fractal-server 2.11.1__py3-none-any.whl → 2.12.0a1__py3-none-any.whl

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

@@ -1,195 +0,0 @@
-from pathlib import Path
-from typing import Optional
-
-from fastapi import APIRouter
-from fastapi import Depends
-from fastapi import Response
-from fastapi import status
-from fastapi.responses import StreamingResponse
-from sqlmodel import select
-
-from .....zip_tools import _zip_folder_to_byte_stream_iterator
-from ....db import AsyncSession
-from ....db import get_async_db
-from ....models.v1 import ApplyWorkflow
-from ....models.v1 import JobStatusTypeV1
-from ....models.v1 import Project
-from ....runner.filenames import WORKFLOW_LOG_FILENAME
-from ....schemas.v1 import ApplyWorkflowReadV1
-from ...aux._job import _write_shutdown_file
-from ...aux._runner import _check_shutdown_is_supported
-from ._aux_functions import _get_job_check_owner
-from ._aux_functions import _get_project_check_owner
-from ._aux_functions import _get_workflow_check_owner
-from fractal_server.app.models import UserOAuth
-from fractal_server.app.routes.auth import current_active_user
-
-router = APIRouter()
-
-
-@router.get("/job/", response_model=list[ApplyWorkflowReadV1])
-async def get_user_jobs(
-    user: UserOAuth = Depends(current_active_user),
-    log: bool = True,
-    db: AsyncSession = Depends(get_async_db),
-) -> list[ApplyWorkflowReadV1]:
-    """
-    Returns all the jobs of the current user
-    """
-    stm = select(ApplyWorkflow)
-    stm = stm.join(Project).where(
-        Project.user_list.any(UserOAuth.id == user.id)
-    )
-    res = await db.execute(stm)
-    job_list = res.scalars().all()
-    await db.close()
-    if not log:
-        for job in job_list:
-            setattr(job, "log", None)
-
-    return job_list
-
-
-@router.get(
-    "/project/{project_id}/workflow/{workflow_id}/job/",
-    response_model=list[ApplyWorkflowReadV1],
-)
-async def get_workflow_jobs(
-    project_id: int,
-    workflow_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[list[ApplyWorkflowReadV1]]:
-    """
-    Returns all the jobs related to a specific workflow
-    """
-    await _get_workflow_check_owner(
-        project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
-    )
-    stm = select(ApplyWorkflow).where(ApplyWorkflow.workflow_id == workflow_id)
-    res = await db.execute(stm)
-    job_list = res.scalars().all()
-    return job_list
-
-
-@router.get(
-    "/project/{project_id}/job/{job_id}/",
-    response_model=ApplyWorkflowReadV1,
-)
-async def read_job(
-    project_id: int,
-    job_id: int,
-    show_tmp_logs: bool = False,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[ApplyWorkflowReadV1]:
-    """
-    Return info on an existing job
-    """
-
-    output = await _get_job_check_owner(
-        project_id=project_id,
-        job_id=job_id,
-        user_id=user.id,
-        db=db,
-    )
-    job = output["job"]
-    await db.close()
-
-    if show_tmp_logs and (job.status == JobStatusTypeV1.SUBMITTED):
-        try:
-            with open(f"{job.working_dir}/{WORKFLOW_LOG_FILENAME}", "r") as f:
-                job.log = f.read()
-        except FileNotFoundError:
-            pass
-
-    return job
-
-
-@router.get(
-    "/project/{project_id}/job/{job_id}/download/",
-    response_class=StreamingResponse,
-)
-async def download_job_logs(
-    project_id: int,
-    job_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> StreamingResponse:
-    """
-    Download job folder
-    """
-    output = await _get_job_check_owner(
-        project_id=project_id,
-        job_id=job_id,
-        user_id=user.id,
-        db=db,
-    )
-    job = output["job"]
-
-    # Create and return byte stream for zipped log folder
-    PREFIX_ZIP = Path(job.working_dir).name
-    zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    return StreamingResponse(
-        _zip_folder_to_byte_stream_iterator(folder=job.working_dir),
-        media_type="application/x-zip-compressed",
-        headers={"Content-Disposition": f"attachment;filename={zip_filename}"},
-    )
-
-
-@router.get(
-    "/project/{project_id}/job/",
-    response_model=list[ApplyWorkflowReadV1],
-)
-async def get_job_list(
-    project_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    log: bool = True,
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[list[ApplyWorkflowReadV1]]:
-    """
-    Get job list for given project
-    """
-    project = await _get_project_check_owner(
-        project_id=project_id, user_id=user.id, db=db
-    )
-
-    stm = select(ApplyWorkflow).where(ApplyWorkflow.project_id == project.id)
-    res = await db.execute(stm)
-    job_list = res.scalars().all()
-    await db.close()
-    if not log:
-        for job in job_list:
-            setattr(job, "log", None)
-
-    return job_list
-
-
-@router.get(
-    "/project/{project_id}/job/{job_id}/stop/",
-    status_code=202,
-)
-async def stop_job(
-    project_id: int,
-    job_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Response:
-    """
-    Stop execution of a workflow job.
-    """
-
-    _check_shutdown_is_supported()
-
-    # Get job from DB
-    output = await _get_job_check_owner(
-        project_id=project_id,
-        job_id=job_id,
-        user_id=user.id,
-        db=db,
-    )
-    job = output["job"]
-
-    _write_shutdown_file(job=job)
-
-    return Response(status_code=status.HTTP_202_ACCEPTED)

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

@@ -1,475 +0,0 @@
-import json
-import os
-from datetime import timedelta
-from datetime import timezone
-from typing import Optional
-
-from fastapi import APIRouter
-from fastapi import BackgroundTasks
-from fastapi import Depends
-from fastapi import HTTPException
-from fastapi import Request
-from fastapi import Response
-from fastapi import status
-from sqlmodel import select
-
-from .....config import get_settings
-from .....logger import set_logger
-from .....syringe import Inject
-from ....db import AsyncSession
-from ....db import get_async_db
-from ....models.v1 import ApplyWorkflow
-from ....models.v1 import Dataset
-from ....models.v1 import LinkUserProject
-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,
-)
-from ....runner.v1 import submit_workflow
-from ....runner.v1 import validate_workflow_compatibility
-from ....schemas.v1 import ApplyWorkflowCreateV1
-from ....schemas.v1 import ApplyWorkflowReadV1
-from ....schemas.v1 import JobStatusTypeV1
-from ....schemas.v1 import ProjectCreateV1
-from ....schemas.v1 import ProjectReadV1
-from ....schemas.v1 import ProjectUpdateV1
-from ...aux.validate_user_settings import validate_user_settings
-from ._aux_functions import _check_project_exists
-from ._aux_functions import _get_dataset_check_owner
-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 clean_app_job_list_v1
-from fractal_server.app.models import UserOAuth
-from fractal_server.app.routes.auth import current_active_user
-from fractal_server.app.routes.auth import current_active_verified_user
-
-router = APIRouter()
-logger = set_logger(__name__)
-
-
-@router.get("/", response_model=list[ProjectReadV1])
-async def get_list_project(
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> list[Project]:
-    """
-    Return list of projects user is member of
-    """
-    stm = (
-        select(Project)
-        .join(LinkUserProject)
-        .where(LinkUserProject.user_id == user.id)
-    )
-    res = await db.execute(stm)
-    project_list = res.scalars().all()
-    await db.close()
-    return project_list
-
-
-@router.post("/", response_model=ProjectReadV1, status_code=201)
-async def create_project(
-    project: ProjectCreateV1,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[ProjectReadV1]:
-    """
-    Create new poject
-    """
-    _raise_if_v1_is_read_only()
-    # Check that there is no project with the same user and name
-    await _check_project_exists(
-        project_name=project.name, user_id=user.id, db=db
-    )
-
-    db_project = Project(**project.dict())
-    db_project.user_list.append(user)
-
-    db.add(db_project)
-    await db.commit()
-    await db.refresh(db_project)
-    await db.close()
-
-    return db_project
-
-
-@router.get("/{project_id}/", response_model=ProjectReadV1)
-async def read_project(
-    project_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[ProjectReadV1]:
-    """
-    Return info on an existing project
-    """
-    project = await _get_project_check_owner(
-        project_id=project_id, user_id=user.id, db=db
-    )
-    await db.close()
-    return project
-
-
-@router.patch("/{project_id}/", response_model=ProjectReadV1)
-async def update_project(
-    project_id: int,
-    project_update: ProjectUpdateV1,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-):
-    _raise_if_v1_is_read_only()
-    project = await _get_project_check_owner(
-        project_id=project_id, user_id=user.id, db=db
-    )
-
-    # Check that there is no project with the same user and name
-    if project_update.name is not None:
-        await _check_project_exists(
-            project_name=project_update.name, user_id=user.id, db=db
-        )
-
-    for key, value in project_update.dict(exclude_unset=True).items():
-        setattr(project, key, value)
-
-    await db.commit()
-    await db.refresh(project)
-    await db.close()
-    return project
-
-
-@router.delete("/{project_id}/", status_code=204)
-async def delete_project(
-    project_id: int,
-    user: UserOAuth = Depends(current_active_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Response:
-    """
-    Delete project
-    """
-    _raise_if_v1_is_read_only()
-    project = await _get_project_check_owner(
-        project_id=project_id, user_id=user.id, db=db
-    )
-
-    # Fail if there exist jobs that are submitted and in relation with the
-    # current project.
-    stm = _get_submitted_jobs_statement().where(
-        ApplyWorkflow.project_id == project_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 project {project.id} because it "
-                f"is linked to active job(s) {string_ids}."
-            ),
-        )
-
-    # Cascade operations
-
-    # Workflows
-    stm = select(Workflow).where(Workflow.project_id == project_id)
-    res = await db.execute(stm)
-    workflows = res.scalars().all()
-    for wf in workflows:
-        # Cascade operations: set foreign-keys to null for jobs which are in
-        # relationship with the current workflow
-        stm = select(ApplyWorkflow).where(ApplyWorkflow.workflow_id == wf.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(wf)
-
-    # Dataset
-    stm = select(Dataset).where(Dataset.project_id == project_id)
-    res = await db.execute(stm)
-    datasets = res.scalars().all()
-    for ds in datasets:
-        # Cascade operations: set foreign-keys to null for jobs which are in
-        # relationship with the current dataset
-        # input_dataset
-        stm = select(ApplyWorkflow).where(
-            ApplyWorkflow.input_dataset_id == ds.id
-        )
-        res = await db.execute(stm)
-        jobs = res.scalars().all()
-        for job in jobs:
-            job.input_dataset_id = None
-            await db.merge(job)
-        await db.commit()
-        # output_dataset
-        stm = select(ApplyWorkflow).where(
-            ApplyWorkflow.output_dataset_id == ds.id
-        )
-        res = await db.execute(stm)
-        jobs = res.scalars().all()
-        for job in jobs:
-            job.output_dataset_id = None
-            await db.merge(job)
-        await db.commit()
-        await db.delete(ds)
-
-    # Job
-    stm = select(ApplyWorkflow).where(ApplyWorkflow.project_id == project_id)
-    res = await db.execute(stm)
-    jobs = res.scalars().all()
-    for job in jobs:
-        job.project_id = None
-        await db.merge(job)
-
-    await db.commit()
-
-    await db.delete(project)
-    await db.commit()
-
-    return Response(status_code=status.HTTP_204_NO_CONTENT)
-
-
-@router.post(
-    "/{project_id}/workflow/{workflow_id}/apply/",
-    status_code=status.HTTP_202_ACCEPTED,
-    response_model=ApplyWorkflowReadV1,
-)
-async def apply_workflow(
-    project_id: int,
-    workflow_id: int,
-    apply_workflow: ApplyWorkflowCreateV1,
-    background_tasks: BackgroundTasks,
-    input_dataset_id: int,
-    output_dataset_id: int,
-    request: Request,
-    user: UserOAuth = Depends(current_active_verified_user),
-    db: AsyncSession = Depends(get_async_db),
-) -> Optional[ApplyWorkflowReadV1]:
-    _raise_if_v1_is_read_only()
-    settings = Inject(get_settings)
-
-    # Remove non-submitted V1 jobs from the app state when the list grows
-    # beyond a threshold
-    if (
-        len(request.app.state.jobsV1)
-        > settings.FRACTAL_API_MAX_JOB_LIST_LENGTH
-    ):
-        new_jobs_list = await clean_app_job_list_v1(
-            db, request.app.state.jobsV1
-        )
-        request.app.state.jobsV1 = new_jobs_list
-
-    output = await _get_dataset_check_owner(
-        project_id=project_id,
-        dataset_id=input_dataset_id,
-        user_id=user.id,
-        db=db,
-    )
-    project = output["project"]
-    input_dataset = output["dataset"]
-
-    output = await _get_dataset_check_owner(
-        project_id=project_id,
-        dataset_id=output_dataset_id,
-        user_id=user.id,
-        db=db,
-    )
-    output_dataset = output["dataset"]
-    if output_dataset.read_only:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                "Cannot apply workflow because output dataset "
-                f"({output_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
-    )
-
-    if not workflow.task_list:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=f"Workflow {workflow_id} has empty task list",
-        )
-
-    # Set values of first_task_index and last_task_index
-    num_tasks = len(workflow.task_list)
-    try:
-        first_task_index, last_task_index = set_start_and_last_task_index(
-            num_tasks,
-            first_task_index=apply_workflow.first_task_index,
-            last_task_index=apply_workflow.last_task_index,
-        )
-        apply_workflow.first_task_index = first_task_index
-        apply_workflow.last_task_index = last_task_index
-    except ValueError as e:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                "Invalid values for first_task_index or last_task_index "
-                f"(with {num_tasks=}).\n"
-                f"Original error: {str(e)}"
-            ),
-        )
-
-    # Validate user settings
-    FRACTAL_RUNNER_BACKEND = settings.FRACTAL_RUNNER_BACKEND
-    user_settings = await validate_user_settings(
-        user=user, backend=FRACTAL_RUNNER_BACKEND, db=db
-    )
-
-    # Check that datasets have the right number of resources
-    if not input_dataset.resource_list:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail="Input dataset has empty resource_list",
-        )
-    if len(output_dataset.resource_list) != 1:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                "Output dataset must have a single resource, "
-                f"but it has {len(output_dataset.resource_list)}"
-            ),
-        )
-
-    try:
-        validate_workflow_compatibility(
-            workflow=workflow,
-            input_dataset=input_dataset,
-            output_dataset=output_dataset,
-            first_task_index=apply_workflow.first_task_index,
-            last_task_index=apply_workflow.last_task_index,
-        )
-    except TypeError as e:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=str(e)
-        )
-
-    # Check that no other job with the same output_dataset_id is SUBMITTED
-    stm = (
-        select(ApplyWorkflow)
-        .where(ApplyWorkflow.output_dataset_id == output_dataset_id)
-        .where(ApplyWorkflow.status == JobStatusTypeV1.SUBMITTED)
-    )
-    res = await db.execute(stm)
-    if res.scalars().all():
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                f"Output dataset {output_dataset_id} is already in use "
-                "in submitted job(s)."
-            ),
-        )
-
-    if apply_workflow.slurm_account is not None:
-        if apply_workflow.slurm_account not in user_settings.slurm_accounts:
-            raise HTTPException(
-                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                detail=(
-                    f"SLURM account '{apply_workflow.slurm_account}' is not "
-                    "among those available to the current user"
-                ),
-            )
-    else:
-        if len(user_settings.slurm_accounts) > 0:
-            apply_workflow.slurm_account = user_settings.slurm_accounts[0]
-
-    # Add new ApplyWorkflow object to DB
-    job = ApplyWorkflow(
-        project_id=project_id,
-        input_dataset_id=input_dataset_id,
-        output_dataset_id=output_dataset_id,
-        workflow_id=workflow_id,
-        user_email=user.email,
-        input_dataset_dump=dict(
-            **json.loads(
-                input_dataset.json(exclude={"resource_list", "history"})
-            ),
-            resource_list=[
-                resource.model_dump()
-                for resource in input_dataset.resource_list
-            ],
-        ),
-        output_dataset_dump=dict(
-            **json.loads(
-                output_dataset.json(exclude={"resource_list", "history"})
-            ),
-            resource_list=[
-                resource.model_dump()
-                for resource in output_dataset.resource_list
-            ],
-        ),
-        workflow_dump=json.loads(workflow.json(exclude={"task_list"})),
-        project_dump=json.loads(project.json(exclude={"user_list"})),
-        **apply_workflow.dict(),
-    )
-
-    # Rate Limiting:
-    # raise `429 TOO MANY REQUESTS` if this endpoint has been called with the
-    # same database keys (Project, Workflow and Datasets) during the last
-    # `settings.FRACTAL_API_SUBMIT_RATE_LIMIT` seconds.
-    stm = (
-        select(ApplyWorkflow)
-        .where(ApplyWorkflow.project_id == project_id)
-        .where(ApplyWorkflow.workflow_id == workflow_id)
-        .where(ApplyWorkflow.input_dataset_id == input_dataset_id)
-        .where(ApplyWorkflow.output_dataset_id == output_dataset_id)
-    )
-    res = await db.execute(stm)
-    db_jobs = res.scalars().all()
-    if db_jobs and any(
-        abs(
-            job.start_timestamp
-            - db_job.start_timestamp.replace(tzinfo=timezone.utc)
-        )
-        < timedelta(seconds=settings.FRACTAL_API_SUBMIT_RATE_LIMIT)
-        for db_job in db_jobs
-    ):
-        raise HTTPException(
-            status_code=status.HTTP_429_TOO_MANY_REQUESTS,
-            detail=(
-                f"The endpoint 'POST /api/v1/project/{project_id}/workflow/"
-                f"{workflow_id}/apply/' "
-                "was called several times within an interval of less "
-                f"than {settings.FRACTAL_API_SUBMIT_RATE_LIMIT} seconds, using"
-                " the same foreign keys. If it was intentional, please wait "
-                "and try again."
-            ),
-        )
-
-    db.add(job)
-    await db.commit()
-    await db.refresh(job)
-
-    cache_dir = (
-        f"{user_settings.project_dir}/.fractal_cache"
-        if user_settings.project_dir is not None
-        else None
-    )
-
-    background_tasks.add_task(
-        submit_workflow,
-        workflow_id=workflow.id,
-        input_dataset_id=input_dataset.id,
-        output_dataset_id=output_dataset.id,
-        job_id=job.id,
-        worker_init=apply_workflow.worker_init,
-        slurm_user=user_settings.slurm_user,
-        user_cache_dir=cache_dir,
-    )
-    request.app.state.jobsV1.append(job.id)
-    logger.info(
-        f"Current worker's pid is {os.getpid()}. "
-        f"Current status of worker job's list "
-        f"{request.app.state.jobsV1}"
-    )
-    await db.close()
-
-    return job