fractal-server 2.0.0a10__py3-none-any.whl → 2.0.0a12__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.0a10"
+__VERSION__ = "2.0.0a12"

fractal_server/app/models/__init__.py

@@ -2,6 +2,8 @@
 `models` module
 """
 from .security import *  # noqa: F401, F403
-from .state import State  # noqa: F401
-from .v1 import *  # noqa: F401, F403
-from .v2 import *  # noqa: F401, F403
+from .v1 import Project  # noqa: F401
+from .v2 import ProjectV2  # noqa: F401
+
+# We include the project models to avoid issues with LinkUserProject
+# (sometimes taking place in alembic autogenerate)

fractal_server/app/models/v1/__init__.py

@@ -6,6 +6,7 @@ from .dataset import Resource  # noqa: F401
 from .job import ApplyWorkflow  # noqa: F403, F401
 from .job import JobStatusTypeV1  # noqa: F401, F403
 from .project import Project  # noqa: F403, F401
+from .state import State  # noqa: F403, F401
 from .task import Task  # noqa: F403, F401
 from .workflow import Workflow  # noqa: F401, F403
 from .workflow import WorkflowTask  # noqa: F401, F403

fractal_server/app/models/{state.py → v1/state.py}

@@ -8,8 +8,8 @@ from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
-from ...utils import get_timestamp
-from ..schemas.v1 import _StateBase
+from ....utils import get_timestamp
+from ...schemas.state import _StateBase
 
 
 class State(_StateBase, SQLModel, table=True):

fractal_server/app/models/v2/__init__.py

@@ -2,6 +2,7 @@
 v2 `models` module
 """
 from ..linkuserproject import LinkUserProjectV2
+from .collection_state import CollectionStateV2
 from .dataset import DatasetV2
 from .job import JobV2
 from .project import ProjectV2
@@ -14,6 +15,7 @@ __all__ = [
     "DatasetV2",
     "JobV2",
     "ProjectV2",
+    "CollectionStateV2",
     "TaskV2",
     "WorkflowTaskV2",
     "WorkflowV2",

fractal_server/app/models/v2/collection_state.py

@@ -0,0 +1,21 @@
+from datetime import datetime
+from typing import Any
+from typing import Optional
+
+from sqlalchemy import Column
+from sqlalchemy.types import DateTime
+from sqlalchemy.types import JSON
+from sqlmodel import Field
+from sqlmodel import SQLModel
+
+from ....utils import get_timestamp
+
+
+class CollectionStateV2(SQLModel, table=True):
+
+    id: Optional[int] = Field(default=None, primary_key=True)
+    data: dict[str, Any] = Field(sa_column=Column(JSON), default={})
+    timestamp: datetime = Field(
+        default_factory=get_timestamp,
+        sa_column=Column(DateTime(timezone=True)),
+    )

fractal_server/app/models/v2/job.py

@@ -9,7 +9,7 @@ from sqlmodel import Field
 from sqlmodel import SQLModel
 
 from ....utils import get_timestamp
-from ...schemas.v1 import JobStatusTypeV1
+from ...schemas.v2 import JobStatusTypeV2
 
 
 class JobV2(SQLModel, table=True):
@@ -47,5 +47,5 @@ class JobV2(SQLModel, table=True):
     end_timestamp: Optional[datetime] = Field(
         default=None, sa_column=Column(DateTime(timezone=True))
     )
-    status: str = JobStatusTypeV1.SUBMITTED
+    status: str = JobStatusTypeV2.SUBMITTED
     log: Optional[str] = None

fractal_server/app/models/v2/workflowtask.py

@@ -2,7 +2,6 @@ from typing import Any
 from typing import Literal
 from typing import Optional
 
-from pydantic import validator
 from sqlalchemy import Column
 from sqlalchemy.types import JSON
 from sqlmodel import Field
@@ -48,41 +47,3 @@ class WorkflowTaskV2(SQLModel, table=True):
     task_legacy: Optional[Task] = Relationship(
         sa_relationship_kwargs=dict(lazy="selectin")
     )
-
-    @validator("args_non_parallel")
-    def validate_args_non_parallel(cls, value):
-        if value is None:
-            return
-        forbidden_args_keys = {
-            "zarr_dir",
-            "zarr_url",
-            "zarr_urls",
-            "init_args",
-        }
-        args_keys = set(value.keys())
-        intersect_keys = forbidden_args_keys.intersection(args_keys)
-        if intersect_keys:
-            raise ValueError(
-                "`args` contains the following forbidden keys: "
-                f"{intersect_keys}"
-            )
-        return value
-
-    @validator("args_parallel")
-    def validate_args_parallel(cls, value):
-        if value is None:
-            return
-        forbidden_args_keys = {
-            "zarr_dir",
-            "zarr_url",
-            "zarr_urls",
-            "init_args",
-        }
-        args_keys = set(value.keys())
-        intersect_keys = forbidden_args_keys.intersection(args_keys)
-        if intersect_keys:
-            raise ValueError(
-                "`args` contains the following forbidden keys: "
-                f"{intersect_keys}"
-            )
-        return value

fractal_server/app/routes/admin/v1.py

@@ -20,12 +20,12 @@ from ....syringe import Inject
 from ....utils import get_timestamp
 from ...db import AsyncSession
 from ...db import get_async_db
-from ...models import ApplyWorkflow
-from ...models import Dataset
-from ...models import JobStatusTypeV1
-from ...models import Project
-from ...models import Workflow
 from ...models.security import UserOAuth as User
+from ...models.v1 import ApplyWorkflow
+from ...models.v1 import Dataset
+from ...models.v1 import JobStatusTypeV1
+from ...models.v1 import Project
+from ...models.v1 import Workflow
 from ...runner.filenames import WORKFLOW_LOG_FILENAME
 from ...schemas.v1 import ApplyWorkflowReadV1
 from ...schemas.v1 import ApplyWorkflowUpdateV1

fractal_server/app/routes/admin/v2.py

@@ -20,13 +20,13 @@ from ....syringe import Inject
 from ....utils import get_timestamp
 from ...db import AsyncSession
 from ...db import get_async_db
-from ...models import JobStatusTypeV1
 from ...models.security import UserOAuth as User
 from ...models.v1 import Task
 from ...models.v2 import JobV2
 from ...models.v2 import ProjectV2
 from ...runner.filenames import WORKFLOW_LOG_FILENAME
 from ...schemas.v2 import JobReadV2
+from ...schemas.v2 import JobStatusTypeV2
 from ...schemas.v2 import JobUpdateV2
 from ...schemas.v2 import ProjectReadV2
 from ...security import current_active_superuser
@@ -90,7 +90,7 @@ async def view_job(
     project_id: Optional[int] = None,
     dataset_id: Optional[int] = None,
     workflow_id: Optional[int] = None,
-    status: Optional[JobStatusTypeV1] = None,
+    status: Optional[JobStatusTypeV2] = None,
     start_timestamp_min: Optional[datetime] = None,
     start_timestamp_max: Optional[datetime] = None,
     end_timestamp_min: Optional[datetime] = None,
@@ -175,7 +175,7 @@ async def view_single_job(
         )
     await db.close()
 
-    if show_tmp_logs and (job.status == JobStatusTypeV1.SUBMITTED):
+    if show_tmp_logs and (job.status == JobStatusTypeV2.SUBMITTED):
         try:
             with open(f"{job.working_dir}/{WORKFLOW_LOG_FILENAME}", "r") as f:
                 job.log = f.read()
@@ -208,7 +208,7 @@ async def update_job(
             detail=f"Job {job_id} not found",
         )
 
-    if job_update.status != JobStatusTypeV1.FAILED:
+    if job_update.status != JobStatusTypeV2.FAILED:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
             detail=f"Cannot set job status to {job_update.status}",

fractal_server/app/routes/api/v1/_aux_functions.py

@@ -12,13 +12,13 @@ from sqlmodel import select
 from sqlmodel.sql.expression import SelectOfScalar
 
 from ....db import AsyncSession
-from ....models import ApplyWorkflow
-from ....models import Dataset
 from ....models import LinkUserProject
-from ....models import Project
-from ....models import Task
-from ....models import Workflow
-from ....models import WorkflowTask
+from ....models.v1 import ApplyWorkflow
+from ....models.v1 import Dataset
+from ....models.v1 import Project
+from ....models.v1 import Task
+from ....models.v1 import Workflow
+from ....models.v1 import WorkflowTask
 from ....schemas.v1 import JobStatusTypeV1
 from ....security import User
 

fractal_server/app/routes/api/v1/dataset.py

@@ -13,10 +13,10 @@ from sqlmodel import select
 
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import ApplyWorkflow
-from ....models import Dataset
-from ....models import Project
-from ....models import Resource
+from ....models.v1 import ApplyWorkflow
+from ....models.v1 import Dataset
+from ....models.v1 import Project
+from ....models.v1 import Resource
 from ....runner.filenames import HISTORY_FILENAME
 from ....schemas.v1 import DatasetCreateV1
 from ....schemas.v1 import DatasetReadV1

fractal_server/app/routes/api/v1/project.py

@@ -18,11 +18,11 @@ from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import ApplyWorkflow
-from ....models import Dataset
 from ....models import LinkUserProject
-from ....models import Project
-from ....models import Workflow
+from ....models.v1 import ApplyWorkflow
+from ....models.v1 import Dataset
+from ....models.v1 import Project
+from ....models.v1 import Workflow
 from ....runner.set_start_and_last_task_index import (
     set_start_and_last_task_index,
 )

fractal_server/app/routes/api/v1/task.py

@@ -11,8 +11,8 @@ from sqlmodel import select
 from .....logger import set_logger
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import Task
-from ....models import WorkflowTask
+from ....models.v1 import Task
+from ....models.v1 import WorkflowTask
 from ....models.v2 import TaskV2
 from ....schemas.v1 import TaskCreateV1
 from ....schemas.v1 import TaskReadV1

fractal_server/app/routes/api/v1/task_collection.py

@@ -17,9 +17,9 @@ from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import State
-from ....models import Task
-from ....schemas.v1 import StateRead
+from ....models.v1 import State
+from ....models.v1 import Task
+from ....schemas.state import StateRead
 from ....schemas.v1 import TaskCollectPipV1
 from ....schemas.v1 import TaskCollectStatusV1
 from ....security import current_active_user

fractal_server/app/routes/api/v1/workflow.py

@@ -23,10 +23,10 @@ from .....logger import close_logger
 from .....logger import set_logger
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import ApplyWorkflow
-from ....models import Project
-from ....models import Task
-from ....models import Workflow
+from ....models.v1 import ApplyWorkflow
+from ....models.v1 import Project
+from ....models.v1 import Task
+from ....models.v1 import Workflow
 from ....schemas.v1 import WorkflowCreateV1
 from ....schemas.v1 import WorkflowExportV1
 from ....schemas.v1 import WorkflowImportV1

fractal_server/app/routes/api/v1/workflowtask.py

@@ -22,7 +22,7 @@ from fastapi import status
 
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import Task
+from ....models.v1 import Task
 from ....schemas.v1 import WorkflowTaskCreateV1
 from ....schemas.v1 import WorkflowTaskReadV1
 from ....schemas.v1 import WorkflowTaskUpdateV1

fractal_server/app/routes/api/v2/_aux_functions.py

@@ -21,7 +21,7 @@ from ....models.v2 import ProjectV2
 from ....models.v2 import TaskV2
 from ....models.v2 import WorkflowTaskV2
 from ....models.v2 import WorkflowV2
-from ....schemas.v1 import JobStatusTypeV1
+from ....schemas.v2 import JobStatusTypeV2
 from ....security import User
 from fractal_server.images import Filters
 
@@ -384,7 +384,7 @@ def _get_submitted_jobs_statement() -> SelectOfScalar:
         A sqlmodel statement that selects all `Job`s with
         `Job.status` equal to `submitted`.
     """
-    stm = select(JobV2).where(JobV2.status == JobStatusTypeV1.SUBMITTED)
+    stm = select(JobV2).where(JobV2.status == JobStatusTypeV2.SUBMITTED)
     return stm
 
 

fractal_server/app/routes/api/v2/dataset.py

@@ -270,6 +270,16 @@ async def import_dataset(
         db=db,
     )
 
+    for image in dataset.images:
+        if not image.zarr_url.startswith(dataset.zarr_dir):
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                detail=(
+                    f"Cannot import dataset: zarr_url {image.zarr_url} is not "
+                    f"relative to zarr_dir={dataset.zarr_dir}."
+                ),
+            )
+
     # Create new Dataset
     db_dataset = DatasetV2(
         project_id=project_id,

fractal_server/app/routes/api/v2/job.py

@@ -12,7 +12,7 @@ from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v2 import JobV2
 from ....models.v2 import ProjectV2
-from ....runner.filenames import WORKFLOW_LOG_FILENAME  # FIXME
+from ....runner.filenames import WORKFLOW_LOG_FILENAME
 from ....schemas.v2 import JobReadV2
 from ....schemas.v2 import JobStatusTypeV2
 from ....security import current_active_user

fractal_server/app/routes/api/v2/project.py

@@ -5,11 +5,8 @@ from fastapi import Depends
 from fastapi import HTTPException
 from fastapi import Response
 from fastapi import status
-from sqlalchemy.exc import IntegrityError
 from sqlmodel import select
 
-from .....logger import close_logger
-from .....logger import set_logger
 from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v2 import DatasetV2
@@ -65,20 +62,11 @@ async def create_project(
 
     db_project = ProjectV2(**project.dict())
     db_project.user_list.append(user)
-    try:
-        db.add(db_project)
-        await db.commit()
-        await db.refresh(db_project)
-        await db.close()
-    except IntegrityError as e:
-        await db.rollback()
-        logger = set_logger("create_project")
-        logger.error(str(e))
-        close_logger(logger)
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=str(e),
-        )
+
+    db.add(db_project)
+    await db.commit()
+    await db.refresh(db_project)
+    await db.close()
 
     return db_project
 

fractal_server/app/routes/api/v2/submit.py

@@ -17,7 +17,7 @@ from ....db import get_async_db
 from ....models.v2 import JobV2
 from ....runner.set_start_and_last_task_index import (
     set_start_and_last_task_index,
-)  # FIXME V2
+)
 from ....runner.v2 import submit_workflow
 from ....schemas.v2 import JobCreateV2
 from ....schemas.v2 import JobReadV2

fractal_server/app/routes/api/v2/task_collection.py

@@ -17,9 +17,9 @@ from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import State
+from ....models.v2 import CollectionStateV2
 from ....models.v2 import TaskV2
-from ....schemas import StateRead
+from ....schemas.state import StateRead
 from ....schemas.v2 import TaskCollectPipV2
 from ....schemas.v2 import TaskCollectStatusV2
 from ....security import current_active_user
@@ -151,7 +151,7 @@ async def collect_tasks_pip(
                 ),
             )
         task_collect_status.info = "Already installed"
-        state = State(data=task_collect_status.sanitised_dict())
+        state = CollectionStateV2(data=task_collect_status.sanitised_dict())
         response.status_code == status.HTTP_200_OK
         await db.close()
         return state
@@ -181,7 +181,7 @@ async def collect_tasks_pip(
     # Create State object (after casting venv_path to string)
     collection_status_dict = collection_status.dict()
     collection_status_dict["venv_path"] = str(collection_status.venv_path)
-    state = State(data=collection_status_dict)
+    state = CollectionStateV2(data=collection_status_dict)
     db.add(state)
     await db.commit()
     await db.refresh(state)
@@ -220,7 +220,7 @@ async def check_collection_status(
     """
     logger = set_logger(logger_name="check_collection_status")
     logger.debug(f"Querying state for state.id={state_id}")
-    state = await db.get(State, state_id)
+    state = await db.get(CollectionStateV2, state_id)
     if not state:
         await db.close()
         raise HTTPException(

fractal_server/app/routes/api/v2/workflowtask.py

@@ -46,6 +46,11 @@ async def create_workflowtask(
 
     if new_task.is_legacy_task is True:
         task = await db.get(Task, task_id)
+        if not task:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Task {task_id} not found.",
+            )
         if not task.is_v2_compatible:
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
@@ -53,16 +58,11 @@ async def create_workflowtask(
             )
     else:
         task = await db.get(TaskV2, task_id)
-
-    if not task:
-        if new_task.is_legacy_task:
-            error = f"Task {task_id} not found."
-        else:
-            error = f"TaskV2 {task_id} not found."
-
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail=error
-        )
+        if not task:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"TaskV2 {task_id} not found.",
+            )
 
     if new_task.is_legacy_task is True or task.type == "parallel":
         if (

fractal_server/app/routes/aux/_job.py

@@ -3,7 +3,7 @@ from pathlib import Path
 from zipfile import ZIP_DEFLATED
 from zipfile import ZipFile
 
-from ...models import ApplyWorkflow
+from ...models.v1 import ApplyWorkflow
 from ...runner.filenames import SHUTDOWN_FILENAME
 
 

fractal_server/app/runner/task_files.py

@@ -42,7 +42,7 @@ class TaskFiles:
     workflow_dir: Path
     workflow_dir_user: Path
     task_order: Optional[int] = None
-    component: Optional[str] = None  # FIXME: this is actually for V1 only
+    component: Optional[str] = None
 
     file_prefix: str
     args: Path

fractal_server/app/runner/v1/__init__.py

@@ -26,10 +26,10 @@ from ....logger import set_logger
 from ....syringe import Inject
 from ....utils import get_timestamp
 from ...db import DB
-from ...models import ApplyWorkflow
-from ...models import Dataset
-from ...models import Workflow
-from ...models import WorkflowTask
+from ...models.v1 import ApplyWorkflow
+from ...models.v1 import Dataset
+from ...models.v1 import Workflow
+from ...models.v1 import WorkflowTask
 from ...schemas.v1 import JobStatusTypeV1
 from ..exceptions import JobExecutionError
 from ..exceptions import TaskExecutionError

fractal_server/app/runner/v1/_common.py

@@ -21,8 +21,8 @@ from typing import Optional
 from ....config import get_settings
 from ....logger import get_logger
 from ....syringe import Inject
-from ...models import Task
-from ...models import WorkflowTask
+from ...models.v1 import Task
+from ...models.v1 import WorkflowTask
 from ...schemas.v1 import WorkflowTaskStatusTypeV1
 from ..exceptions import JobExecutionError
 from ..exceptions import TaskExecutionError

fractal_server/app/runner/v1/_local/__init__.py

@@ -23,11 +23,11 @@ from pathlib import Path
 from typing import Any
 from typing import Optional
 
-from ....models import Workflow  # FIXME: this is v1 specific
+from ....models.v1 import Workflow
 from ...async_wrap import async_wrap
 from ...set_start_and_last_task_index import set_start_and_last_task_index
-from .._common import execute_tasks  # FIXME: this is v1 specific
-from ..common import TaskParameters  # FIXME: this is v1 specific
+from .._common import execute_tasks
+from ..common import TaskParameters
 from ._submit_setup import _local_submit_setup
 from .executor import FractalThreadPoolExecutor