fractal-server 2.14.5__py3-none-any.whl → 2.14.7__py3-none-any.whl

fractal_server/tasks/v2/ssh/collect.py

@@ -2,8 +2,8 @@ import logging
 import time
 from pathlib import Path
 from tempfile import TemporaryDirectory
-from typing import Optional
 
+from ....ssh._fabric import SingleUseFractalSSH
 from ..utils_background import _prepare_tasks_metadata
 from ..utils_background import fail_and_cleanup
 from ..utils_database import create_db_tasks_and_update_task_group_sync
@@ -16,7 +16,7 @@ from fractal_server.app.schemas.v2 import WheelFile
 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 FractalSSH
+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
 from fractal_server.tasks.v2.utils_background import get_current_log
@@ -36,9 +36,9 @@ def collect_ssh(
     *,
     task_group_id: int,
     task_group_activity_id: int,
-    fractal_ssh: FractalSSH,
+    ssh_config: SSHConfig,
     tasks_base_dir: str,
-    wheel_file: Optional[WheelFile] = None,
+    wheel_file: WheelFile | None = None,
 ) -> None:
     """
     Collect a task package over SSH
@@ -54,7 +54,7 @@ def collect_ssh(
     Arguments:
         task_group_id:
         task_group_activity_id:
-        fractal_ssh:
+        ssh_config:
         tasks_base_dir:
             Only used as a `safe_root` in `remove_dir`, and typically set to
             `user_settings.ssh_tasks_dir`.
@@ -65,256 +65,267 @@ def collect_ssh(
 
     # Work within a temporary folder, where also logs will be placed
     with TemporaryDirectory() as tmpdir:
-        LOGGER_NAME = "task_collection_ssh"
         log_file_path = Path(tmpdir) / "log"
         logger = set_logger(
             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:
+                # Get main objects from db
+                activity = db.get(TaskGroupActivityV2, task_group_activity_id)
+                task_group = db.get(TaskGroupV2, task_group_id)
+                if activity is None or task_group is None:
+                    # Use `logging` directly
+                    logging.error(
+                        "Cannot find database rows with "
+                        f"{task_group_id=} and {task_group_activity_id=}:\n"
+                        f"{task_group=}\n{activity=}. Exit."
+                    )
+                    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
+                try:
+                    fractal_ssh.check_connection()
+                except Exception as e:
+                    logger.error("Cannot establish SSH connection.")
+                    fail_and_cleanup(
+                        task_group=task_group,
+                        task_group_activity=activity,
+                        logger_name=LOGGER_NAME,
+                        log_file_path=log_file_path,
+                        exception=e,
+                        db=db,
+                    )
+                    return
+
+                # Check that the (remote) task_group path does not exist
+                if fractal_ssh.remote_exists(task_group.path):
+                    error_msg = f"{task_group.path} already exists."
+                    logger.error(error_msg)
+                    fail_and_cleanup(
+                        task_group=task_group,
+                        task_group_activity=activity,
+                        logger_name=LOGGER_NAME,
+                        log_file_path=log_file_path,
+                        exception=FileExistsError(error_msg),
+                        db=db,
+                    )
+                    return
+
+                try:
+                    # 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`)
+                    script_dir_remote = (
+                        Path(task_group.path) / SCRIPTS_SUBFOLDER
+                    ).as_posix()
+                    fractal_ssh.mkdir(folder=task_group.path, parents=True)
+                    fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
+
+                    # Write wheel file locally and send it to remote path,
+                    # and set task_group.wheel_path
+                    if wheel_file is not None:
+                        wheel_filename = wheel_file.filename
+                        wheel_path = (
+                            Path(task_group.path) / wheel_filename
+                        ).as_posix()
+                        tmp_wheel_path = (
+                            Path(tmpdir) / wheel_filename
+                        ).as_posix()
+                        logger.info(
+                            f"Write wheel-file contents into {tmp_wheel_path}"
+                        )
+                        with open(tmp_wheel_path, "wb") as f:
+                            f.write(wheel_file.contents)
+                        fractal_ssh.send_file(
+                            local=tmp_wheel_path,
+                            remote=wheel_path,
+                        )
+                        task_group.wheel_path = wheel_path
+                        task_group = add_commit_refresh(obj=task_group, db=db)
+
+                    replacements = get_collection_replacements(
+                        task_group=task_group,
+                        python_bin=get_python_interpreter_v2(
+                            python_version=task_group.python_version
+                        ),
+                    )
+
+                    # Prepare common arguments for _customize_and_run_template
+                    common_args = dict(
+                        replacements=replacements,
+                        script_dir_local=(
+                            Path(tmpdir) / SCRIPTS_SUBFOLDER
+                        ).as_posix(),
+                        script_dir_remote=script_dir_remote,
+                        prefix=(
+                            f"{int(time.time())}_"
+                            f"{TaskGroupActivityActionV2.COLLECT}"
+                        ),
+                        fractal_ssh=fractal_ssh,
+                        logger_name=LOGGER_NAME,
+                    )
+
+                    logger.info("installing - START")
+
+                    # Set status to ONGOING and refresh logs
+                    activity.status = TaskGroupActivityStatusV2.ONGOING
+                    activity.log = get_current_log(log_file_path)
+                    activity = add_commit_refresh(obj=activity, db=db)
+
+                    # Run script 1
+                    stdout = _customize_and_run_template(
+                        template_filename="1_create_venv.sh",
+                        **common_args,
+                    )
+                    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",
+                        **common_args,
+                    )
+                    activity.log = get_current_log(log_file_path)
+                    activity = add_commit_refresh(obj=activity, db=db)
 
-        with next(get_sync_db()) as db:
-            # Get main objects from db
-            activity = db.get(TaskGroupActivityV2, task_group_activity_id)
-            task_group = db.get(TaskGroupV2, task_group_id)
-            if activity is None or task_group is None:
-                # Use `logging` directly
-                logging.error(
-                    "Cannot find database rows with "
-                    f"{task_group_id=} and {task_group_activity_id=}:\n"
-                    f"{task_group=}\n{activity=}. Exit."
-                )
-                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
-            try:
-                fractal_ssh.check_connection()
-            except Exception as e:
-                logger.error("Cannot establish SSH connection.")
-                fail_and_cleanup(
-                    task_group=task_group,
-                    task_group_activity=activity,
-                    logger_name=LOGGER_NAME,
-                    log_file_path=log_file_path,
-                    exception=e,
-                    db=db,
-                )
-                return
-
-            # Check that the (remote) task_group path does not exist
-            if fractal_ssh.remote_exists(task_group.path):
-                error_msg = f"{task_group.path} already exists."
-                logger.error(error_msg)
-                fail_and_cleanup(
-                    task_group=task_group,
-                    task_group_activity=activity,
-                    logger_name=LOGGER_NAME,
-                    log_file_path=log_file_path,
-                    exception=FileExistsError(error_msg),
-                    db=db,
-                )
-                return
-
-            try:
-                # 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`)
-                script_dir_remote = (
-                    Path(task_group.path) / SCRIPTS_SUBFOLDER
-                ).as_posix()
-                fractal_ssh.mkdir(folder=task_group.path, parents=True)
-                fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
-
-                # Write wheel file locally and send it to remote path,
-                # and set task_group.wheel_path
-                if wheel_file is not None:
-                    wheel_filename = wheel_file.filename
-                    wheel_path = (
-                        Path(task_group.path) / wheel_filename
+                    # Run script 3
+                    pip_freeze_stdout = _customize_and_run_template(
+                        template_filename="3_pip_freeze.sh",
+                        **common_args,
+                    )
+                    activity.log = get_current_log(log_file_path)
+                    activity = add_commit_refresh(obj=activity, db=db)
+
+                    # Run script 4
+                    stdout = _customize_and_run_template(
+                        template_filename="4_pip_show.sh",
+                        **common_args,
+                    )
+                    activity.log = get_current_log(log_file_path)
+                    activity = add_commit_refresh(obj=activity, db=db)
+
+                    # Run script 5
+                    venv_info = _customize_and_run_template(
+                        template_filename="5_get_venv_size_and_file_number.sh",
+                        **common_args,
+                    )
+                    venv_size, venv_file_number = venv_info.split()
+                    activity.log = get_current_log(log_file_path)
+                    activity = add_commit_refresh(obj=activity, db=db)
+
+                    pkg_attrs = parse_script_pip_show_stdout(stdout)
+
+                    for key, value in pkg_attrs.items():
+                        logger.debug(f"parsed from pip-show: {key}={value}")
+                    # Check package_name match between pip show and task-group
+                    package_name_pip_show = pkg_attrs.get("package_name")
+                    package_name_task_group = task_group.pkg_name
+                    compare_package_names(
+                        pkg_name_pip_show=package_name_pip_show,
+                        pkg_name_task_group=package_name_task_group,
+                        logger_name=LOGGER_NAME,
+                    )
+                    # Extract/drop parsed attributes
+                    package_name = package_name_task_group
+                    python_bin = pkg_attrs.pop("python_bin")
+                    package_root_parent_remote = pkg_attrs.pop(
+                        "package_root_parent"
+                    )
+                    manifest_path_remote = pkg_attrs.pop("manifest_path")
+
+                    # TODO SSH: Use more robust logic to determine
+                    # `package_root`. Examples: use `importlib.util.find_spec`
+                    # or parse the output of `pip show --files {package_name}`.
+                    package_name_underscore = package_name.replace("-", "_")
+                    package_root_remote = (
+                        Path(package_root_parent_remote)
+                        / package_name_underscore
                     ).as_posix()
-                    tmp_wheel_path = (Path(tmpdir) / wheel_filename).as_posix()
+
+                    # Read and validate remote manifest file
+                    pkg_manifest_dict = fractal_ssh.read_remote_json_file(
+                        manifest_path_remote
+                    )
+                    logger.info(f"Loaded {manifest_path_remote=}")
+                    pkg_manifest = ManifestV2(**pkg_manifest_dict)
+                    logger.info("Manifest is a valid ManifestV2")
+
+                    logger.info("_prepare_tasks_metadata - start")
+                    task_list = _prepare_tasks_metadata(
+                        package_manifest=pkg_manifest,
+                        package_version=task_group.version,
+                        package_root=Path(package_root_remote),
+                        python_bin=Path(python_bin),
+                    )
+                    logger.info("_prepare_tasks_metadata - end")
+
                     logger.info(
-                        f"Write wheel-file contents into {tmp_wheel_path}"
+                        "create_db_tasks_and_update_task_group - " "start"
                     )
-                    with open(tmp_wheel_path, "wb") as f:
-                        f.write(wheel_file.contents)
-                    fractal_ssh.send_file(
-                        local=tmp_wheel_path,
-                        remote=wheel_path,
+                    create_db_tasks_and_update_task_group_sync(
+                        task_list=task_list,
+                        task_group_id=task_group.id,
+                        db=db,
                     )
-                    task_group.wheel_path = wheel_path
-                    task_group = add_commit_refresh(obj=task_group, db=db)
+                    logger.info("create_db_tasks_and_update_task_group - end")
 
-                replacements = get_collection_replacements(
-                    task_group=task_group,
-                    python_bin=get_python_interpreter_v2(
-                        python_version=task_group.python_version
-                    ),
-                )
-
-                # Prepare common arguments for `_customize_and_run_template``
-                common_args = dict(
-                    replacements=replacements,
-                    script_dir_local=(
-                        Path(tmpdir) / SCRIPTS_SUBFOLDER
-                    ).as_posix(),
-                    script_dir_remote=script_dir_remote,
-                    prefix=(
-                        f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.COLLECT.value}"
-                    ),
-                    fractal_ssh=fractal_ssh,
-                    logger_name=LOGGER_NAME,
-                )
-
-                logger.info("installing - START")
-
-                # Set status to ONGOING and refresh logs
-                activity.status = TaskGroupActivityStatusV2.ONGOING
-                activity.log = get_current_log(log_file_path)
-                activity = add_commit_refresh(obj=activity, db=db)
-
-                # Run script 1
-                stdout = _customize_and_run_template(
-                    template_filename="1_create_venv.sh",
-                    **common_args,
-                )
-                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",
-                    **common_args,
-                )
-                activity.log = get_current_log(log_file_path)
-                activity = add_commit_refresh(obj=activity, db=db)
-
-                # Run script 3
-                pip_freeze_stdout = _customize_and_run_template(
-                    template_filename="3_pip_freeze.sh",
-                    **common_args,
-                )
-                activity.log = get_current_log(log_file_path)
-                activity = add_commit_refresh(obj=activity, db=db)
-
-                # Run script 4
-                stdout = _customize_and_run_template(
-                    template_filename="4_pip_show.sh",
-                    **common_args,
-                )
-                activity.log = get_current_log(log_file_path)
-                activity = add_commit_refresh(obj=activity, db=db)
-
-                # Run script 5
-                venv_info = _customize_and_run_template(
-                    template_filename="5_get_venv_size_and_file_number.sh",
-                    **common_args,
-                )
-                venv_size, venv_file_number = venv_info.split()
-                activity.log = get_current_log(log_file_path)
-                activity = add_commit_refresh(obj=activity, db=db)
-
-                pkg_attrs = parse_script_pip_show_stdout(stdout)
-
-                for key, value in pkg_attrs.items():
-                    logger.debug(f"parsed from pip-show: {key}={value}")
-                # Check package_name match between pip show and task-group
-                package_name_pip_show = pkg_attrs.get("package_name")
-                package_name_task_group = task_group.pkg_name
-                compare_package_names(
-                    pkg_name_pip_show=package_name_pip_show,
-                    pkg_name_task_group=package_name_task_group,
-                    logger_name=LOGGER_NAME,
-                )
-                # Extract/drop parsed attributes
-                package_name = package_name_task_group
-                python_bin = pkg_attrs.pop("python_bin")
-                package_root_parent_remote = pkg_attrs.pop(
-                    "package_root_parent"
-                )
-                manifest_path_remote = pkg_attrs.pop("manifest_path")
-
-                # TODO SSH: Use more robust logic to determine `package_root`.
-                # Examples: use `importlib.util.find_spec`, or parse the output
-                # of `pip show --files {package_name}`.
-                package_name_underscore = package_name.replace("-", "_")
-                package_root_remote = (
-                    Path(package_root_parent_remote) / package_name_underscore
-                ).as_posix()
-
-                # Read and validate remote manifest file
-                pkg_manifest_dict = fractal_ssh.read_remote_json_file(
-                    manifest_path_remote
-                )
-                logger.info(f"Loaded {manifest_path_remote=}")
-                pkg_manifest = ManifestV2(**pkg_manifest_dict)
-                logger.info("Manifest is a valid ManifestV2")
-
-                logger.info("_prepare_tasks_metadata - start")
-                task_list = _prepare_tasks_metadata(
-                    package_manifest=pkg_manifest,
-                    package_version=task_group.version,
-                    package_root=Path(package_root_remote),
-                    python_bin=Path(python_bin),
-                )
-                logger.info("_prepare_tasks_metadata - end")
-
-                logger.info("create_db_tasks_and_update_task_group - " "start")
-                create_db_tasks_and_update_task_group_sync(
-                    task_list=task_list,
-                    task_group_id=task_group.id,
-                    db=db,
-                )
-                logger.info("create_db_tasks_and_update_task_group - end")
-
-                # Update task_group data
-                logger.info(
-                    "Add pip_freeze, venv_size and venv_file_number "
-                    "to TaskGroupV2 - start"
-                )
-                task_group.pip_freeze = pip_freeze_stdout
-                task_group.venv_size_in_kB = int(venv_size)
-                task_group.venv_file_number = int(venv_file_number)
-                task_group = add_commit_refresh(obj=task_group, db=db)
-                logger.info(
-                    "Add pip_freeze, venv_size and venv_file_number "
-                    "to TaskGroupV2 - end"
-                )
-
-                # Finalize (write metadata to DB)
-                logger.info("finalising - START")
-                activity.status = TaskGroupActivityStatusV2.OK
-                activity.timestamp_ended = get_timestamp()
-                activity = add_commit_refresh(obj=activity, db=db)
-                logger.info("finalising - END")
-                logger.info("END")
-                reset_logger_handlers(logger)
-
-            except Exception as collection_e:
-                # Delete corrupted package dir
-                try:
-                    logger.info(f"Now delete remote folder {task_group.path}")
-                    fractal_ssh.remove_folder(
-                        folder=task_group.path,
-                        safe_root=tasks_base_dir,
+                    # Update task_group data
+                    logger.info(
+                        "Add pip_freeze, venv_size and venv_file_number "
+                        "to TaskGroupV2 - start"
                     )
-                    logger.info(f"Deleted remoted folder {task_group.path}")
-                except Exception as e_rm:
-                    logger.error(
-                        "Removing folder failed. "
-                        f"Original error:\n{str(e_rm)}"
+                    task_group.pip_freeze = pip_freeze_stdout
+                    task_group.venv_size_in_kB = int(venv_size)
+                    task_group.venv_file_number = int(venv_file_number)
+                    task_group = add_commit_refresh(obj=task_group, db=db)
+                    logger.info(
+                        "Add pip_freeze, venv_size and venv_file_number "
+                        "to TaskGroupV2 - end"
+                    )
+
+                    # Finalize (write metadata to DB)
+                    logger.info("finalising - START")
+                    activity.status = TaskGroupActivityStatusV2.OK
+                    activity.timestamp_ended = get_timestamp()
+                    activity = add_commit_refresh(obj=activity, db=db)
+                    logger.info("finalising - END")
+                    logger.info("END")
+                    reset_logger_handlers(logger)
+
+                except Exception as collection_e:
+                    # Delete corrupted package dir
+                    try:
+                        logger.info(
+                            f"Now delete remote folder {task_group.path}"
+                        )
+                        fractal_ssh.remove_folder(
+                            folder=task_group.path,
+                            safe_root=tasks_base_dir,
+                        )
+                        logger.info(
+                            f"Deleted remoted folder {task_group.path}"
+                        )
+                    except Exception as e_rm:
+                        logger.error(
+                            "Removing folder failed. "
+                            f"Original error:\n{str(e_rm)}"
+                        )
+                    fail_and_cleanup(
+                        task_group=task_group,
+                        task_group_activity=activity,
+                        log_file_path=log_file_path,
+                        logger_name=LOGGER_NAME,
+                        exception=collection_e,
+                        db=db,
                     )
-                fail_and_cleanup(
-                    task_group=task_group,
-                    task_group_activity=activity,
-                    log_file_path=log_file_path,
-                    logger_name=LOGGER_NAME,
-                    exception=collection_e,
-                    db=db,
-                )
-    return