fractal-server 2.15.0a3__py3-none-any.whl → 2.15.0a5__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.15.0a3"
+__VERSION__ = "2.15.0a5"

fractal_server/app/routes/admin/v2/task_group_lifecycle.py

@@ -2,7 +2,6 @@ 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
 
@@ -51,7 +50,6 @@ async def deactivate_task_group(
     task_group_id: int,
     background_tasks: BackgroundTasks,
     response: Response,
-    request: Request,
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:
@@ -157,7 +155,6 @@ async def reactivate_task_group(
     task_group_id: int,
     background_tasks: BackgroundTasks,
     response: Response,
-    request: Request,
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:

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

@@ -333,6 +333,28 @@ async def _verify_non_duplication_group_constraint(
         )
 
 
+async def _verify_non_duplication_group_path(
+    path: str | None,
+    db: AsyncSession,
+) -> None:
+    """
+    Verify uniqueness of non-`None` `TaskGroupV2.path`
+    """
+    if path is None:
+        return
+    stm = select(TaskGroupV2.id).where(TaskGroupV2.path == path)
+    res = await db.execute(stm)
+    duplicate_ids = res.scalars().all()
+    if duplicate_ids:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                f"Other TaskGroups already have {path=}: "
+                f"{sorted(duplicate_ids)}."
+            ),
+        )
+
+
 async def _add_warnings_to_workflow_tasks(
     wftask_list: list[WorkflowTaskV2], user_id: int, db: AsyncSession
 ) -> list[dict[str, Any]]:

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

@@ -7,14 +7,12 @@ from fastapi import Depends
 from fastapi import File
 from fastapi import Form
 from fastapi import HTTPException
-from fastapi import Request
 from fastapi import Response
 from fastapi import status
 from fastapi import UploadFile
 from pydantic import BaseModel
 from pydantic import model_validator
 from pydantic import ValidationError
-from sqlmodel import select
 
 from .....config import get_settings
 from .....logger import reset_logger_handlers
@@ -32,6 +30,7 @@ from ...aux.validate_user_settings import validate_user_settings
 from ._aux_functions_task_lifecycle import get_package_version_from_pypi
 from ._aux_functions_tasks import _get_valid_user_group_id
 from ._aux_functions_tasks import _verify_non_duplication_group_constraint
+from ._aux_functions_tasks import _verify_non_duplication_group_path
 from ._aux_functions_tasks import _verify_non_duplication_user_constraint
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import TaskGroupActivityV2
@@ -151,7 +150,6 @@ def parse_request_data(
     response_model=TaskGroupActivityV2Read,
 )
 async def collect_tasks_pip(
-    request: Request,
     response: Response,
     background_tasks: BackgroundTasks,
     request_data: CollectionRequestData = Depends(parse_request_data),
@@ -293,18 +291,10 @@ async def collect_tasks_pip(
         version=task_group_attrs["version"],
         db=db,
     )
-
-    # Verify that task-group path is unique
-    stm = select(TaskGroupV2).where(TaskGroupV2.path == task_group_path)
-    res = await db.execute(stm)
-    for conflicting_task_group in res.scalars().all():
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                f"Another task-group already has path={task_group_path}.\n"
-                f"{conflicting_task_group=}"
-            ),
-        )
+    await _verify_non_duplication_group_path(
+        path=task_group_attrs["path"],
+        db=db,
+    )
 
     # On-disk checks
 

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

@@ -6,12 +6,9 @@ from fastapi import BackgroundTasks
 from fastapi import Depends
 from fastapi import Form
 from fastapi import HTTPException
-from fastapi import Request
 from fastapi import Response
 from fastapi import status
 from fastapi import UploadFile
-from pydantic import ValidationError
-from sqlmodel import select
 
 from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
@@ -24,6 +21,9 @@ from fractal_server.app.routes.api.v2._aux_functions_tasks import (
 from fractal_server.app.routes.api.v2._aux_functions_tasks import (
     _verify_non_duplication_group_constraint,
 )
+from fractal_server.app.routes.api.v2._aux_functions_tasks import (
+    _verify_non_duplication_group_path,
+)
 from fractal_server.app.routes.api.v2._aux_functions_tasks import (
     _verify_non_duplication_user_constraint,
 )
@@ -35,7 +35,6 @@ from fractal_server.app.schemas.v2 import FractalUploadedFile
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
 from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
 from fractal_server.app.schemas.v2 import TaskGroupActivityV2Read
-from fractal_server.app.schemas.v2 import TaskGroupCreateV2StrictPixi
 from fractal_server.app.schemas.v2.task_group import TaskGroupV2OriginEnum
 from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
@@ -81,7 +80,6 @@ def validate_pkgname_and_version(filename: str) -> tuple[str, str]:
     response_model=TaskGroupActivityV2Read,
 )
 async def collect_task_pixi(
-    request: Request,
     response: Response,
     background_tasks: BackgroundTasks,
     file: UploadFile,
@@ -147,13 +145,6 @@ async def collect_task_pixi(
         version=version,
         path=task_group_path,
     )
-    try:
-        TaskGroupCreateV2StrictPixi(**task_group_attrs)
-    except ValidationError as e:
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=f"Invalid task-group object. Original error: {e}",
-        )
 
     await _verify_non_duplication_user_constraint(
         user_id=user.id,
@@ -167,18 +158,10 @@ async def collect_task_pixi(
         version=task_group_attrs["version"],
         db=db,
     )
-
-    # FIXME: to be removed with issue #2634
-    stm = select(TaskGroupV2).where(TaskGroupV2.path == task_group_path)
-    res = await db.execute(stm)
-    for conflicting_task_group in res.scalars().all():
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                f"Another task-group already has path={task_group_path}.\n"
-                f"{conflicting_task_group=}"
-            ),
-        )
+    await _verify_non_duplication_group_path(
+        path=task_group_attrs["path"],
+        db=db,
+    )
 
     if settings.FRACTAL_RUNNER_BACKEND != "slurm_ssh":
         if Path(task_group_path).exists():

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

@@ -12,6 +12,7 @@ from pydantic.types import AwareDatetime
 from sqlmodel import or_
 from sqlmodel import select
 
+from ._aux_functions_task_lifecycle import check_no_ongoing_activity
 from ._aux_functions_tasks import _get_task_group_full_access
 from ._aux_functions_tasks import _get_task_group_read_access
 from ._aux_functions_tasks import _verify_non_duplication_group_constraint
@@ -216,6 +217,8 @@ async def delete_task_group(
         db=db,
     )
 
+    await check_no_ongoing_activity(task_group_id=task_group_id, db=db)
+
     stm = select(WorkflowTaskV2).where(
         WorkflowTaskV2.task_id.in_({task.id for task in task_group.task_list})
     )

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

@@ -2,7 +2,6 @@ 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
 
@@ -48,7 +47,6 @@ async def deactivate_task_group(
     task_group_id: int,
     background_tasks: BackgroundTasks,
     response: Response,
-    request: Request,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:
@@ -168,7 +166,6 @@ async def reactivate_task_group(
     task_group_id: int,
     background_tasks: BackgroundTasks,
     response: Response,
-    request: Request,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:

fractal_server/app/schemas/v2/__init__.py

@@ -41,7 +41,6 @@ from .task_group import TaskGroupActivityStatusV2  # noqa F401
 from .task_group import TaskGroupActivityV2Read  # noqa F401
 from .task_group import TaskGroupCreateV2  # noqa F401
 from .task_group import TaskGroupCreateV2Strict  # noqa F401
-from .task_group import TaskGroupCreateV2StrictPixi  # noqa F401
 from .task_group import TaskGroupReadV2  # noqa F401
 from .task_group import TaskGroupUpdateV2  # noqa F401
 from .task_group import TaskGroupV2OriginEnum  # noqa F401

fractal_server/app/schemas/v2/task_group.py

@@ -62,15 +62,6 @@ class TaskGroupCreateV2Strict(TaskGroupCreateV2):
     python_version: NonEmptyStr
 
 
-class TaskGroupCreateV2StrictPixi(TaskGroupCreateV2):
-    """
-    A strict version of TaskGroupCreateV2, to be used for pixi task collection.
-    """
-
-    path: AbsolutePathStr
-    pixi_version: NonEmptyStr
-
-
 class TaskGroupReadV2(BaseModel):
     id: int
     task_list: list[TaskReadV2]

fractal_server/config.py

@@ -65,8 +65,36 @@ class MailSettings(BaseModel):
 
 
 class PixiSettings(BaseModel):
-    default_version: str
+    """
+    Configuration for Pixi task collection
+
+    See https://pixi.sh/latest/reference/cli/pixi/install/#config-options for
+    `pixi install` concurrency options.
+    See https://docs.rs/tokio/latest/tokio/#cpu-bound-tasks-and-blocking-code
+    for `tokio` configuration.
+
+    versions:
+        Available `pixi` versions and their `PIXI_HOME` folders.
+    default_version:
+        Default `pixi` version to use for task collection - must be one
+        of `versions` keys.
+    PIXI_CONCURRENT_SOLVES:
+        Value of `--concurrent-solves` for `pixi install`.
+    PIXI_CONCURRENT_DOWNLOADS:
+        Value of `--concurrent-downloads for `pixi install`.
+    TOKIO_WORKER_THREADS:
+        From tokio docs, "The core threads are where all asynchronous code
+        runs, and Tokio will by default spawn one for each CPU core. You can
+        use the environment variable TOKIO_WORKER_THREADS to override the
+        default value."
+    """
+
     versions: DictStrStr
+    default_version: str
+
+    PIXI_CONCURRENT_SOLVES: int = 4
+    PIXI_CONCURRENT_DOWNLOADS: int = 4
+    TOKIO_WORKER_THREADS: int = 2
 
     @model_validator(mode="after")
     def check_pixi_settings(self):

fractal_server/tasks/v2/local/_utils.py

@@ -31,7 +31,7 @@ def _customize_and_run_template(
             f"Invalid {template_filename=} (it must end with '.sh')."
         )
 
-    script_filename = f"{prefix}{template_filename}"
+    script_filename = f"{prefix}_{template_filename}"
     script_path_local = Path(script_dir) / script_filename
     # Read template
     customize_template(
@@ -50,10 +50,6 @@ def check_task_files_exist(task_list: list[TaskCreateV2]) -> None:
     """
     Check that the modules listed in task commands point to existing files.
 
-    Note: commands may be like `/one/python /another/task.py` or
-    `/one/pixi [...] /another/task.py`, and in both cases `split()[-1]`
-    returns `/another/task.py`.
-
     Args:
         task_list:
     """

fractal_server/tasks/v2/local/collect.py

@@ -67,20 +67,17 @@ def collect_local(
             log_file_path=log_file_path,
         )
 
+        logger.info("START")
         with next(get_sync_db()) as db:
-            success, task_group, activity = get_activity_and_task_group(
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
                 task_group_activity_id=task_group_activity_id,
                 task_group_id=task_group_id,
                 db=db,
+                logger_name=LOGGER_NAME,
             )
-            if not success:
+            if not db_objects_ok:
                 return
 
-            # Log some info
-            logger.info("START")
-            for key, value in task_group.model_dump().items():
-                logger.debug(f"task_group.{key}: {value}")
-
             # Check that the (local) task_group path does exist
             if Path(task_group.path).exists():
                 error_msg = f"{task_group.path} already exists."
@@ -130,7 +127,7 @@ def collect_local(
                     ).as_posix(),
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.COLLECT}_"
+                        f"{TaskGroupActivityActionV2.COLLECT}"
                     ),
                     logger_name=LOGGER_NAME,
                 )

fractal_server/tasks/v2/local/collect_pixi.py

@@ -27,6 +27,7 @@ from fractal_server.tasks.v2.utils_background import (
 from fractal_server.tasks.v2.utils_background import get_current_log
 from fractal_server.tasks.v2.utils_background import prepare_tasks_metadata
 from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
+from fractal_server.utils import execute_command_sync
 from fractal_server.utils import get_timestamp
 
 
@@ -47,22 +48,19 @@ def collect_local_pixi(
             log_file_path=log_file_path,
         )
 
+        logger.info("START")
         with next(get_sync_db()) as db:
-            success, task_group, activity = get_activity_and_task_group(
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
                 task_group_activity_id=task_group_activity_id,
                 task_group_id=task_group_id,
                 db=db,
+                logger_name=LOGGER_NAME,
             )
-            if not success:
+            if not db_objects_ok:
                 return
 
-            logger.info("START")
-            for key, value in task_group.model_dump(
-                exclude={"env_info"}
-            ).items():
-                logger.debug(f"task_group.{key}: {value}")
-
             if Path(task_group.path).exists():
+                # We handle this before the try/except to avoid the rmtree
                 error_msg = f"{task_group.path} already exists."
                 logger.error(error_msg)
                 fail_and_cleanup(
@@ -100,13 +98,26 @@ def collect_local_pixi(
                             task_group.pkg_name.replace("-", "_"),
                         ),
                         ("__SOURCE_DIR_NAME__", SOURCE_DIR_NAME),
+                        ("__FROZEN_OPTION__", ""),
+                        (
+                            "__TOKIO_WORKER_THREADS__",
+                            str(settings.pixi.TOKIO_WORKER_THREADS),
+                        ),
+                        (
+                            "__PIXI_CONCURRENT_SOLVES__",
+                            str(settings.pixi.PIXI_CONCURRENT_SOLVES),
+                        ),
+                        (
+                            "__PIXI_CONCURRENT_DOWNLOADS__",
+                            str(settings.pixi.PIXI_CONCURRENT_DOWNLOADS),
+                        ),
                     },
                     script_dir=Path(
                         task_group.path, SCRIPTS_SUBFOLDER
                     ).as_posix(),
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.COLLECT}_"
+                        f"{TaskGroupActivityActionV2.COLLECT}"
                     ),
                     logger_name=LOGGER_NAME,
                 )
@@ -148,6 +159,14 @@ def collect_local_pixi(
                     "project_python_wrapper"
                 ]
 
+                # Make task folder 755
+                source_dir = Path(task_group.path, SOURCE_DIR_NAME).as_posix()
+                command = f"chmod 755 {source_dir} -R"
+                execute_command_sync(
+                    command=command,
+                    logger_name=LOGGER_NAME,
+                )
+
                 # Read and validate manifest
                 # NOTE: we are only supporting the manifest path being relative
                 # to the top-level folder
@@ -215,17 +234,14 @@ def collect_local_pixi(
                 reset_logger_handlers(logger)
 
             except Exception as collection_e:
-                # Delete corrupted package dir
                 try:
                     logger.info(f"Now delete folder {task_group.path}")
                     shutil.rmtree(task_group.path)
                     logger.info(f"Deleted folder {task_group.path}")
                 except Exception as rm_e:
                     logger.error(
-                        "Removing folder failed.\n"
-                        f"Original error:\n{str(rm_e)}"
+                        f"Removing folder failed. Original error: {str(rm_e)}"
                     )
-
                 fail_and_cleanup(
                     task_group=task_group,
                     task_group_activity=activity,

fractal_server/tasks/v2/local/deactivate.py

@@ -46,21 +46,17 @@ def deactivate_local(
             log_file_path=log_file_path,
         )
 
+        logger.debug("START")
         with next(get_sync_db()) as db:
-            success, task_group, activity = get_activity_and_task_group(
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
                 task_group_activity_id=task_group_activity_id,
                 task_group_id=task_group_id,
                 db=db,
+                logger_name=LOGGER_NAME,
             )
-            if not success:
+            if not db_objects_ok:
                 return
 
-            # Log some info
-            logger.debug("START")
-
-            for key, value in task_group.model_dump().items():
-                logger.debug(f"task_group.{key}: {value}")
-
             # Check that the (local) task_group venv_path does exist
             if not Path(task_group.venv_path).exists():
                 error_msg = f"{task_group.venv_path} does not exist."
@@ -100,7 +96,7 @@ def deactivate_local(
                         ).as_posix(),
                         prefix=(
                             f"{int(time.time())}_"
-                            f"{TaskGroupActivityActionV2.DEACTIVATE}_"
+                            f"{TaskGroupActivityActionV2.DEACTIVATE}"
                         ),
                         logger_name=LOGGER_NAME,
                     )

fractal_server/tasks/v2/local/deactivate_pixi.py

@@ -40,23 +40,17 @@ def deactivate_local_pixi(
             log_file_path=log_file_path,
         )
 
+        logger.debug("START")
         with next(get_sync_db()) as db:
-            success, task_group, activity = get_activity_and_task_group(
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
                 task_group_activity_id=task_group_activity_id,
                 task_group_id=task_group_id,
                 db=db,
+                logger_name=LOGGER_NAME,
             )
-            if not success:
+            if not db_objects_ok:
                 return
 
-            # Log some info
-            logger.debug("START")
-
-            for key, value in task_group.model_dump(
-                exclude={"env_info"}
-            ).items():
-                logger.debug(f"task_group.{key}: {value}")
-
             source_dir = Path(task_group.path, SOURCE_DIR_NAME)
             if not source_dir.exists():
                 error_msg = f"'{source_dir.as_posix()}' does not exist."

fractal_server/tasks/v2/local/reactivate.py

@@ -47,21 +47,17 @@ def reactivate_local(
             log_file_path=log_file_path,
         )
 
+        logger.debug("START")
         with next(get_sync_db()) as db:
-            success, task_group, activity = get_activity_and_task_group(
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
                 task_group_activity_id=task_group_activity_id,
                 task_group_id=task_group_id,
                 db=db,
+                logger_name=LOGGER_NAME,
             )
-            if not success:
+            if not db_objects_ok:
                 return
 
-            # Log some info
-            logger.debug("START")
-
-            for key, value in task_group.model_dump().items():
-                logger.debug(f"task_group.{key}: {value}")
-
             # Check that the (local) task_group venv_path does not exist
             if Path(task_group.venv_path).exists():
                 error_msg = f"{task_group.venv_path} already exists."
@@ -100,7 +96,7 @@ def reactivate_local(
                     ).as_posix(),
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.REACTIVATE}_"
+                        f"{TaskGroupActivityActionV2.REACTIVATE}"
                     ),
                     logger_name=LOGGER_NAME,
                 )

fractal_server/tasks/v2/local/reactivate_pixi.py

@@ -18,6 +18,7 @@ from fractal_server.tasks.utils import get_log_path
 from fractal_server.tasks.v2.local._utils import _customize_and_run_template
 from fractal_server.tasks.v2.utils_background import get_current_log
 from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
+from fractal_server.utils import execute_command_sync
 from fractal_server.utils import get_timestamp
 
 
@@ -45,23 +46,17 @@ def reactivate_local_pixi(
             logger_name=LOGGER_NAME,
             log_file_path=log_file_path,
         )
+        logger.debug("START")
         with next(get_sync_db()) as db:
-            success, task_group, activity = get_activity_and_task_group(
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
                 task_group_activity_id=task_group_activity_id,
                 task_group_id=task_group_id,
                 db=db,
+                logger_name=LOGGER_NAME,
             )
-            if not success:
+            if not db_objects_ok:
                 return
 
-            # Log some info
-            logger.debug("START")
-
-            for key, value in task_group.model_dump(
-                exclude={"env_info"}
-            ).items():
-                logger.debug(f"task_group.{key}: {value}")
-
             source_dir = Path(task_group.path, SOURCE_DIR_NAME).as_posix()
             if Path(source_dir).exists():
                 error_msg = f"{source_dir} already exists."
@@ -94,7 +89,19 @@ def reactivate_local_pixi(
                             task_group.pkg_name.replace("-", "_"),
                         ),
                         ("__SOURCE_DIR_NAME__", SOURCE_DIR_NAME),
-                        ("__FROZEN_OPTION__", "true"),
+                        ("__FROZEN_OPTION__", "--frozen"),
+                        (
+                            "__TOKIO_WORKER_THREADS__",
+                            str(settings.pixi.TOKIO_WORKER_THREADS),
+                        ),
+                        (
+                            "__PIXI_CONCURRENT_SOLVES__",
+                            str(settings.pixi.PIXI_CONCURRENT_SOLVES),
+                        ),
+                        (
+                            "__PIXI_CONCURRENT_DOWNLOADS__",
+                            str(settings.pixi.PIXI_CONCURRENT_DOWNLOADS),
+                        ),
                     },
                     script_dir=Path(
                         task_group.path, SCRIPTS_SUBFOLDER
@@ -128,7 +135,7 @@ def reactivate_local_pixi(
                 activity.log = get_current_log(log_file_path)
                 activity = add_commit_refresh(obj=activity, db=db)
 
-                # Run script 3
+                # Run script 3 - post-install
                 _customize_and_run_template(
                     template_filename="pixi_3_post_install.sh",
                     **common_args,
@@ -136,6 +143,14 @@ def reactivate_local_pixi(
                 activity.log = get_current_log(log_file_path)
                 activity = add_commit_refresh(obj=activity, db=db)
 
+                # Make task folder 755
+                source_dir = Path(task_group.path, SOURCE_DIR_NAME).as_posix()
+                command = f"chmod 755 {source_dir} -R"
+                execute_command_sync(
+                    command=command,
+                    logger_name=LOGGER_NAME,
+                )
+
                 activity.log = get_current_log(log_file_path)
                 activity.status = TaskGroupActivityStatusV2.OK
                 activity.timestamp_ended = get_timestamp()
@@ -154,8 +169,8 @@ def reactivate_local_pixi(
                     logger.info(f"Deleted folder {source_dir}")
                 except Exception as rm_e:
                     logger.error(
-                        "Removing folder failed.\n"
-                        f"Original error:\n{str(rm_e)}"
+                        "Removing folder failed. "
+                        f"Original error: {str(rm_e)}"
                     )
 
                 fail_and_cleanup(