fractal-server 2.13.0__py3-none-any.whl → 2.14.0__py3-none-any.whl

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

@@ -417,3 +417,69 @@ async def clean_app_job_list_v2(
         if job.status == JobStatusTypeV2.SUBMITTED
     ]
     return submitted_job_ids
+
+
+async def _get_dataset_or_404(
+    *,
+    dataset_id: int,
+    db: AsyncSession,
+) -> DatasetV2:
+    """
+    Get a dataset or raise 404.
+
+    Args:
+        dataset_id:
+        db:
+    """
+    ds = await db.get(DatasetV2, dataset_id)
+    if ds is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"Dataset {dataset_id} not found.",
+        )
+    else:
+        return ds
+
+
+async def _get_workflow_or_404(
+    *,
+    workflow_id: int,
+    db: AsyncSession,
+) -> WorkflowV2:
+    """
+    Get a workflow or raise 404.
+
+    Args:
+        workflow_id:
+        db:
+    """
+    wf = await db.get(WorkflowV2, workflow_id)
+    if wf is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"Workflow {workflow_id} not found.",
+        )
+    else:
+        return wf
+
+
+async def _get_workflowtask_or_404(
+    *,
+    workflowtask_id: int,
+    db: AsyncSession,
+) -> WorkflowTaskV2:
+    """
+    Get a workflow task or raise 404.
+
+    Args:
+        workflowtask_id:
+        db:
+    """
+    wftask = await db.get(WorkflowTaskV2, workflowtask_id)
+    if wftask is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"WorkflowTask {workflowtask_id} not found.",
+        )
+    else:
+        return wftask

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

@@ -0,0 +1,166 @@
+from pathlib import Path
+from typing import Literal
+
+from fastapi import HTTPException
+from fastapi import status
+
+from fractal_server.app.db import AsyncSession
+from fractal_server.app.models import WorkflowTaskV2
+from fractal_server.app.models.v2 import DatasetV2
+from fractal_server.app.models.v2 import HistoryRun
+from fractal_server.app.models.v2 import HistoryUnit
+from fractal_server.app.models.v2 import WorkflowV2
+from fractal_server.app.routes.api.v2._aux_functions import _get_dataset_or_404
+from fractal_server.app.routes.api.v2._aux_functions import (
+    _get_project_check_owner,
+)
+from fractal_server.app.routes.api.v2._aux_functions import (
+    _get_workflow_or_404,
+)
+from fractal_server.app.routes.api.v2._aux_functions import (
+    _get_workflowtask_or_404,
+)
+from fractal_server.logger import set_logger
+
+
+logger = set_logger(__name__)
+
+
+async def get_history_unit_or_404(
+    *, history_unit_id: int, db: AsyncSession
+) -> HistoryUnit:
+    """
+    Get an existing HistoryUnit  or raise a 404.
+
+    Arguments:
+        history_unit_id: The `HistoryUnit` id
+        db: An asynchronous db session
+    """
+    history_unit = await db.get(HistoryUnit, history_unit_id)
+    if history_unit is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"HistoryUnit {history_unit_id} not found",
+        )
+    return history_unit
+
+
+async def get_history_run_or_404(
+    *, history_run_id: int, db: AsyncSession
+) -> HistoryRun:
+    """
+    Get an existing HistoryRun  or raise a 404.
+
+    Arguments:
+        history_run_id:
+        db:
+    """
+    history_run = await db.get(HistoryRun, history_run_id)
+    if history_run is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"HistoryRun {history_run_id} not found",
+        )
+    return history_run
+
+
+def read_log_file(
+    *,
+    logfile: str | None,
+    wftask: WorkflowTaskV2,
+    dataset_id: int,
+):
+    if logfile is None or not Path(logfile).exists():
+        logger.debug(
+            f"Logs for task '{wftask.task.name}' in dataset "
+            f"{dataset_id} are not available ({logfile=})."
+        )
+        return (
+            f"Logs for task '{wftask.task.name}' in dataset "
+            f"{dataset_id} are not available."
+        )
+
+    try:
+        with open(logfile, "r") as f:
+            return f.read()
+    except Exception as e:
+        return (
+            f"Error while retrieving logs for task '{wftask.task.name}' "
+            f"in dataset {dataset_id}. Original error: {str(e)}."
+        )
+
+
+async def _verify_workflow_and_dataset_access(
+    *,
+    project_id: int,
+    workflow_id: int,
+    dataset_id: int,
+    user_id: int,
+    db: AsyncSession,
+) -> dict[Literal["dataset", "workflow"], DatasetV2 | WorkflowV2]:
+    """
+    Verify user access to a dataset/workflow pair.
+
+    Args:
+        dataset_id:
+        workflow_task_id:
+        user_id:
+        db:
+    """
+    await _get_project_check_owner(
+        project_id=project_id,
+        user_id=user_id,
+        db=db,
+    )
+    workflow = await _get_workflow_or_404(
+        workflow_id=workflow_id,
+        db=db,
+    )
+    if workflow.project_id != project_id:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail="Workflow does not belong to expected project.",
+        )
+    dataset = await _get_dataset_or_404(
+        dataset_id=dataset_id,
+        db=db,
+    )
+    if dataset.project_id != project_id:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail="Dataset does not belong to expected project.",
+        )
+
+    return dict(dataset=dataset, workflow=workflow)
+
+
+async def get_wftask_check_owner(
+    *,
+    project_id: int,
+    dataset_id: int,
+    workflowtask_id: int,
+    user_id: int,
+    db: AsyncSession,
+) -> WorkflowTaskV2:
+    """
+    Verify user access for the history of this dataset and workflowtask.
+
+    Args:
+        project_id:
+        dataset_id:
+        workflow_task_id:
+        user_id:
+        db:
+    """
+    wftask = await _get_workflowtask_or_404(
+        workflowtask_id=workflowtask_id,
+        db=db,
+    )
+    await _verify_workflow_and_dataset_access(
+        project_id=project_id,
+        dataset_id=dataset_id,
+        workflow_id=wftask.workflow_id,
+        user_id=user_id,
+        db=db,
+    )
+    return wftask

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

@@ -55,7 +55,7 @@ async def get_package_version_from_pypi(
             f"A TimeoutException occurred while getting {url}.\n"
             f"Original error: {str(e)}."
         )
-        logger.error(error_msg)
+        logger.warning(error_msg)
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
             detail=error_msg,
@@ -65,7 +65,7 @@ async def get_package_version_from_pypi(
             f"An unknown error occurred while getting {url}. "
             f"Original error: {str(e)}."
         )
-        logger.error(error_msg)
+        logger.warning(error_msg)
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
             detail=error_msg,
@@ -85,7 +85,7 @@ async def get_package_version_from_pypi(
         latest_version = response_data["info"]["version"]
         available_releases = response_data["releases"].keys()
     except KeyError as e:
-        logger.error(
+        logger.warning(
             f"A KeyError occurred while getting {url}. "
             f"Original error: {str(e)}."
         )

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

@@ -47,7 +47,6 @@ async def create_dataset(
     )
 
     if dataset.zarr_dir is None:
-
         if user.settings.project_dir is None:
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
@@ -91,7 +90,6 @@ async def create_dataset(
 )
 async def read_dataset_list(
     project_id: int,
-    history: bool = True,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> Optional[list[DatasetReadV2]]:
@@ -110,9 +108,6 @@ async def read_dataset_list(
     res = await db.execute(stm)
     dataset_list = res.scalars().all()
     await db.close()
-    if not history:
-        for ds in dataset_list:
-            setattr(ds, "history", [])
     return dataset_list
 
 
@@ -217,14 +212,6 @@ async def delete_dataset(
             ),
         )
 
-    # Cascade operations: set foreign-keys to null for jobs which are in
-    # relationship with the current dataset
-    stm = select(JobV2).where(JobV2.dataset_id == dataset_id)
-    res = await db.execute(stm)
-    jobs = res.scalars().all()
-    for job in jobs:
-        job.dataset_id = None
-
     # Delete dataset
     await db.delete(dataset)
     await db.commit()
@@ -234,7 +221,6 @@ async def delete_dataset(
 
 @router.get("/dataset/", response_model=list[DatasetReadV2])
 async def get_user_datasets(
-    history: bool = True,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[DatasetReadV2]:
@@ -249,9 +235,6 @@ async def get_user_datasets(
     res = await db.execute(stm)
     dataset_list = res.scalars().all()
     await db.close()
-    if not history:
-        for ds in dataset_list:
-            setattr(ds, "history", [])
     return dataset_list