(workflow_router_v2, tags=["V2 Workflow"])
 router_api_v2.include_router(workflowtask_router_v2, tags=["V2 WorkflowTask"])

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/routes/api/v2/submit.py

@@ -59,15 +59,6 @@ async def apply_workflow(
     project = output["project"]
     dataset = output["dataset"]
 
-    if dataset.read_only:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                "Cannot apply workflow because dataset "
-                f"({dataset_id=}) is read_only."
-            ),
-        )
-
     workflow = await _get_workflow_check_owner(
         project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
     )

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/routes/api/v2/task_collection.py

@@ -137,7 +137,17 @@ async def collect_tasks_pip(
                 detail=(
                     "Cannot collect package. Possible reason: another "
                     "collection of the same package is in progress. "
-                    f"Original error: {e}"
+                    f"Original FileNotFoundError: {e}"
+                ),
+            )
+        except ValidationError as e:
+            await db.close()
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                detail=(
+                    "Cannot collect package. Possible reason: an old version "
+                    "of the same package has already been collected. "
+                    f"Original ValidationError: {e}"
                 ),
             )
         task_collect_status.info = "Already installed"

fractal_server-2.0.0a6/fractal_server/app/routes/api/v2/task_legacy.py

@@ -0,0 +1,59 @@
+from fastapi import APIRouter
+from fastapi import Depends
+from fastapi import HTTPException
+from fastapi import status
+from sqlmodel import select
+
+from .....logger import set_logger
+from ....db import AsyncSession
+from ....db import get_async_db
+from ....models.v1 import Task as TaskV1
+from ....schemas.v2 import TaskLegacyReadV2
+from ....security import current_active_user
+from ....security import User
+
+router = APIRouter()
+
+logger = set_logger(__name__)
+
+
+@router.get("/", response_model=list[TaskLegacyReadV2])
+async def get_list_task_legacy(
+    args_schema: bool = True,
+    only_v2_compatible: bool = False,
+    user: User = Depends(current_active_user),
+    db: AsyncSession = Depends(get_async_db),
+) -> list[TaskLegacyReadV2]:
+    """
+    Get list of available legacy tasks
+    """
+    stm = select(TaskV1)
+    if only_v2_compatible:
+        stm = stm.where(TaskV1.is_v2_compatible)
+    res = await db.execute(stm)
+    task_list = res.scalars().all()
+    await db.close()
+    if args_schema is False:
+        for task in task_list:
+            setattr(task, "args_schema", None)
+
+    return task_list
+
+
+@router.get("/{task_id}/", response_model=TaskLegacyReadV2)
+async def get_task_legacy(
+    task_id: int,
+    user: User = Depends(current_active_user),
+    db: AsyncSession = Depends(get_async_db),
+) -> TaskLegacyReadV2:
+    """
+    Get info on a specific legacy task
+    """
+    task = await db.get(TaskV1, task_id)
+    await db.close()
+    if not task:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"TaskV1[{task_id}] not found",
+        )
+    return task

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/runner/v1/_common.py

@@ -207,7 +207,7 @@ def call_single_task(
         with task_files.metadiff.open("r") as f_metadiff:
             diff_metadata = json.load(f_metadiff)
     except FileNotFoundError as e:
-        logger.error(
+        logger.warning(
             f"Skip collection of updated metadata. Original error: {str(e)}"
         )
         diff_metadata = {}

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/runner/v2/deduplicate_list.py

@@ -1,9 +1,10 @@
 from typing import TypeVar
 
 from ....images import SingleImage
+from ....images import SingleImageTaskOutput
 from .task_interface import InitArgsModel
 
-T = TypeVar("T", SingleImage, InitArgsModel)
+T = TypeVar("T", SingleImage, SingleImageTaskOutput, InitArgsModel)
 
 
 def deduplicate_list(

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/runner/v2/runner.py

@@ -157,6 +157,20 @@ def execute_tasks_v2(
                 updated_types.update(image["types"])
                 updated_types.update(task.output_types)
 
+                # Unset attributes with None value
+                updated_attributes = {
+                    key: value
+                    for key, value in updated_attributes.items()
+                    if value is not None
+                }
+
+                # Validate new image
+                SingleImage(
+                    zarr_url=image["zarr_url"],
+                    types=updated_types,
+                    attributes=updated_attributes,
+                )
+
                 # Update image in the dataset image list
                 tmp_images[original_index]["attributes"] = updated_attributes
                 tmp_images[original_index]["types"] = updated_types
@@ -182,6 +196,11 @@ def execute_tasks_v2(
                         updated_types = copy(original_img["types"])
                 # Update image attributes/types with task output and manifest
                 updated_attributes.update(image["attributes"])
+                updated_attributes = {
+                    key: value
+                    for key, value in updated_attributes.items()
+                    if value is not None
+                }
                 updated_types.update(image["types"])
                 updated_types.update(task.output_types)
                 new_image = dict(

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/runner/v2/task_interface.py

@@ -3,7 +3,7 @@ from typing import Any
 from pydantic import BaseModel
 from pydantic import Field
 
-from ....images import SingleImage
+from ....images import SingleImageTaskOutput
 from fractal_server.images import Filters
 
 
@@ -11,7 +11,9 @@ class TaskOutput(BaseModel):
     class Config:
         extra = "forbid"
 
-    image_list_updates: list[SingleImage] = Field(default_factory=list)
+    image_list_updates: list[SingleImageTaskOutput] = Field(
+        default_factory=list
+    )
     image_list_removals: list[str] = Field(default_factory=list)
     filters: Filters = Field(default_factory=Filters)
 

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/schemas/v1/task.py

@@ -122,7 +122,6 @@ class TaskReadV1(_TaskBaseV1):
     args_schema_version: Optional[str]
     docs_info: Optional[str]
     docs_link: Optional[HttpUrl]
-    is_v2_compatible: bool
 
 
 class TaskCreateV1(_TaskBaseV1):

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/schemas/v2/__init__.py

@@ -17,6 +17,7 @@ from .project import ProjectUpdateV2  # noqa F401
 from .task import TaskCreateV2  # noqa F401
 from .task import TaskExportV2  # noqa F401
 from .task import TaskImportV2  # noqa F401
+from .task import TaskLegacyReadV2  # noqa F401
 from .task import TaskReadV2  # noqa F401
 from .task import TaskUpdateV2  # noqa F401
 from .task_collection import TaskCollectPipV2  # noqa F401

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/schemas/v2/dataset.py

@@ -8,8 +8,8 @@ from pydantic import validator
 
 from .._validators import valstr
 from .._validators import valutc
-from ..v1.project import ProjectReadV1
 from .dumps import WorkflowTaskDumpV2
+from .project import ProjectReadV2
 from .workflowtask import WorkflowTaskStatusTypeV2
 from fractal_server.images import Filters
 
@@ -45,7 +45,6 @@ class DatasetCreateV2(BaseModel, extra=Extra.forbid):
 
     name: str
 
-    read_only: bool = False
     zarr_dir: str
 
     filters: Filters = Field(default_factory=Filters)
@@ -60,10 +59,9 @@ class DatasetReadV2(BaseModel):
     name: str
 
     project_id: int
-    project: ProjectReadV1
+    project: ProjectReadV2
 
     history: list[_DatasetHistoryItemV2]
-    read_only: bool
 
     timestamp_created: datetime
 
@@ -81,7 +79,6 @@ class DatasetUpdateV2(BaseModel):
         extra = "forbid"
 
     name: Optional[str]
-    read_only: Optional[bool]
     zarr_dir: Optional[str]
     filters: Optional[Filters]
 

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/schemas/v2/dumps.py

@@ -22,7 +22,6 @@ class ProjectDumpV2(BaseModel, extra=Extra.forbid):
 
     id: int
     name: str
-    read_only: bool
     timestamp_created: str
 
 
@@ -80,7 +79,6 @@ class DatasetDumpV2(BaseModel):
     id: int
     name: str
     project_id: int
-    read_only: bool
     timestamp_created: str
 
     zarr_dir: str

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/schemas/v2/project.py

@@ -12,7 +12,6 @@ from .._validators import valutc
 class ProjectCreateV2(BaseModel, extra=Extra.forbid):
 
     name: str
-    read_only: bool = False
     # Validators
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
@@ -21,7 +20,6 @@ class ProjectReadV2(BaseModel):
 
     id: int
     name: str
-    read_only: bool
     timestamp_created: datetime
     # Validators
     _timestamp_created = validator("timestamp_created", allow_reuse=True)(
@@ -32,6 +30,5 @@ class ProjectReadV2(BaseModel):
 class ProjectUpdateV2(BaseModel):
 
     name: Optional[str]
-    read_only: Optional[bool]
     # Validators
     _name = validator("name", allow_reuse=True)(valstr("name"))

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/schemas/v2/task.py

@@ -11,6 +11,7 @@ from pydantic import validator
 
 from .._validators import valdictkeys
 from .._validators import valstr
+from ..v1.task import TaskReadV1
 
 
 class TaskCreateV2(BaseModel, extra=Extra.forbid):
@@ -100,6 +101,10 @@ class TaskReadV2(BaseModel):
     output_types: dict[str, bool]
 
 
+class TaskLegacyReadV2(TaskReadV1):
+    is_v2_compatible: bool
+
+
 class TaskUpdateV2(BaseModel):
 
     name: Optional[str]

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/app/schemas/v2/workflow.py

@@ -7,7 +7,7 @@ from pydantic import validator
 
 from .._validators import valstr
 from .._validators import valutc
-from ..v1.project import ProjectReadV1
+from .project import ProjectReadV2
 from .workflowtask import WorkflowTaskExportV2
 from .workflowtask import WorkflowTaskImportV2
 from .workflowtask import WorkflowTaskReadV2
@@ -27,7 +27,7 @@ class WorkflowReadV2(BaseModel):
     name: str
     project_id: int
     task_list: list[WorkflowTaskReadV2]
-    project: ProjectReadV1
+    project: ProjectReadV2
     timestamp_created: datetime
 
     _timestamp_created = validator("timestamp_created", allow_reuse=True)(

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/images/__init__.py

@@ -1,2 +1,3 @@
 from .models import Filters  # noqa: F401
 from .models import SingleImage  # noqa: F401
+from .models import SingleImageTaskOutput  # noqa: F401

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/fractal_server/images/models.py

@@ -9,7 +9,16 @@ from pydantic import validator
 from fractal_server.app.schemas._validators import valdictkeys
 
 
-class SingleImage(BaseModel):
+class SingleImageBase(BaseModel):
+    """
+    Base for SingleImage and SingleImageTaskOutput.
+
+    Attributes:
+        zarr_url:
+        origin:
+        attributes:
+        types:
+    """
 
     zarr_url: str
     origin: Optional[str] = None
@@ -23,6 +32,31 @@ class SingleImage(BaseModel):
     )
     _types = validator("types", allow_reuse=True)(valdictkeys("types"))
 
+
+class SingleImageTaskOutput(SingleImageBase):
+    """
+    `SingleImageBase`, with scalar `attributes` values (`None` included).
+    """
+
+    @validator("attributes")
+    def validate_attributes(
+        cls, v: dict[str, Any]
+    ) -> dict[str, Union[int, float, str, bool, None]]:
+        for key, value in v.items():
+            if not isinstance(value, (int, float, str, bool, type(None))):
+                raise ValueError(
+                    f"SingleImageTaskOutput.attributes[{key}] must be a "
+                    "scalar (int, float, str or bool). "
+                    f"Given {value} ({type(value)})"
+                )
+        return v
+
+
+class SingleImage(SingleImageBase):
+    """
+    `SingleImageBase`, with scalar `attributes` values (`None` excluded).
+    """
+
     @validator("attributes")
     def validate_attributes(
         cls, v: dict[str, Any]

fractal_server-2.0.0a4/fractal_server/migrations/versions/d71e732236cd_v2.py → fractal_server-2.0.0a6/fractal_server/migrations/versions/80e12e1bc4fd_v2.py

@@ -1,8 +1,8 @@
-"""v2
+"""V2
 
-Revision ID: d71e732236cd
+Revision ID: 80e12e1bc4fd
 Revises: 9fd26a2b0de4
-Create Date: 2024-04-05 11:09:17.639183
+Create Date: 2024-04-12 10:13:58.085788
 
 """
 import sqlalchemy as sa
@@ -11,7 +11,7 @@ from alembic import op
 
 
 # revision identifiers, used by Alembic.
-revision = "d71e732236cd"
+revision = "80e12e1bc4fd"
 down_revision = "9fd26a2b0de4"
 branch_labels = None
 depends_on = None
@@ -23,7 +23,6 @@ def upgrade() -> None:
         "projectv2",
         sa.Column("id", sa.Integer(), nullable=False),
         sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
-        sa.Column("read_only", sa.Boolean(), nullable=False),
         sa.Column(
             "timestamp_created", sa.DateTime(timezone=True), nullable=False
         ),
@@ -81,7 +80,6 @@ def upgrade() -> None:
         sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column("project_id", sa.Integer(), nullable=False),
         sa.Column("history", sa.JSON(), server_default="[]", nullable=False),
-        sa.Column("read_only", sa.Boolean(), nullable=False),
         sa.Column(
             "timestamp_created", sa.DateTime(timezone=True), nullable=False
         ),

{fractal_server-2.0.0a4 → fractal_server-2.0.0a6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.0.0a4"
+version = "2.0.0a6"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Jacopo Nespolo <jacopo.nespolo@exact-lab.it>",
@@ -86,7 +86,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.0.0a4"
+current_version = "2.0.0a6"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.0.0a4/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.0.0a4"