fractal-server 2.8.1__py3-none-any.whl → 2.9.0__py3-none-any.whl

fractal_server/tasks/v2/collection_ssh.py

@@ -1,352 +0,0 @@
-import os
-from pathlib import Path
-from tempfile import TemporaryDirectory
-
-from sqlalchemy.orm.attributes import flag_modified
-
-from .database_operations import create_db_tasks_and_update_task_group
-from .utils_background import _handle_failure
-from .utils_background import _prepare_tasks_metadata
-from .utils_background import _set_collection_state_data_status
-from fractal_server.app.db import get_sync_db
-from fractal_server.app.models.v2 import CollectionStateV2
-from fractal_server.app.models.v2 import TaskGroupV2
-from fractal_server.app.schemas.v2 import CollectionStatusV2
-from fractal_server.app.schemas.v2.manifest import ManifestV2
-from fractal_server.config import get_settings
-from fractal_server.logger import get_logger
-from fractal_server.logger import set_logger
-from fractal_server.ssh._fabric import FractalSSH
-from fractal_server.syringe import Inject
-from fractal_server.tasks.v2.utils_background import _refresh_logs
-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 customize_template
-from fractal_server.tasks.v2.utils_templates import parse_script_5_stdout
-
-
-def _customize_and_run_template(
-    *,
-    template_name: str,
-    replacements: list[tuple[str, str]],
-    script_dir: str,
-    logger_name: str,
-    fractal_ssh: FractalSSH,
-    tasks_base_dir: str,
-) -> str:
-    """
-    Customize one of the template bash scripts, transfer it to the remote host
-    via SFTP and then run it via SSH.
-
-    Args:
-        script_filename:
-        replacements:
-        tmpdir:
-        logger_name:
-        fractal_ssh:
-    """
-    logger = get_logger(logger_name)
-    logger.debug(f"_customize_and_run_template {template_name} - START")
-
-    script_path_local = Path(script_dir) / template_name
-
-    customize_template(
-        template_name=template_name,
-        replacements=replacements,
-        script_path=script_path_local,
-    )
-
-    # Transfer script to remote host
-    script_path_remote = os.path.join(
-        tasks_base_dir,
-        f"script_{abs(hash(script_dir))}{template_name}",
-    )
-    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"Standard output of '{cmd}':\n{stdout}")
-
-    logger.debug(f"_customize_and_run_template {template_name} - END")
-    return stdout
-
-
-def collect_package_ssh(
-    *,
-    state_id: int,
-    task_group: TaskGroupV2,
-    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 will run within a thread - due to
-    starlette/fastapi handling of background tasks (see
-    https://github.com/encode/starlette/blob/master/starlette/background.py).
-
-
-    Arguments:
-        state_id:
-        task_group:
-        fractal_ssh:
-        tasks_base_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,
-        )
-        logger.debug("START")
-        for key, value in task_group.model_dump().items():
-            logger.debug(f"task_group.{key}: {value}")
-
-        # `remove_venv_folder_upon_failure` is set to True only if
-        # script 1 goes through, which means that the remote folder
-        # `package_env_dir` did not already exist. If this remote
-        # folder already existed, then script 1 fails and the boolean
-        # flag `remove_venv_folder_upon_failure` remains false.
-        remove_venv_folder_upon_failure = False
-
-        # Open a DB session soon, since it is needed for updating `state`
-        with next(get_sync_db()) as db:
-            try:
-                # Prepare replacements for task-collection scripts
-                python_bin = get_python_interpreter_v2(
-                    python_version=task_group.python_version
-                )
-                install_string = task_group.pip_install_string
-                settings = Inject(get_settings)
-                replacements = [
-                    ("__PACKAGE_NAME__", task_group.pkg_name),
-                    ("__TASK_GROUP_DIR__", task_group.path),
-                    ("__PACKAGE_ENV_DIR__", task_group.venv_path),
-                    ("__PYTHON__", python_bin),
-                    ("__INSTALL_STRING__", install_string),
-                    (
-                        "__FRACTAL_MAX_PIP_VERSION__",
-                        settings.FRACTAL_MAX_PIP_VERSION,
-                    ),
-                    (
-                        "__PINNED_PACKAGE_LIST__",
-                        task_group.pinned_package_versions_string,
-                    ),
-                ]
-
-                common_args = dict(
-                    replacements=replacements,
-                    script_dir=tmpdir,
-                    logger_name=LOGGER_NAME,
-                    fractal_ssh=fractal_ssh,
-                    tasks_base_dir=tasks_base_dir,
-                )
-
-                fractal_ssh.check_connection()
-
-                logger.debug("installing - START")
-                _set_collection_state_data_status(
-                    state_id=state_id,
-                    new_status=CollectionStatusV2.INSTALLING,
-                    logger_name=LOGGER_NAME,
-                    db=db,
-                )
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-                db.close()
-                # Create remote folder (note that because of `parents=True` we
-                # are in the `no error if existing, make parent directories as
-                # needed` scenario)
-                fractal_ssh.mkdir(folder=tasks_base_dir, parents=True)
-
-                stdout = _customize_and_run_template(
-                    template_name="_1_create_venv.sh",
-                    **common_args,
-                )
-                remove_venv_folder_upon_failure = True
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-
-                stdout = _customize_and_run_template(
-                    template_name="_2_preliminary_pip_operations.sh",
-                    **common_args,
-                )
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-                stdout = _customize_and_run_template(
-                    template_name="_3_pip_install.sh",
-                    **common_args,
-                )
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-                stdout_pip_freeze = _customize_and_run_template(
-                    template_name="_4_pip_freeze.sh",
-                    **common_args,
-                )
-                logger.debug("installing - END")
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-                logger.debug("collecting - START")
-                _set_collection_state_data_status(
-                    state_id=state_id,
-                    new_status=CollectionStatusV2.COLLECTING,
-                    logger_name=LOGGER_NAME,
-                    db=db,
-                )
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-
-                stdout = _customize_and_run_template(
-                    template_name="_5_pip_show.sh",
-                    **common_args,
-                )
-                pkg_attrs = parse_script_5_stdout(stdout)
-                for key, value in pkg_attrs.items():
-                    logger.debug(
-                        f"collecting - 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,
-                )
-
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-
-                # 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")
-
-                # FIXME 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"collecting - loaded {manifest_path_remote=}")
-                pkg_manifest = ManifestV2(**pkg_manifest_dict)
-                logger.info("collecting - manifest is a valid ManifestV2")
-
-                logger.info("collecting - _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("collecting - _prepare_tasks_metadata - end")
-
-                logger.info(
-                    "collecting - 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(
-                    "collecting - create_db_tasks_and_update_task_group - end"
-                )
-
-                logger.debug("collecting - END")
-                _refresh_logs(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    db=db,
-                )
-
-                # Finalize (write metadata to DB)
-                logger.debug("finalising - START")
-
-                collection_state = db.get(CollectionStateV2, state_id)
-                collection_state.data["log"] = log_file_path.open("r").read()
-                collection_state.data["freeze"] = stdout_pip_freeze
-                collection_state.data["status"] = CollectionStatusV2.OK
-                flag_modified(collection_state, "data")
-                db.commit()
-                logger.debug("finalising - END")
-                logger.debug("END")
-
-            except Exception as collection_e:
-                # Delete corrupted package dir
-                if remove_venv_folder_upon_failure:
-                    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)}"
-                        )
-                else:
-                    logger.info(
-                        "Not trying to remove remote folder "
-                        f"{task_group.path}."
-                    )
-                _handle_failure(
-                    state_id=state_id,
-                    log_file_path=log_file_path,
-                    logger_name=LOGGER_NAME,
-                    exception=collection_e,
-                    db=db,
-                    task_group_id=task_group.id,
-                )
-    return

fractal_server/tasks/v2/templates/_1_create_venv.sh

@@ -1,42 +0,0 @@
-set -e
-
-write_log(){
-    TIMESTAMP=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
-    echo "[collect-task, $TIMESTAMP] $1"
-}
-
-
-# Variables to be filled within fractal-server
-TASK_GROUP_DIR=__TASK_GROUP_DIR__
-PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
-PYTHON=__PYTHON__
-
-TIME_START=$(date +%s)
-
-# Check that task-group and venv folders do not exist
-for DIR_TO_BE_CHECKED in "$TASK_GROUP_DIR" "$PACKAGE_ENV_DIR";
-do
-    if [ -d "$DIR_TO_BE_CHECKED" ]; then
-        write_log "ERROR: Folder $DIR_TO_BE_CHECKED already exists. Exit."
-        exit 1
-    fi
-done
-
-write_log "START mkdir -p $PACKAGE_ENV_DIR"
-mkdir -p $PACKAGE_ENV_DIR
-write_log "END   mkdir -p $PACKAGE_ENV_DIR"
-echo
-
-
-# Create venv
-write_log "START create venv in ${PACKAGE_ENV_DIR}"
-"$PYTHON" -m venv "$PACKAGE_ENV_DIR" --copies
-write_log "END   create venv in ${PACKAGE_ENV_DIR}"
-echo
-
-# End
-TIME_END=$(date +%s)
-write_log "All good up to here."
-write_log "Elapsed: $((TIME_END - TIME_START)) seconds"
-write_log "Exit."
-echo