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320 | def collect_ssh(
*,
task_group_id: int,
task_group_activity_id: int,
fractal_ssh: FractalSSH,
tasks_base_dir: str,
wheel_file: Optional[WheelFile] = None,
) -> None:
"""
Collect a task package over SSH
This function runs as a background task, therefore exceptions must be
handled.
NOTE: since this function is 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`.
wheel_file:
"""
# 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:
# 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.debug(
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.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
|