fractal-server 2.11.1__py3-none-any.whl → 2.12.0a0__py3-none-any.whl

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

@@ -1,355 +0,0 @@
-# Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and
-# University of Zurich
-#
-# Original author(s):
-# Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
-# Marco Franzon <marco.franzon@exact-lab.it>
-# Tommaso Comparin <tommaso.comparin@exact-lab.it>
-#
-# This file is part of Fractal and was originally developed by eXact lab S.r.l.
-# <exact-lab.it> under contract with Liberali Lab from the Friedrich Miescher
-# Institute for Biomedical Research and Pelkmans Lab from the University of
-# Zurich.
-from typing import Optional
-
-from fastapi import APIRouter
-from fastapi import Depends
-from fastapi import HTTPException
-from fastapi import Response
-from fastapi import status
-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.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
-from ....schemas.v1 import WorkflowReadV1
-from ....schemas.v1 import WorkflowTaskCreateV1
-from ....schemas.v1 import WorkflowUpdateV1
-from ._aux_functions import _check_workflow_exists
-from ._aux_functions import _get_project_check_owner
-from ._aux_functions import _get_submitted_jobs_statement
-from ._aux_functions import _get_workflow_check_owner
-from ._aux_functions import _raise_if_v1_is_read_only
-from ._aux_functions import _workflow_insert_task
-from fractal_server.app.models import UserOAuth
-from fractal_server.app.routes.auth import current_active_user
-
-
-router = APIRouter()
-
-
-@router.get(
-    "/project/{project_id}/workflow/",
-    response_model=list[WorkflowReadV1],
-)
-async def get_workflow_list(
-    project_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[list[WorkflowReadV1]]:
-    """
-    Get workflow list for given project
-    """
-    # Access control
-    project = await _get_project_check_owner(
-        project_id=project_id, user_id=user.id, db=db
-    )
-    # Find workflows of the current project. Note: this select/where approach
-    # has much better scaling than refreshing all elements of
-    # `project.workflow_list` - ref
-    # https://github.com/fractal-analytics-platform/fractal-server/pull/1082#issuecomment-1856676097.
-    stm = select(Workflow).where(Workflow.project_id == project.id)
-    workflow_list = (await db.execute(stm)).scalars().all()
-    return workflow_list
-
-
-@router.post(
-    "/project/{project_id}/workflow/",
-    response_model=WorkflowReadV1,
-    status_code=status.HTTP_201_CREATED,
-)
-async def create_workflow(
-    project_id: int,
-    workflow: WorkflowCreateV1,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowReadV1]:
-    """
-    Create a workflow, associate to a project
-    """
-    _raise_if_v1_is_read_only()
-    await _get_project_check_owner(
-        project_id=project_id,
-        user_id=user.id,
-        db=db,
-    )
-    await _check_workflow_exists(
-        name=workflow.name, project_id=project_id, db=db
-    )
-
-    db_workflow = Workflow(project_id=project_id, **workflow.dict())
-    db.add(db_workflow)
-    await db.commit()
-    await db.refresh(db_workflow)
-    await db.close()
-    return db_workflow
-
-
-@router.get(
-    "/project/{project_id}/workflow/{workflow_id}/",
-    response_model=WorkflowReadV1,
-)
-async def read_workflow(
-    project_id: int,
-    workflow_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowReadV1]:
-    """
-    Get info on an existing workflow
-    """
-
-    workflow = await _get_workflow_check_owner(
-        project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
-    )
-
-    return workflow
-
-
-@router.patch(
-    "/project/{project_id}/workflow/{workflow_id}/",
-    response_model=WorkflowReadV1,
-)
-async def update_workflow(
-    project_id: int,
-    workflow_id: int,
-    patch: WorkflowUpdateV1,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowReadV1]:
-    """
-    Edit a workflow
-    """
-    _raise_if_v1_is_read_only()
-    workflow = await _get_workflow_check_owner(
-        project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
-    )
-
-    if patch.name:
-        await _check_workflow_exists(
-            name=patch.name, project_id=project_id, db=db
-        )
-
-    for key, value in patch.dict(exclude_unset=True).items():
-        if key == "reordered_workflowtask_ids":
-            current_workflowtask_ids = [
-                wftask.id for wftask in workflow.task_list
-            ]
-            num_tasks = len(workflow.task_list)
-            if len(value) != num_tasks or set(value) != set(
-                current_workflowtask_ids
-            ):
-                raise HTTPException(
-                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                    detail=(
-                        "`reordered_workflowtask_ids` must be a permutation of"
-                        f" {current_workflowtask_ids} (given {value})"
-                    ),
-                )
-            for ind_wftask in range(num_tasks):
-                new_order = value.index(workflow.task_list[ind_wftask].id)
-                workflow.task_list[ind_wftask].order = new_order
-        else:
-            setattr(workflow, key, value)
-
-    await db.commit()
-    await db.refresh(workflow)
-    await db.close()
-
-    return workflow
-
-
-@router.delete(
-    "/project/{project_id}/workflow/{workflow_id}/",
-    status_code=status.HTTP_204_NO_CONTENT,
-)
-async def delete_workflow(
-    project_id: int,
-    workflow_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Response:
-    """
-    Delete a workflow
-    """
-    _raise_if_v1_is_read_only()
-    workflow = await _get_workflow_check_owner(
-        project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
-    )
-
-    # Fail if there exist jobs that are submitted and in relation with the
-    # current workflow.
-    stm = _get_submitted_jobs_statement().where(
-        ApplyWorkflow.workflow_id == workflow.id
-    )
-    res = await db.execute(stm)
-    jobs = res.scalars().all()
-    if jobs:
-        string_ids = str([job.id for job in jobs])[1:-1]
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                f"Cannot delete workflow {workflow.id} because it "
-                f"is linked to active job(s) {string_ids}."
-            ),
-        )
-
-    # Cascade operations: set foreign-keys to null for jobs which are in
-    # relationship with the current workflow
-    stm = select(ApplyWorkflow).where(ApplyWorkflow.workflow_id == workflow_id)
-    res = await db.execute(stm)
-    jobs = res.scalars().all()
-    for job in jobs:
-        job.workflow_id = None
-        await db.merge(job)
-    await db.commit()
-
-    # Delete workflow
-    await db.delete(workflow)
-    await db.commit()
-
-    return Response(status_code=status.HTTP_204_NO_CONTENT)
-
-
-@router.get(
-    "/project/{project_id}/workflow/{workflow_id}/export/",
-    response_model=WorkflowExportV1,
-)
-async def export_worfklow(
-    project_id: int,
-    workflow_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowExportV1]:
-    """
-    Export an existing workflow, after stripping all IDs
-    """
-    workflow = await _get_workflow_check_owner(
-        project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
-    )
-    # Emit a warning when exporting a workflow with custom tasks
-    logger = set_logger(None)
-    for wftask in workflow.task_list:
-        if wftask.task.owner is not None:
-            logger.warning(
-                f"Custom tasks (like the one with id={wftask.task.id} and "
-                f'source="{wftask.task.source}") are not meant to be '
-                "portable; re-importing this workflow may not work as "
-                "expected."
-            )
-    close_logger(logger)
-
-    await db.close()
-    return workflow
-
-
-@router.post(
-    "/project/{project_id}/workflow/import/",
-    response_model=WorkflowReadV1,
-    status_code=status.HTTP_201_CREATED,
-)
-async def import_workflow(
-    project_id: int,
-    workflow: WorkflowImportV1,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowReadV1]:
-    """
-    Import an existing workflow into a project
-
-    Also create all required objects (i.e. Workflow and WorkflowTask's) along
-    the way.
-    """
-    _raise_if_v1_is_read_only()
-    # Preliminary checks
-    await _get_project_check_owner(
-        project_id=project_id,
-        user_id=user.id,
-        db=db,
-    )
-
-    await _check_workflow_exists(
-        name=workflow.name, project_id=project_id, db=db
-    )
-
-    # Check that all required tasks are available
-    tasks = [wf_task.task for wf_task in workflow.task_list]
-    source_to_id = {}
-    for task in tasks:
-        source = task.source
-        if source not in source_to_id.keys():
-            stm = select(Task).where(Task.source == source)
-            tasks_by_source = (await db.execute(stm)).scalars().all()
-            if len(tasks_by_source) != 1:
-                raise HTTPException(
-                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                    detail=(
-                        f"Found {len(tasks_by_source)} tasks with {source=}."
-                    ),
-                )
-            source_to_id[source] = tasks_by_source[0].id
-
-    # Create new Workflow (with empty task_list)
-    db_workflow = Workflow(
-        project_id=project_id,
-        **workflow.dict(exclude_none=True, exclude={"task_list"}),
-    )
-    db.add(db_workflow)
-    await db.commit()
-    await db.refresh(db_workflow)
-
-    # Insert tasks
-    async with db:
-        for _, wf_task in enumerate(workflow.task_list):
-            # Identify task_id
-            source = wf_task.task.source
-            task_id = source_to_id[source]
-            # Prepare new_wf_task
-            new_wf_task = WorkflowTaskCreateV1(
-                **wf_task.dict(exclude_none=True),
-            )
-            # Insert task
-            await _workflow_insert_task(
-                **new_wf_task.dict(),
-                workflow_id=db_workflow.id,
-                task_id=task_id,
-                db=db,
-            )
-
-    await db.close()
-    return db_workflow
-
-
-@router.get("/workflow/", response_model=list[WorkflowReadV1])
-async def get_user_workflows(
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> list[WorkflowReadV1]:
-    """
-    Returns all the workflows of the current user
-    """
-    stm = select(Workflow)
-    stm = stm.join(Project).where(
-        Project.user_list.any(UserOAuth.id == user.id)
-    )
-    res = await db.execute(stm)
-    workflow_list = res.scalars().all()
-    return workflow_list

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

@@ -1,187 +0,0 @@
-# Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and
-# University of Zurich
-#
-# Original author(s):
-# Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
-# Marco Franzon <marco.franzon@exact-lab.it>
-# Tommaso Comparin <tommaso.comparin@exact-lab.it>
-# Yuri Chiucconi <yuri.chiucconi@exact-lab.it>
-#
-# This file is part of Fractal and was originally developed by eXact lab S.r.l.
-# <exact-lab.it> under contract with Liberali Lab from the Friedrich Miescher
-# Institute for Biomedical Research and Pelkmans Lab from the University of
-# Zurich.
-from copy import deepcopy
-from typing import Optional
-
-from fastapi import APIRouter
-from fastapi import Depends
-from fastapi import HTTPException
-from fastapi import Response
-from fastapi import status
-
-from ....db import AsyncSession
-from ....db import get_async_db
-from ....models.v1 import Task
-from ....schemas.v1 import WorkflowTaskCreateV1
-from ....schemas.v1 import WorkflowTaskReadV1
-from ....schemas.v1 import WorkflowTaskUpdateV1
-from ._aux_functions import _get_workflow_check_owner
-from ._aux_functions import _get_workflow_task_check_owner
-from ._aux_functions import _raise_if_v1_is_read_only
-from ._aux_functions import _workflow_insert_task
-from fractal_server.app.models import UserOAuth
-from fractal_server.app.routes.auth import current_active_user
-
-router = APIRouter()
-
-
-@router.post(
-    "/project/{project_id}/workflow/{workflow_id}/wftask/",
-    response_model=WorkflowTaskReadV1,
-    status_code=status.HTTP_201_CREATED,
-)
-async def create_workflowtask(
-    project_id: int,
-    workflow_id: int,
-    task_id: int,
-    new_task: WorkflowTaskCreateV1,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowTaskReadV1]:
-    """
-    Add a WorkflowTask to a Workflow
-    """
-    _raise_if_v1_is_read_only()
-    workflow = await _get_workflow_check_owner(
-        project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
-    )
-
-    # Check that task exists
-    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.",
-        )
-
-    async with db:
-        workflow_task = await _workflow_insert_task(
-            **new_task.dict(),
-            workflow_id=workflow.id,
-            task_id=task_id,
-            db=db,
-        )
-
-    await db.close()
-    return workflow_task
-
-
-@router.get(
-    "/project/{project_id}/workflow/{workflow_id}/wftask/{workflow_task_id}/",
-    response_model=WorkflowTaskReadV1,
-)
-async def read_workflowtask(
-    project_id: int,
-    workflow_id: int,
-    workflow_task_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-):
-    workflow_task, _ = await _get_workflow_task_check_owner(
-        project_id=project_id,
-        workflow_task_id=workflow_task_id,
-        workflow_id=workflow_id,
-        user_id=user.id,
-        db=db,
-    )
-    return workflow_task
-
-
-@router.patch(
-    "/project/{project_id}/workflow/{workflow_id}/wftask/{workflow_task_id}/",
-    response_model=WorkflowTaskReadV1,
-)
-async def update_workflowtask(
-    project_id: int,
-    workflow_id: int,
-    workflow_task_id: int,
-    workflow_task_update: WorkflowTaskUpdateV1,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowTaskReadV1]:
-    """
-    Edit a WorkflowTask of a Workflow
-    """
-    _raise_if_v1_is_read_only()
-    db_workflow_task, db_workflow = await _get_workflow_task_check_owner(
-        project_id=project_id,
-        workflow_task_id=workflow_task_id,
-        workflow_id=workflow_id,
-        user_id=user.id,
-        db=db,
-    )
-
-    for key, value in workflow_task_update.dict(exclude_unset=True).items():
-        if key == "args":
-
-            # Get default arguments via a Task property method
-            default_args = deepcopy(
-                db_workflow_task.task.default_args_from_args_schema
-            )
-            # Override default_args with args value items
-            actual_args = default_args.copy()
-            if value is not None:
-                for k, v in value.items():
-                    actual_args[k] = v
-            if not actual_args:
-                actual_args = None
-            setattr(db_workflow_task, key, actual_args)
-        elif key == "meta":
-            current_meta = deepcopy(db_workflow_task.meta) or {}
-            current_meta.update(value)
-            setattr(db_workflow_task, key, current_meta)
-        else:
-            raise HTTPException(
-                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail=f"patch_workflow_task endpoint cannot set {key=}",
-            )
-
-    await db.commit()
-    await db.refresh(db_workflow_task)
-    await db.close()
-
-    return db_workflow_task
-
-
-@router.delete(
-    "/project/{project_id}/workflow/{workflow_id}/wftask/{workflow_task_id}/",
-    status_code=status.HTTP_204_NO_CONTENT,
-)
-async def delete_workflowtask(
-    project_id: int,
-    workflow_id: int,
-    workflow_task_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Response:
-    """
-    Delete a WorkflowTask of a Workflow
-    """
-    _raise_if_v1_is_read_only()
-    db_workflow_task, db_workflow = await _get_workflow_task_check_owner(
-        project_id=project_id,
-        workflow_task_id=workflow_task_id,
-        workflow_id=workflow_id,
-        user_id=user.id,
-        db=db,
-    )
-
-    await db.delete(db_workflow_task)
-    await db.commit()
-
-    await db.refresh(db_workflow)
-    db_workflow.task_list.reorder()
-    await db.commit()
-
-    return Response(status_code=status.HTTP_204_NO_CONTENT)

fractal_server/app/runner/async_wrap_v1.py

@@ -1,27 +0,0 @@
-import asyncio
-from functools import partial
-from functools import wraps
-from typing import Callable
-
-
-def async_wrap_v1(func: Callable) -> Callable:
-    """
-    Wrap a synchronous callable in an async task
-
-    Ref: [issue #140](https://github.com/fractal-analytics-platform/fractal-server/issues/140)
-    and [this StackOverflow answer](https://stackoverflow.com/q/43241221/19085332).
-
-    Returns:
-        async_wrapper:
-            A factory that allows wrapping a blocking callable within a
-            coroutine.
-    """  # noqa: E501
-
-    @wraps(func)
-    async def async_wrapper(*args, loop=None, executor=None, **kwargs):
-        if loop is None:
-            loop = asyncio.get_event_loop()
-        pfunc = partial(func, *args, **kwargs)
-        return await loop.run_in_executor(executor, pfunc)
-
-    return async_wrapper