fractal-server 2.7.1__py3-none-any.whl → 2.8.1__py3-none-any.whl

fractal_server/tasks/v1/utils.py

@@ -2,7 +2,7 @@ from pathlib import Path
 from typing import Optional
 
 from fractal_server.logger import get_logger
-from fractal_server.utils import execute_command
+from fractal_server.utils import execute_command_async
 
 
 def get_python_interpreter_v1(version: Optional[str] = None) -> str:
@@ -57,7 +57,7 @@ async def _init_venv_v1(
     logger.debug(f"[_init_venv] {path=}")
     interpreter = get_python_interpreter_v1(version=python_version)
     logger.debug(f"[_init_venv] {interpreter=}")
-    await execute_command(
+    await execute_command_async(
         cwd=path,
         command=f"{interpreter} -m venv venv",
         logger_name=logger_name,

fractal_server/tasks/v2/collection_local.py

@@ -0,0 +1,357 @@
+import json
+import shutil
+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 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 import TaskReadV2
+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.syringe import Inject
+from fractal_server.tasks.utils import get_log_path
+from fractal_server.tasks.v2.utils_background import _handle_failure
+from fractal_server.tasks.v2.utils_background import _prepare_tasks_metadata
+from fractal_server.tasks.v2.utils_background import _refresh_logs
+from fractal_server.tasks.v2.utils_background import (
+    _set_collection_state_data_status,
+)
+from fractal_server.tasks.v2.utils_background import check_task_files_exist
+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
+from fractal_server.utils import execute_command_sync
+
+
+def _customize_and_run_template(
+    script_filename: str,
+    replacements: list[tuple[str, str]],
+    script_dir: str,
+    logger_name: str,
+) -> str:
+    """
+    Customize one of the template bash scripts.
+
+    Args:
+        script_filename:
+        replacements:
+        script_dir:
+        logger_name:
+    """
+    logger = get_logger(logger_name)
+    logger.debug(f"_customize_and_run_template {script_filename} - START")
+
+    script_path_local = Path(script_dir) / script_filename
+    # Read template
+    customize_template(
+        template_name=script_filename,
+        replacements=replacements,
+        script_path=script_path_local,
+    )
+
+    cmd = f"bash {script_path_local}"
+    logger.debug(f"Now run '{cmd}' ")
+
+    stdout = execute_command_sync(command=cmd)
+
+    logger.debug(f"Standard output of '{cmd}':\n{stdout}")
+    logger.debug(f"_customize_and_run_template {script_filename} - END")
+
+    return stdout
+
+
+def collect_package_local(
+    *,
+    state_id: int,
+    task_group: TaskGroupV2,
+) -> None:
+    """
+    Collect a task package.
+
+    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:
+    """
+
+    # Create the task_group path
+    with TemporaryDirectory() as tmpdir:
+
+        # Setup logger in tmpdir
+        LOGGER_NAME = "task_collection_local"
+        log_file_path = get_log_path(Path(tmpdir))
+        logger = set_logger(
+            logger_name=LOGGER_NAME,
+            log_file_path=log_file_path,
+        )
+
+        # Log some info
+        logger.debug("START")
+        for key, value in task_group.model_dump().items():
+            logger.debug(f"task_group.{key}: {value}")
+
+        # Open a DB session
+        with next(get_sync_db()) as db:
+
+            # Check that the task_group path does not exist
+            if Path(task_group.path).exists():
+                error_msg = f"{task_group.path} already exists."
+                logger.error(error_msg)
+                _handle_failure(
+                    state_id=state_id,
+                    logger_name=LOGGER_NAME,
+                    log_file_path=log_file_path,
+                    exception=FileExistsError(error_msg),
+                    db=db,
+                    task_group_id=task_group.id,
+                )
+                return
+
+            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=task_group.path,
+                    logger_name=LOGGER_NAME,
+                )
+
+                logger.debug("installing - START")
+                _set_collection_state_data_status(
+                    state_id=state_id,
+                    new_status=CollectionStatusV2.INSTALLING,
+                    logger_name=LOGGER_NAME,
+                    db=db,
+                )
+
+                # Create main path for task group
+                Path(task_group.path).mkdir(parents=True)
+                logger.debug(f"Created {task_group.path}")
+
+                # Create venv
+                logger.debug(
+                    (f"START - Create python venv {task_group.venv_path}")
+                )
+                cmd = (
+                    f"python{task_group.python_version} -m venv "
+                    f"{task_group.venv_path} --copies"
+                )
+                stdout = execute_command_sync(command=cmd)
+                logger.debug(
+                    (f"END - Create python venv folder {task_group.venv_path}")
+                )
+                _refresh_logs(
+                    state_id=state_id,
+                    log_file_path=log_file_path,
+                    db=db,
+                )
+                # Close db connections before long pip related operations
+                # Warning this expunge all ORM objects.
+                # https://docs.sqlalchemy.org/en/20/orm/session_api.html#sqlalchemy.orm.Session.close
+                db.close()
+
+                stdout = _customize_and_run_template(
+                    script_filename="_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(
+                    script_filename="_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(
+                    script_filename="_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(
+                    script_filename="_5_pip_show.sh",
+                    **common_args,
+                )
+                _refresh_logs(
+                    state_id=state_id,
+                    log_file_path=log_file_path,
+                    db=db,
+                )
+
+                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,
+                )
+                # Extract/drop parsed attributes
+                package_name = package_name_task_group
+                python_bin = pkg_attrs.pop("python_bin")
+                package_root_parent = pkg_attrs.pop("package_root_parent")
+
+                # TODO : 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 = (
+                    Path(package_root_parent) / package_name_underscore
+                ).as_posix()
+
+                # Read and validate manifest file
+                manifest_path = pkg_attrs.pop("manifest_path")
+                logger.info(f"collecting - now loading {manifest_path=}")
+                with open(manifest_path) as json_data:
+                    pkg_manifest_dict = json.load(json_data)
+                logger.info(f"collecting - loaded {manifest_path=}")
+                logger.info("collecting - now validating manifest content")
+                pkg_manifest = ManifestV2(**pkg_manifest_dict)
+                logger.info("collecting - validated manifest content")
+                _refresh_logs(
+                    state_id=state_id,
+                    log_file_path=log_file_path,
+                    db=db,
+                )
+
+                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),
+                    python_bin=Path(python_bin),
+                )
+                check_task_files_exist(task_list=task_list)
+                logger.info("collecting - _prepare_tasks_metadata - end")
+                _refresh_logs(
+                    state_id=state_id,
+                    log_file_path=log_file_path,
+                    db=db,
+                )
+
+                logger.info(
+                    "collecting - create_db_tasks_and_update_task_group - "
+                    "start"
+                )
+                task_group = 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")
+
+                # Finalize (write metadata to DB)
+                logger.debug("finalising - START")
+
+                _refresh_logs(
+                    state_id=state_id,
+                    log_file_path=log_file_path,
+                    db=db,
+                )
+                collection_state = db.get(CollectionStateV2, state_id)
+                collection_state.data["freeze"] = stdout_pip_freeze
+                collection_state.data["status"] = CollectionStatusV2.OK
+                # FIXME: The `task_list` key is likely not used by any client,
+                # we should consider dropping it
+                task_read_list = [
+                    TaskReadV2(**task.model_dump()).dict()
+                    for task in task_group.task_list
+                ]
+                collection_state.data["task_list"] = task_read_list
+                flag_modified(collection_state, "data")
+                db.commit()
+                logger.debug("finalising - END")
+                logger.debug("END")
+
+            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)}"
+                    )
+
+                _handle_failure(
+                    state_id=state_id,
+                    logger_name=LOGGER_NAME,
+                    log_file_path=log_file_path,
+                    exception=collection_e,
+                    db=db,
+                    task_group_id=task_group.id,
+                )
+    return