fractal-server 2.15.0a3__py3-none-any.whl → 2.15.0a4__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.15.0a3"
+__VERSION__ = "2.15.0a4"

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/task_collection.py

@@ -7,7 +7,6 @@ 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
@@ -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),

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

@@ -6,11 +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
@@ -35,7 +33,6 @@ 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 +78,6 @@ 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 +143,6 @@ 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,
@@ -168,7 +157,7 @@ async def collect_task_pixi(
         db=db,
     )
 
-    # FIXME: to be removed with issue #2634
+    # NOTE: 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():

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/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

@@ -47,22 +47,19 @@ 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 +97,14 @@ def collect_local_pixi(
                             task_group.pkg_name.replace("-", "_"),
                         ),
                         ("__SOURCE_DIR_NAME__", SOURCE_DIR_NAME),
+                        ("__FROZEN_OPTION__", ""),
                     },
                     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,
                 )
@@ -215,17 +213,14 @@ 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

@@ -45,23 +45,17 @@ 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 +88,7 @@ def reactivate_local_pixi(
                             task_group.pkg_name.replace("-", "_"),
                         ),
                         ("__SOURCE_DIR_NAME__", SOURCE_DIR_NAME),
-                        ("__FROZEN_OPTION__", "true"),
+                        ("__FROZEN_OPTION__", "--frozen"),
                     },
                     script_dir=Path(
                         task_group.path, SCRIPTS_SUBFOLDER
@@ -128,7 +122,7 @@ 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,
@@ -154,8 +148,8 @@ 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(

fractal_server/tasks/v2/ssh/_utils.py

@@ -1,6 +1,10 @@
 import os
 from pathlib import Path
 
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from ..utils_background import fail_and_cleanup
+from fractal_server.app.models.v2 import TaskGroupActivityV2
 from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.logger import get_logger
 from fractal_server.ssh._fabric import FractalSSH
@@ -10,7 +14,7 @@ from fractal_server.tasks.v2.utils_templates import customize_template
 def _customize_and_run_template(
     *,
     template_filename: str,
-    replacements: list[tuple[str, str]],
+    replacements: set[tuple[str, str]],
     script_dir_local: str,
     prefix: str,
     fractal_ssh: FractalSSH,
@@ -66,7 +70,10 @@ def _customize_and_run_template(
 
 
 def _copy_wheel_file_ssh(
-    *, task_group: TaskGroupV2, fractal_ssh: FractalSSH, logger_name: str
+    *,
+    task_group: TaskGroupV2,
+    fractal_ssh: FractalSSH,
+    logger_name: str,
 ) -> str:
     """
     Handle the situation where `task_group.archive_path` is not part of
@@ -81,7 +88,41 @@ def _copy_wheel_file_ssh(
         Path(task_group.path) / Path(task_group.archive_path).name
     ).as_posix()
     cmd = f"cp {source} {dest}"
-    logger.debug(f"[_copy_wheel_file] START {source=} {dest=}")
+    logger.debug(f"[_copy_wheel_file_ssh] START {source=} {dest=}")
     fractal_ssh.run_command(cmd=cmd)
-    logger.debug(f"[_copy_wheel_file] END {source=} {dest=}")
+    logger.debug(f"[_copy_wheel_file_ssh] END {source=} {dest=}")
     return dest
+
+
+def check_ssh_or_fail_and_cleanup(
+    *,
+    fractal_ssh: FractalSSH,
+    task_group: TaskGroupV2,
+    task_group_activity: TaskGroupActivityV2,
+    logger_name: str,
+    log_file_path: Path,
+    db: AsyncSession,
+) -> bool:
+    """
+    Check SSH connection.
+
+    Returns:
+        Whether SSH connection is OK.
+    """
+    try:
+        fractal_ssh.check_connection()
+        return True
+    except Exception as e:
+        logger = get_logger(logger_name=logger_name)
+        logger.error(
+            "Cannot establish SSH connection. " f"Original error: {str(e)}"
+        )
+        fail_and_cleanup(
+            task_group=task_group,
+            task_group_activity=task_group_activity,
+            logger_name=logger_name,
+            log_file_path=log_file_path,
+            exception=e,
+            db=db,
+        )
+        return False

fractal_server/tasks/v2/ssh/collect.py

@@ -2,11 +2,11 @@ import time
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
-from ....ssh._fabric import SingleUseFractalSSH
 from ..utils_background import fail_and_cleanup
 from ..utils_background import get_activity_and_task_group
 from ..utils_background import prepare_tasks_metadata
 from ..utils_database import create_db_tasks_and_update_task_group_sync
+from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.schemas.v2 import FractalUploadedFile
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
@@ -14,6 +14,7 @@ from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
 from fractal_server.app.schemas.v2.manifest import ManifestV2
 from fractal_server.logger import reset_logger_handlers
 from fractal_server.logger import set_logger
+from fractal_server.ssh._fabric import SingleUseFractalSSH
 from fractal_server.ssh._fabric import SSHConfig
 from fractal_server.tasks.v2.ssh._utils import _customize_and_run_template
 from fractal_server.tasks.v2.utils_background import add_commit_refresh
@@ -68,43 +69,39 @@ def collect_ssh(
             logger_name=LOGGER_NAME,
             log_file_path=log_file_path,
         )
-        with SingleUseFractalSSH(
-            ssh_config=ssh_config,
-            logger_name=LOGGER_NAME,
-        ) as fractal_ssh:
-
-            with next(get_sync_db()) as db:
-                success, task_group, activity = get_activity_and_task_group(
-                    task_group_activity_id=task_group_activity_id,
-                    task_group_id=task_group_id,
-                    db=db,
-                )
-                if not success:
-                    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 SSH connection works
+        logger.info("START")
+        with next(get_sync_db()) as db:
+            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 db_objects_ok:
+                return
+
+            with SingleUseFractalSSH(
+                ssh_config=ssh_config,
+                logger_name=LOGGER_NAME,
+            ) as fractal_ssh:
+
                 try:
-                    fractal_ssh.check_connection()
-                except Exception as e:
-                    logger.error("Cannot establish SSH connection.")
-                    fail_and_cleanup(
+                    # Check SSH connection
+                    ssh_ok = check_ssh_or_fail_and_cleanup(
+                        fractal_ssh=fractal_ssh,
                         task_group=task_group,
                         task_group_activity=activity,
                         logger_name=LOGGER_NAME,
                         log_file_path=log_file_path,
-                        exception=e,
                         db=db,
                     )
-                    return
-
-                try:
+                    if not ssh_ok:
+                        return
 
                     # Check that the (remote) task_group path does not exist
+                    # NOTE: this is not part of the try/except below, in order
+                    # to avoid removing the existing folder (as part of the
+                    # exception-handling).
                     if fractal_ssh.remote_exists(task_group.path):
                         error_msg = f"{task_group.path} already exists."
                         logger.error(error_msg)
@@ -119,9 +116,7 @@ def collect_ssh(
                         return
 
                     # Create remote `task_group.path` and `script_dir_remote`
-                    # folders (note that because of `parents=True` we  are in
-                    # the `no error if existing, make parent directories as
-                    # needed` scenario for `mkdir`)
+                    # folders
                     script_dir_remote = (
                         Path(task_group.path) / SCRIPTS_SUBFOLDER
                     ).as_posix()
@@ -139,8 +134,7 @@ def collect_ssh(
                             Path(tmpdir) / wheel_filename
                         ).as_posix()
                         logger.info(
-                            "Write wheel-file contents into "
-                            f"{tmp_archive_path}"
+                            f"Write wheel file into {tmp_archive_path}"
                         )
                         with open(tmp_archive_path, "wb") as f:
                             f.write(wheel_file.contents)
@@ -161,8 +155,8 @@ def collect_ssh(
                     # Prepare common arguments for _customize_and_run_template
                     common_args = dict(
                         replacements=replacements,
-                        script_dir_local=(
-                            Path(tmpdir) / SCRIPTS_SUBFOLDER
+                        script_dir_local=Path(
+                            tmpdir, SCRIPTS_SUBFOLDER
                         ).as_posix(),
                         script_dir_remote=script_dir_remote,
                         prefix=(
@@ -187,6 +181,7 @@ def collect_ssh(
                     )
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
+
                     # Run script 2
                     stdout = _customize_and_run_template(
                         template_filename="2_pip_install.sh",
@@ -315,7 +310,7 @@ def collect_ssh(
                     except Exception as e_rm:
                         logger.error(
                             "Removing folder failed. "
-                            f"Original error:\n{str(e_rm)}"
+                            f"Original error: {str(e_rm)}"
                         )
                     fail_and_cleanup(
                         task_group=task_group,