fractal-server 2.8.0__py3-none-any.whl → 2.9.0__py3-none-any.whl

fractal_server/tasks/v2/ssh/_utils.py

@@ -0,0 +1,87 @@
+import os
+from pathlib import Path
+
+from fractal_server.app.models.v2 import TaskGroupV2
+from fractal_server.logger import get_logger
+from fractal_server.ssh._fabric import FractalSSH
+from fractal_server.tasks.v2.utils_templates import customize_template
+
+
+def _customize_and_run_template(
+    *,
+    template_filename: str,
+    replacements: list[tuple[str, str]],
+    script_dir_local: str,
+    prefix: str,
+    fractal_ssh: FractalSSH,
+    script_dir_remote: str,
+    logger_name: str,
+) -> str:
+    """
+    Customize one of the template bash scripts, transfer it to the remote host
+    via SFTP and then run it via SSH.
+
+    Args:
+        template_filename: Filename of the template file (ends with ".sh").
+        replacements: Dictionary of replacements.
+        script_dir: Local folder where the script will be placed.
+        prefix: Prefix for the script filename.
+        fractal_ssh: FractalSSH object
+        script_dir_remote: Remote scripts directory
+    """
+    logger = get_logger(logger_name=logger_name)
+    logger.debug(f"_customize_and_run_template {template_filename} - START")
+    # Prepare name and path of script
+    if not template_filename.endswith(".sh"):
+        raise ValueError(
+            f"Invalid {template_filename=} (it must end with '.sh')."
+        )
+    script_filename = f"{prefix}_{template_filename}"
+    script_path_local = (Path(script_dir_local) / script_filename).as_posix()
+
+    customize_template(
+        template_name=template_filename,
+        replacements=replacements,
+        script_path=script_path_local,
+    )
+
+    # Transfer script to remote host
+    script_path_remote = os.path.join(
+        script_dir_remote,
+        script_filename,
+    )
+    logger.debug(f"Now transfer {script_path_local=} over SSH.")
+    fractal_ssh.send_file(
+        local=script_path_local,
+        remote=script_path_remote,
+    )
+
+    # Execute script remotely
+    cmd = f"bash {script_path_remote}"
+    logger.debug(f"Now run '{cmd}' over SSH.")
+    stdout = fractal_ssh.run_command(cmd=cmd)
+
+    logger.debug(f"_customize_and_run_template {template_filename} - END")
+    return stdout
+
+
+def _copy_wheel_file_ssh(
+    *, task_group: TaskGroupV2, fractal_ssh: FractalSSH, logger_name: str
+) -> str:
+    """
+    Handle the situation where `task_group.wheel_path` is not part of
+    `task_group.path`, by copying `wheel_path` into `path`.
+
+    Returns:
+        The new `wheel_path`.
+    """
+    logger = get_logger(logger_name=logger_name)
+    source = task_group.wheel_path
+    dest = (
+        Path(task_group.path) / Path(task_group.wheel_path).name
+    ).as_posix()
+    cmd = f"cp {source} {dest}"
+    logger.debug(f"[_copy_wheel_file] START {source=} {dest=}")
+    fractal_ssh.run_command(cmd=cmd)
+    logger.debug(f"[_copy_wheel_file] END {source=} {dest=}")
+    return dest

fractal_server/tasks/v2/ssh/collect.py

@@ -0,0 +1,311 @@
+import logging
+import time
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+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
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models.v2 import TaskGroupActivityV2
+from fractal_server.app.models.v2 import TaskGroupV2
+from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
+from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
+from fractal_server.app.schemas.v2.manifest import ManifestV2
+from fractal_server.logger import set_logger
+from fractal_server.ssh._fabric import FractalSSH
+from fractal_server.tasks.v2.ssh._utils import _copy_wheel_file_ssh
+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
+from fractal_server.tasks.v2.utils_package_names import compare_package_names
+from fractal_server.tasks.v2.utils_python_interpreter import (
+    get_python_interpreter_v2,
+)
+from fractal_server.tasks.v2.utils_templates import get_collection_replacements
+from fractal_server.tasks.v2.utils_templates import (
+    parse_script_pip_show_stdout,
+)
+from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
+from fractal_server.utils import get_timestamp
+
+LOGGER_NAME = __name__
+
+
+def collect_ssh(
+    *,
+    task_group_id: int,
+    task_group_activity_id: int,
+    fractal_ssh: FractalSSH,
+    tasks_base_dir: str,
+) -> None:
+    """
+    Collect a task package over SSH
+
+    This function is run as a background task, therefore exceptions must be
+    handled.
+
+    NOTE: by making this function sync, it runs within a thread - due to
+    starlette/fastapi handling of background tasks (see
+    https://github.com/encode/starlette/blob/master/starlette/background.py).
+
+
+    Arguments:
+        task_group_id:
+        task_group_activity_id:
+        fractal_ssh:
+        tasks_base_dir:
+            Only used as a `safe_root` in `remove_dir`, and typically set to
+            `user_settings.ssh_tasks_dir`.
+    """
+
+    # 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 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.debug("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:
+
+                # Prepare replacements for templates
+                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``
+                script_dir_remote = (
+                    Path(task_group.path) / SCRIPTS_SUBFOLDER
+                ).as_posix()
+                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,
+                )
+
+                # 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`)
+                fractal_ssh.mkdir(folder=task_group.path, parents=True)
+                fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
+
+                # Copy wheel file into task group path
+                if task_group.wheel_path:
+                    new_wheel_path = _copy_wheel_file_ssh(
+                        task_group=task_group,
+                        fractal_ssh=fractal_ssh,
+                        logger_name=LOGGER_NAME,
+                    )
+                    task_group.wheel_path = new_wheel_path
+                    task_group = add_commit_refresh(obj=task_group, db=db)
+
+                logger.debug("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(
+                    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.debug("finalising - START")
+                activity.status = TaskGroupActivityStatusV2.OK
+                activity.timestamp_ended = get_timestamp()
+                activity = add_commit_refresh(obj=activity, db=db)
+                logger.debug("finalising - END")
+                logger.debug("END")
+
+                logger.debug("END")
+
+            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,
+                )
+    return

fractal_server/tasks/v2/ssh/deactivate.py

@@ -0,0 +1,253 @@
+import logging
+import time
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+from ..utils_background import add_commit_refresh
+from ..utils_background import fail_and_cleanup
+from ..utils_templates import get_collection_replacements
+from ._utils import _copy_wheel_file_ssh
+from ._utils import _customize_and_run_template
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models.v2 import TaskGroupActivityV2
+from fractal_server.app.models.v2 import TaskGroupV2
+from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
+from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
+from fractal_server.logger import set_logger
+from fractal_server.ssh._fabric import FractalSSH
+from fractal_server.tasks.utils import get_log_path
+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 get_timestamp
+
+LOGGER_NAME = __name__
+
+
+def deactivate_ssh(
+    *,
+    task_group_activity_id: int,
+    task_group_id: int,
+    fractal_ssh: FractalSSH,
+    tasks_base_dir: str,
+) -> None:
+    """
+    Deactivate a task group venv.
+
+    This function is run as a background task, therefore exceptions must be
+    handled.
+
+    Arguments:
+        task_group_id:
+        task_group_activity_id:
+        fractal_ssh:
+        tasks_base_dir:
+            Only used as a `safe_root` in `remove_dir`, and typically set to
+            `user_settings.ssh_tasks_dir`.
+    """
+
+    with TemporaryDirectory() as tmpdir:
+        log_file_path = get_log_path(Path(tmpdir))
+        logger = set_logger(
+            logger_name=LOGGER_NAME,
+            log_file_path=log_file_path,
+        )
+
+        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.debug("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 (local) task_group venv_path does exist
+            if not fractal_ssh.remote_exists(task_group.venv_path):
+                error_msg = f"{task_group.venv_path} does not exist."
+                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=FileNotFoundError(error_msg),
+                    db=db,
+                )
+                return
+
+            try:
+
+                activity.status = TaskGroupActivityStatusV2.ONGOING
+                activity = add_commit_refresh(obj=activity, db=db)
+
+                if task_group.pip_freeze is None:
+                    logger.warning(
+                        "Recreate pip-freeze information, since "
+                        f"{task_group.pip_freeze=}. NOTE: this should only "
+                        "happen for task groups created before 2.9.0."
+                    )
+
+                    # Prepare replacements for templates
+                    replacements = get_collection_replacements(
+                        task_group=task_group,
+                        python_bin="/not/applicable",
+                    )
+
+                    # Define script_dir_remote and create it if missing
+                    script_dir_remote = (
+                        Path(task_group.path) / SCRIPTS_SUBFOLDER
+                    ).as_posix()
+                    fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
+
+                    # Prepare 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.DEACTIVATE}"
+                        ),
+                        fractal_ssh=fractal_ssh,
+                        logger_name=LOGGER_NAME,
+                    )
+
+                    # Run `pip freeze`
+                    pip_freeze_stdout = _customize_and_run_template(
+                        template_filename="3_pip_freeze.sh",
+                        **common_args,
+                    )
+
+                    # Update pip-freeze data
+                    logger.info("Add pip freeze stdout to TaskGroupV2 - start")
+                    activity.log = get_current_log(log_file_path)
+                    activity = add_commit_refresh(obj=activity, db=db)
+                    task_group.pip_freeze = pip_freeze_stdout
+                    task_group = add_commit_refresh(obj=task_group, db=db)
+                    logger.info("Add pip freeze stdout to TaskGroupV2 - end")
+
+                # Handle some specific cases for wheel-file case
+                if task_group.origin == TaskGroupV2OriginEnum.WHEELFILE:
+
+                    logger.info(
+                        f"Handle specific cases for {task_group.origin=}."
+                    )
+
+                    # Blocking situation: `wheel_path` is not set or points
+                    # to a missing path
+                    if (
+                        task_group.wheel_path is None
+                        or not fractal_ssh.remote_exists(task_group.wheel_path)
+                    ):
+                        error_msg = (
+                            "Invalid wheel path for task group with "
+                            f"{task_group_id=}. {task_group.wheel_path=} is "
+                            "unset or does not exist."
+                        )
+                        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=FileNotFoundError(error_msg),
+                            db=db,
+                        )
+                        return
+
+                    # Recoverable situation: `wheel_path` was not yet copied
+                    # over to the correct server-side folder
+                    wheel_path_parent_dir = Path(task_group.wheel_path).parent
+                    if wheel_path_parent_dir != Path(task_group.path):
+                        logger.warning(
+                            f"{wheel_path_parent_dir.as_posix()} differs from "
+                            f"{task_group.path}. NOTE: this should only "
+                            "happen for task groups created before 2.9.0."
+                        )
+
+                        if task_group.wheel_path not in task_group.pip_freeze:
+                            raise ValueError(
+                                f"Cannot find {task_group.wheel_path=} in "
+                                "pip-freeze data. Exit."
+                            )
+
+                        logger.info(
+                            f"Now copy wheel file into {task_group.path}."
+                        )
+                        new_wheel_path = _copy_wheel_file_ssh(
+                            task_group=task_group,
+                            fractal_ssh=fractal_ssh,
+                            logger_name=LOGGER_NAME,
+                        )
+                        logger.info(f"Copied wheel file to {new_wheel_path}.")
+
+                        task_group.wheel_path = new_wheel_path
+                        new_pip_freeze = task_group.pip_freeze.replace(
+                            task_group.wheel_path,
+                            new_wheel_path,
+                        )
+                        task_group.pip_freeze = new_pip_freeze
+                        task_group = add_commit_refresh(obj=task_group, db=db)
+                        logger.info(
+                            "Updated `wheel_path` and `pip_freeze` "
+                            "task-group attributes."
+                        )
+
+                # We now have all required information for reactivating the
+                # virtual environment at a later point
+
+                # Actually mark the task group as non-active
+                logger.info("Now setting `active=False`.")
+                task_group.active = False
+                task_group = add_commit_refresh(obj=task_group, db=db)
+
+                # Proceed with deactivation
+                logger.info(f"Now removing {task_group.venv_path}.")
+                fractal_ssh.remove_folder(
+                    folder=task_group.venv_path,
+                    safe_root=tasks_base_dir,
+                )
+                logger.info(f"All good, {task_group.venv_path} removed.")
+                activity.status = TaskGroupActivityStatusV2.OK
+                activity.log = get_current_log(log_file_path)
+                activity.timestamp_ended = get_timestamp()
+                activity = add_commit_refresh(obj=activity, db=db)
+
+            except Exception as e:
+                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