fractal-server 2.0.0a9__py3-none-any.whl → 2.0.0a10__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -1 +1 @@
1
- __VERSION__ = "2.0.0a9"
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+ __VERSION__ = "2.0.0a10"
@@ -7,6 +7,7 @@ from .dataset import router as dataset_router_v2
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  from .images import router as images_routes_v2
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  from .job import router as job_router_v2
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  from .project import router as project_router_v2
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+ from .status import router as status_router_v2
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  from .submit import router as submit_job_router_v2
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  from .task import router as task_router_v2
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  from .task_collection import router as task_collection_router_v2
@@ -30,3 +31,4 @@ router_api_v2.include_router(
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  )
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  router_api_v2.include_router(workflow_router_v2, tags=["V2 Workflow"])
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  router_api_v2.include_router(workflowtask_router_v2, tags=["V2 WorkflowTask"])
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+ router_api_v2.include_router(status_router_v2, tags=["V2 Status"])
@@ -1,5 +1,3 @@
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- import json
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- from pathlib import Path
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1
  from typing import Optional
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2
 
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3
  from fastapi import APIRouter
@@ -19,15 +17,11 @@ from ....schemas.v2 import DatasetReadV2
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  from ....schemas.v2 import DatasetUpdateV2
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  from ....schemas.v2.dataset import DatasetExportV2
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  from ....schemas.v2.dataset import DatasetImportV2
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- from ....schemas.v2.dataset import DatasetStatusReadV2
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- from ....schemas.v2.dataset import WorkflowTaskStatusTypeV2
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  from ....security import current_active_user
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  from ....security import User
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  from ._aux_functions import _get_dataset_check_owner
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  from ._aux_functions import _get_project_check_owner
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  from ._aux_functions import _get_submitted_jobs_statement
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- from ._aux_functions import _get_workflow_check_owner
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- from fractal_server.app.runner.filenames import HISTORY_FILENAME
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25
 
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  router = APIRouter()
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27
 
@@ -228,100 +222,6 @@ async def get_user_datasets(
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  return dataset_list
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223
 
230
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231
- @router.get(
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- "/project/{project_id}/dataset/{dataset_id}/status/",
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- response_model=DatasetStatusReadV2,
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- )
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- async def get_workflowtask_status(
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- project_id: int,
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- dataset_id: int,
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- user: User = Depends(current_active_user),
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- db: AsyncSession = Depends(get_async_db),
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- ) -> Optional[DatasetStatusReadV2]:
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- """
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- Extract the status of all `WorkflowTask`s that ran on a given `DatasetV2`.
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- """
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- # Get the dataset DB entry
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- output = await _get_dataset_check_owner(
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- project_id=project_id,
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- dataset_id=dataset_id,
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- user_id=user.id,
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- db=db,
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- )
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- dataset = output["dataset"]
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-
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- # Check whether there exists a job such that
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- # 1. `job.dataset_id == dataset_id`, and
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- # 2. `job.status` is submitted
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- # If one such job exists, it will be used later. If there are multiple
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- # jobs, raise an error.
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- stm = _get_submitted_jobs_statement().where(JobV2.dataset_id == dataset_id)
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- res = await db.execute(stm)
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- running_jobs = res.scalars().all()
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- if len(running_jobs) == 0:
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- running_job = None
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- elif len(running_jobs) == 1:
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- running_job = running_jobs[0]
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- else:
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- string_ids = str([job.id for job in running_jobs])[1:-1]
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- raise HTTPException(
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- status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
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- detail=(
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- f"Cannot get WorkflowTaskV2 statuses as DatasetV2 {dataset.id}"
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- f" is linked to multiple active jobs: {string_ids}."
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- ),
273
- )
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-
275
- # Initialize empty dictionary for WorkflowTaskV2 status
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- workflow_tasks_status_dict: dict = {}
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-
278
- # Lowest priority: read status from DB, which corresponds to jobs that are
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- # not running
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- history = dataset.history
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- for history_item in history:
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- wftask_id = history_item["workflowtask"]["id"]
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- wftask_status = history_item["status"]
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- workflow_tasks_status_dict[wftask_id] = wftask_status
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-
286
- # If a job is running, then gather more up-to-date information
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- if running_job is not None:
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- # Get the workflow DB entry
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- running_workflow = await _get_workflow_check_owner(
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- project_id=project_id,
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- workflow_id=running_job.workflow_id,
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- user_id=user.id,
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- db=db,
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- )
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- # Mid priority: Set all WorkflowTask's that are part of the running job
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- # as "submitted"
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- start = running_job.first_task_index
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- end = running_job.last_task_index + 1
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- for wftask in running_workflow.task_list[start:end]:
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- workflow_tasks_status_dict[
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- wftask.id
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- ] = WorkflowTaskStatusTypeV2.SUBMITTED
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-
304
- # Highest priority: Read status updates coming from the running-job
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- # temporary file. Note: this file only contains information on
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- # # WorkflowTask's that ran through successfully.
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- tmp_file = Path(running_job.working_dir) / HISTORY_FILENAME
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- try:
309
- with tmp_file.open("r") as f:
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- history = json.load(f)
311
- except FileNotFoundError:
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- history = []
313
- for history_item in history:
314
- wftask_id = history_item["workflowtask"]["id"]
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- wftask_status = history_item["status"]
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- workflow_tasks_status_dict[wftask_id] = wftask_status
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-
318
- response_body = DatasetStatusReadV2(status=workflow_tasks_status_dict)
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- return response_body
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-
321
-
322
- # /api/v2/project/{project_id}/dataset/{dataset_id}/export/
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-
324
-
325
225
  @router.get(
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  "/project/{project_id}/dataset/{dataset_id}/export/",
327
227
  response_model=DatasetExportV2,
@@ -0,0 +1,150 @@
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+ import json
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+ from pathlib import Path
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+ from typing import Optional
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+
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+ from fastapi import APIRouter
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+ from fastapi import Depends
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+ from fastapi import HTTPException
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+ from fastapi import status
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+
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+ from ....db import AsyncSession
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+ from ....db import get_async_db
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+ from ....models.v2 import JobV2
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+ from ....schemas.v2.dataset import WorkflowTaskStatusTypeV2
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+ from ....schemas.v2.status import StatusReadV2
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+ from ....security import current_active_user
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+ from ....security import User
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+ from ._aux_functions import _get_dataset_check_owner
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+ from ._aux_functions import _get_submitted_jobs_statement
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+ from ._aux_functions import _get_workflow_check_owner
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+ from fractal_server.app.runner.filenames import HISTORY_FILENAME
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+
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+ router = APIRouter()
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+
24
+
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+ @router.get(
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+ "/project/{project_id}/status/",
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+ response_model=StatusReadV2,
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+ )
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+ async def get_workflowtask_status(
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+ project_id: int,
31
+ dataset_id: int,
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+ workflow_id: int,
33
+ user: User = Depends(current_active_user),
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+ db: AsyncSession = Depends(get_async_db),
35
+ ) -> Optional[StatusReadV2]:
36
+ """
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+ Extract the status of all `WorkflowTaskV2` of a given `WorkflowV2` that ran
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+ on a given `DatasetV2`.
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+
40
+ *NOTE*: the current endpoint is not guaranteed to provide consistent
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+ results if the workflow task list is modified in a non-trivial way
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+ (that is, by adding intermediate tasks, removing tasks, or changing their
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+ order). See fractal-server GitHub issues: 793, 1083.
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+ """
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+ # Get the dataset DB entry
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+ output = await _get_dataset_check_owner(
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+ project_id=project_id,
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+ dataset_id=dataset_id,
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+ user_id=user.id,
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+ db=db,
51
+ )
52
+ dataset = output["dataset"]
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+
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+ # Get the workflow DB entry
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+ workflow = await _get_workflow_check_owner(
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+ project_id=project_id,
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+ workflow_id=workflow_id,
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+ user_id=user.id,
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+ db=db,
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+ )
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+
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+ # Check whether there exists a submitted job associated to this
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+ # workflow/dataset pair. If it does exist, it will be used later.
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+ # If there are multiple jobs, raise an error.
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+ stm = _get_submitted_jobs_statement()
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+ stm = stm.where(JobV2.dataset_id == dataset_id)
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+ stm = stm.where(JobV2.workflow_id == workflow_id)
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+ res = await db.execute(stm)
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+ running_jobs = res.scalars().all()
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+ if len(running_jobs) == 0:
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+ running_job = None
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+ elif len(running_jobs) == 1:
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+ running_job = running_jobs[0]
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+ else:
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+ string_ids = str([job.id for job in running_jobs])[1:-1]
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+ raise HTTPException(
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+ status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
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+ detail=(
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+ f"Cannot get WorkflowTaskV2 statuses as DatasetV2 {dataset.id}"
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+ f" is linked to multiple active jobs: {string_ids}."
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+ ),
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+ )
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+
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+ # Initialize empty dictionary for WorkflowTaskV2 status
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+ workflow_tasks_status_dict: dict = {}
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+
87
+ # Lowest priority: read status from DB, which corresponds to jobs that are
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+ # not running
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+ history = dataset.history
90
+ for history_item in history:
91
+ wftask_id = history_item["workflowtask"]["id"]
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+ wftask_status = history_item["status"]
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+ workflow_tasks_status_dict[wftask_id] = wftask_status
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+
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+ if running_job is None:
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+ # If no job is running, the chronological-last history item is also the
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+ # positional-last workflow task to be included in the response.
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+ if len(dataset.history) > 0:
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+ last_valid_wftask_id = dataset.history[-1]["workflowtask"]["id"]
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+ else:
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+ last_valid_wftask_id = None
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+ else:
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+ # If a job is running, then gather more up-to-date information
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+
105
+ # Mid priority: Set all WorkflowTask's that are part of the running job
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+ # as "submitted"
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+ start = running_job.first_task_index
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+ end = running_job.last_task_index + 1
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+ for wftask in workflow.task_list[start:end]:
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+ workflow_tasks_status_dict[
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+ wftask.id
112
+ ] = WorkflowTaskStatusTypeV2.SUBMITTED
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+
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+ # The last workflow task that is included in the submitted job is also
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+ # the positional-last workflow task to be included in the response.
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+ last_valid_wftask_id = workflow.task_list[end - 1]
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+
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+ # Highest priority: Read status updates coming from the running-job
119
+ # temporary file. Note: this file only contains information on
120
+ # WorkflowTask's that ran through successfully.
121
+ tmp_file = Path(running_job.working_dir) / HISTORY_FILENAME
122
+ try:
123
+ with tmp_file.open("r") as f:
124
+ history = json.load(f)
125
+ except FileNotFoundError:
126
+ history = []
127
+ for history_item in history:
128
+ wftask_id = history_item["workflowtask"]["id"]
129
+ wftask_status = history_item["status"]
130
+ workflow_tasks_status_dict[wftask_id] = wftask_status
131
+
132
+ # Based on previously-gathered information, clean up the response body
133
+ clean_workflow_tasks_status_dict = {}
134
+ for wf_task in workflow.task_list:
135
+ wf_task_status = workflow_tasks_status_dict.get(wf_task.id)
136
+ if wf_task_status is None:
137
+ # If a wftask ID was not found, ignore it and continue
138
+ continue
139
+ clean_workflow_tasks_status_dict[wf_task.id] = wf_task_status
140
+ if wf_task_status == WorkflowTaskStatusTypeV2.FAILED:
141
+ # Starting from the beginning of `workflow.task_list`, stop the
142
+ # first time that you hit a failed job
143
+ break
144
+ if wf_task.id == last_valid_wftask_id:
145
+ # Starting from the beginning of `workflow.task_list`, stop the
146
+ # first time that you hit `last_valid_wftask_id``
147
+ break
148
+
149
+ response_body = StatusReadV2(status=clean_workflow_tasks_status_dict)
150
+ return response_body
@@ -146,6 +146,9 @@ def run_v2_task_parallel(
146
146
  submit_setup_call: Callable = no_op_submit_setup_call,
147
147
  ) -> TaskOutput:
148
148
 
149
+ if len(images) == 0:
150
+ return TaskOutput()
151
+
149
152
  _check_parallelization_list_size(images)
150
153
 
151
154
  executor_options = _get_executor_options(
@@ -249,6 +252,9 @@ def run_v2_task_compound(
249
252
  # 3/B: parallel part of a compound task
250
253
  _check_parallelization_list_size(parallelization_list)
251
254
 
255
+ if len(parallelization_list) == 0:
256
+ return TaskOutput()
257
+
252
258
  list_function_kwargs = []
253
259
  for ind, parallelization_item in enumerate(parallelization_list):
254
260
  list_function_kwargs.append(
@@ -26,20 +26,6 @@ class _DatasetHistoryItemV2(BaseModel):
26
26
  parallelization: Optional[dict]
27
27
 
28
28
 
29
- class DatasetStatusReadV2(BaseModel):
30
- """
31
- Response type for the
32
- `/project/{project_id}/dataset/{dataset_id}/status/` endpoint
33
- """
34
-
35
- status: Optional[
36
- dict[
37
- str,
38
- WorkflowTaskStatusTypeV2,
39
- ]
40
- ] = None
41
-
42
-
43
29
  # CRUD
44
30
 
45
31
 
@@ -0,0 +1,16 @@
1
+ from pydantic import BaseModel
2
+ from pydantic import Field
3
+
4
+ from .workflowtask import WorkflowTaskStatusTypeV2
5
+
6
+
7
+ class StatusReadV2(BaseModel):
8
+ """
9
+ Response type for the
10
+ `/project/{project_id}/status/` endpoint
11
+ """
12
+
13
+ status: dict[
14
+ str,
15
+ WorkflowTaskStatusTypeV2,
16
+ ] = Field(default_factory=dict)
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: fractal-server
3
- Version: 2.0.0a9
3
+ Version: 2.0.0a10
4
4
  Summary: Server component of the Fractal analytics platform
5
5
  Home-page: https://github.com/fractal-analytics-platform/fractal-server
6
6
  License: BSD-3-Clause
@@ -1,4 +1,4 @@
1
- fractal_server/__init__.py,sha256=igx3UAg7e-LuCe083CY3r_FQooF1tJV_FTJy9JRvzEo,24
1
+ fractal_server/__init__.py,sha256=Ndyws1HQt0rbkLhMYPxRDuKeooalmEoA6oesT2NmbbU,25
2
2
  fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
3
3
  fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
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  fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -34,12 +34,13 @@ fractal_server/app/routes/api/v1/task.py,sha256=4zUXMtq5M95XjaZs1t9oibYHiDIwxpM-
34
34
  fractal_server/app/routes/api/v1/task_collection.py,sha256=_cY3pPRGchdWPuJ1XudMZMVJ0IC0_XVH0XwLTiAbRGg,8873
35
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  fractal_server/app/routes/api/v1/workflow.py,sha256=ZObifWTPi100oRQ1wEER8Sgsr3Neo8QVdCCFQnWMNZ0,10930
36
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  fractal_server/app/routes/api/v1/workflowtask.py,sha256=ox-DIIqYV4K35hCu86eGa2SHnR5IQml-I00UHEwnmHQ,5579
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- fractal_server/app/routes/api/v2/__init__.py,sha256=x56HcY1uBNCgq4BRVj-0j6bAj6OsTN97RNDqY8NefJ8,1373
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+ fractal_server/app/routes/api/v2/__init__.py,sha256=UNgODxoEXfQpQDjvsnMvHaUWbZOrcHhEXNisLcU-0tE,1487
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  fractal_server/app/routes/api/v2/_aux_functions.py,sha256=TCHf3aM-KQxaNJen10CGX1Da5IIra00xRF39FUTU698,14301
39
- fractal_server/app/routes/api/v2/dataset.py,sha256=mgz8746jOhXDdKkNY7dDN3bM0QgXFBMk1VUFqnxU-B0,11573
39
+ fractal_server/app/routes/api/v2/dataset.py,sha256=0JGRnK1DRQKgVA3FDhK8VdoRglLYFxgkMQOaoWI-tiQ,7853
40
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  fractal_server/app/routes/api/v2/images.py,sha256=4r_HblPWyuKSZSJZfn8mbDaLv1ncwZU0gWdKneZcNG4,7894
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  fractal_server/app/routes/api/v2/job.py,sha256=9mXaKCX_N3FXM0GIxdE49nWl_hJZ8CBLBIaMMhaCKOM,5334
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  fractal_server/app/routes/api/v2/project.py,sha256=i9a19HAqE36N92G60ZYgObIP9nv-hR7Jt5nd9Dkhz1g,6024
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+ fractal_server/app/routes/api/v2/status.py,sha256=3bqQejJ3TnIMan5wK6jr9sv4ypsQr9WWU8xqlvTgDCE,5739
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  fractal_server/app/routes/api/v2/submit.py,sha256=iszII5CvWDEjGPTphBgH9FVS1pNb5m11Xc8xozGgjgI,6901
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  fractal_server/app/routes/api/v2/task.py,sha256=gJ0LruSk-Q1iMw8ZOX8C0wrZ4S4DGlQTr_5SdJJud0Q,7130
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  fractal_server/app/routes/api/v2/task_collection.py,sha256=iw74UF8qdQa9pJf0DvSjihng6ri2k2HtW2UhMS_a8Zc,8904
@@ -90,7 +91,7 @@ fractal_server/app/runner/v2/deduplicate_list.py,sha256=-imwO7OB7ATADEnqVbTElUwo
90
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  fractal_server/app/runner/v2/handle_failed_job.py,sha256=M1r3dnrbUMo_AI2qjaVuGhieMAyLh5gcvB10YOBpjvI,5415
91
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  fractal_server/app/runner/v2/merge_outputs.py,sha256=IHuHqbKmk97K35BFvTrKVBs60z3e_--OzXTnsvmA02c,1281
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  fractal_server/app/runner/v2/runner.py,sha256=K6bmWbQRSZwbO6ZI2Bp7wNxYdkHcXxhWwBObMxJ0iSU,12599
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- fractal_server/app/runner/v2/runner_functions.py,sha256=kN_xuaAg4qeRNIXijo30F1WSOo3zbjz5JCuS87EQf4g,10171
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+ fractal_server/app/runner/v2/runner_functions.py,sha256=qVGG9KlH8ObX4Y0kr0q6qE8OpWFwf4RnOHhgPRRdj5M,10293
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  fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=djNKD1y_EE0Q9Jkzh1QdKpjM66JVsLQgX2_zJT0xQlA,3947
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  fractal_server/app/runner/v2/task_interface.py,sha256=TZLVJs6CNFo2lFhr-lsDxe585cEhRv48eA490LS9aqc,1746
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  fractal_server/app/runner/v2/v1_compat.py,sha256=t0ficzAHUFaaeI56nqTb4YEKxfARF7L9Y6ijtJCwjP8,912
@@ -108,11 +109,12 @@ fractal_server/app/schemas/v1/task.py,sha256=7BxOZ_qoRQ8n3YbQpDvB7VMcxB5fSYQmR5R
108
109
  fractal_server/app/schemas/v1/task_collection.py,sha256=uvq9bcMaGD_qHsh7YtcpoSAkVAbw12eY4DocIO3MKOg,3057
109
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  fractal_server/app/schemas/v1/workflow.py,sha256=tuOs5E5Q_ozA8if7YPZ07cQjzqB_QMkBS4u92qo4Ro0,4618
110
111
  fractal_server/app/schemas/v2/__init__.py,sha256=zlCYrplCWwnCL9-BYsExRMfVzhBy21IMBfdHPMgJZYk,1752
111
- fractal_server/app/schemas/v2/dataset.py,sha256=_nnpGqaD7HJNC125jAyPn05iavy5uy4jxEMDB40TXCA,2737
112
+ fractal_server/app/schemas/v2/dataset.py,sha256=MGv0bdzEIQFNy8ARqiDn_neC1mJJTMXFzbb9M5l4xxg,2474
112
113
  fractal_server/app/schemas/v2/dumps.py,sha256=IpIT_2KxJd7qTgW2NllDknGeP7vBAJDfyz1I5p3TytU,2023
113
114
  fractal_server/app/schemas/v2/job.py,sha256=zfF9K3v4jWUJ7M482ta2CkqUJ4tVT4XfVt60p9IRhP0,3250
114
115
  fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Izxk9iL1vtwBJw,6243
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116
  fractal_server/app/schemas/v2/project.py,sha256=u7S4B-bote1oGjzAGiZ-DuQIyeRAGqJsI71Tc1EtYE0,736
117
+ fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
116
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  fractal_server/app/schemas/v2/task.py,sha256=7IfxiZkaVqlARy7WYE_H8m7j_IEcuQaZORUrs6b5YuY,4672
117
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  fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-20wIsmh7G1QOdr05KoDQ,3171
118
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  fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
@@ -159,8 +161,8 @@ fractal_server/tasks/v2/background_operations.py,sha256=zr6j3uoWmCeW2EA9auxWNZ0s
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  fractal_server/tasks/v2/get_collection_data.py,sha256=Qhf2T_aaqAfqu9_KpUSlXsS7EJoZQbEPEreHHa2jco8,502
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  fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
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  fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
162
- fractal_server-2.0.0a9.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
163
- fractal_server-2.0.0a9.dist-info/METADATA,sha256=P8NzTlZ9SHoftxPyngm08c824qK_b9sdIXvfrxt_e5Y,4200
164
- fractal_server-2.0.0a9.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
165
- fractal_server-2.0.0a9.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
166
- fractal_server-2.0.0a9.dist-info/RECORD,,
164
+ fractal_server-2.0.0a10.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
165
+ fractal_server-2.0.0a10.dist-info/METADATA,sha256=rZurMguM3pZbihOJYXyhi3zM3aRVhRrzDc_kuoTh910,4201
166
+ fractal_server-2.0.0a10.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
167
+ fractal_server-2.0.0a10.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
168
+ fractal_server-2.0.0a10.dist-info/RECORD,,