fractal-server 1.4.10__py3-none-any.whl → 2.0.0__py3-none-any.whl

fractal_server/tasks/v2/background_operations.py

@@ -0,0 +1,381 @@
+"""
+The main function exported from this module is `background_collect_pip`, which
+is used as a background task for the task-collection endpoint.
+"""
+import json
+from pathlib import Path
+from shutil import rmtree as shell_rmtree
+
+from ..utils import _init_venv
+from ..utils import _normalize_package_name
+from ..utils import get_collection_log
+from ..utils import get_collection_path
+from ..utils import get_log_path
+from ..utils import slugify_task_name
+from ._TaskCollectPip import _TaskCollectPip
+from fractal_server.app.db import DBSyncSession
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models.v2 import CollectionStateV2
+from fractal_server.app.models.v2 import TaskV2
+from fractal_server.app.schemas.v2 import TaskCollectStatusV2
+from fractal_server.app.schemas.v2 import TaskCreateV2
+from fractal_server.app.schemas.v2 import TaskReadV2
+from fractal_server.logger import close_logger
+from fractal_server.logger import get_logger
+from fractal_server.logger import set_logger
+from fractal_server.utils import execute_command
+
+
+async def _pip_install(
+    venv_path: Path,
+    task_pkg: _TaskCollectPip,
+    logger_name: str,
+) -> Path:
+    """
+    Install package in venv
+
+    Args:
+        venv_path:
+        task_pkg:
+        logger_name:
+
+    Returns:
+        The location of the package.
+    """
+
+    logger = get_logger(logger_name)
+
+    pip = venv_path / "venv/bin/pip"
+
+    extras = f"[{task_pkg.package_extras}]" if task_pkg.package_extras else ""
+
+    if task_pkg.is_local_package:
+        pip_install_str = f"{task_pkg.package_path.as_posix()}{extras}"
+    else:
+        version_string = (
+            f"=={task_pkg.package_version}" if task_pkg.package_version else ""
+        )
+        pip_install_str = f"{task_pkg.package}{extras}{version_string}"
+
+    cmd_install = f"{pip} install {pip_install_str}"
+    cmd_inspect = f"{pip} show {task_pkg.package}"
+
+    await execute_command(
+        cwd=venv_path,
+        command=f"{pip} install --upgrade pip",
+        logger_name=logger_name,
+    )
+    await execute_command(
+        cwd=venv_path, command=cmd_install, logger_name=logger_name
+    )
+    if task_pkg.pinned_package_versions:
+        for (
+            pinned_pkg_name,
+            pinned_pkg_version,
+        ) in task_pkg.pinned_package_versions.items():
+
+            logger.debug(
+                "Specific version required: "
+                f"{pinned_pkg_name}=={pinned_pkg_version}"
+            )
+            logger.debug(
+                "Preliminary check: verify that "
+                f"{pinned_pkg_version} is already installed"
+            )
+            stdout_inspect = await execute_command(
+                cwd=venv_path,
+                command=f"{pip} show {pinned_pkg_name}",
+                logger_name=logger_name,
+            )
+            current_version = next(
+                line.split()[-1]
+                for line in stdout_inspect.split("\n")
+                if line.startswith("Version:")
+            )
+            if current_version != pinned_pkg_version:
+                logger.debug(
+                    f"Currently installed version of {pinned_pkg_name} "
+                    f"({current_version}) differs from pinned version "
+                    f"({pinned_pkg_version}); "
+                    f"install version {pinned_pkg_version}."
+                )
+                await execute_command(
+                    cwd=venv_path,
+                    command=(
+                        f"{pip} install "
+                        f"{pinned_pkg_name}=={pinned_pkg_version}"
+                    ),
+                    logger_name=logger_name,
+                )
+            else:
+                logger.debug(
+                    f"Currently installed version of {pinned_pkg_name} "
+                    f"({current_version}) already matches the pinned version."
+                )
+
+    # Extract package installation path from `pip show`
+    stdout_inspect = await execute_command(
+        cwd=venv_path, command=cmd_inspect, logger_name=logger_name
+    )
+
+    location = Path(
+        next(
+            line.split()[-1]
+            for line in stdout_inspect.split("\n")
+            if line.startswith("Location:")
+        )
+    )
+
+    # NOTE
+    # https://packaging.python.org/en/latest/specifications/recording-installed-packages/
+    # This directory is named as {name}-{version}.dist-info, with name and
+    # version fields corresponding to Core metadata specifications. Both
+    # fields must be normalized (see the name normalization specification and
+    # the version normalization specification), and replace dash (-)
+    # characters with underscore (_) characters, so the .dist-info directory
+    # always has exactly one dash (-) character in its stem, separating the
+    # name and version fields.
+    package_root = location / (task_pkg.package.replace("-", "_"))
+    logger.debug(f"[_pip install] {location=}")
+    logger.debug(f"[_pip install] {task_pkg.package=}")
+    logger.debug(f"[_pip install] {package_root=}")
+    if not package_root.exists():
+        raise RuntimeError(
+            "Could not determine package installation location."
+        )
+    return package_root
+
+
+async def _create_venv_install_package(
+    *,
+    task_pkg: _TaskCollectPip,
+    path: Path,
+    logger_name: str,
+) -> tuple[Path, Path]:
+    """Create venv and install package
+
+    Args:
+        path: the directory in which to create the environment
+        task_pkg: object containing the different metadata required to install
+            the package
+
+    Returns:
+        python_bin: path to venv's python interpreter
+        package_root: the location of the package manifest
+    """
+
+    # Normalize package name
+    task_pkg.package_name = _normalize_package_name(task_pkg.package_name)
+    task_pkg.package = _normalize_package_name(task_pkg.package)
+
+    python_bin = await _init_venv(
+        path=path,
+        python_version=task_pkg.python_version,
+        logger_name=logger_name,
+    )
+    package_root = await _pip_install(
+        venv_path=path, task_pkg=task_pkg, logger_name=logger_name
+    )
+    return python_bin, package_root
+
+
+async def create_package_environment_pip(
+    *,
+    task_pkg: _TaskCollectPip,
+    venv_path: Path,
+    logger_name: str,
+) -> list[TaskCreateV2]:
+    """
+    Create environment, install package, and prepare task list
+    """
+
+    logger = get_logger(logger_name)
+
+    # Normalize package name
+    task_pkg.package_name = _normalize_package_name(task_pkg.package_name)
+    task_pkg.package = _normalize_package_name(task_pkg.package)
+
+    # Only proceed if package, version and manifest attributes are set
+    task_pkg.check()
+
+    try:
+
+        logger.debug("Creating venv and installing package")
+        python_bin, package_root = await _create_venv_install_package(
+            path=venv_path,
+            task_pkg=task_pkg,
+            logger_name=logger_name,
+        )
+        logger.debug("Venv creation and package installation ended correctly.")
+
+        # Prepare task_list with appropriate metadata
+        logger.debug("Creating task list from manifest")
+        task_list = []
+        for t in task_pkg.package_manifest.task_list:
+            # Fill in attributes for TaskCreate
+            task_attributes = {}
+            task_attributes["version"] = task_pkg.package_version
+            task_name_slug = slugify_task_name(t.name)
+            task_attributes[
+                "source"
+            ] = f"{task_pkg.package_source}:{task_name_slug}"
+            # Executables
+            if t.executable_non_parallel is not None:
+                non_parallel_path = package_root / t.executable_non_parallel
+                if not non_parallel_path.exists():
+                    raise FileNotFoundError(
+                        f"Cannot find executable `{non_parallel_path}` "
+                        f"for task `{t.name}`"
+                    )
+                task_attributes[
+                    "command_non_parallel"
+                ] = f"{python_bin.as_posix()} {non_parallel_path.as_posix()}"
+            if t.executable_parallel is not None:
+                parallel_path = package_root / t.executable_parallel
+                if not parallel_path.exists():
+                    raise FileNotFoundError(
+                        f"Cannot find executable `{parallel_path}` "
+                        f"for task `{t.name}`"
+                    )
+                task_attributes[
+                    "command_parallel"
+                ] = f"{python_bin.as_posix()} {parallel_path.as_posix()}"
+
+            manifest = task_pkg.package_manifest
+            if manifest.has_args_schemas:
+                task_attributes[
+                    "args_schema_version"
+                ] = manifest.args_schema_version
+
+            this_task = TaskCreateV2(
+                **t.dict(
+                    exclude={"executable_non_parallel", "executable_parallel"}
+                ),
+                **task_attributes,
+            )
+            task_list.append(this_task)
+        logger.debug("Task list created correctly")
+    except Exception as e:
+        logger.error("Task manifest loading failed")
+        raise e
+    return task_list
+
+
+def _get_task_type(task: TaskCreateV2) -> str:
+    if task.command_non_parallel is None:
+        return "parallel"
+    elif task.command_parallel is None:
+        return "non_parallel"
+    else:
+        return "compound"
+
+
+async def _insert_tasks(
+    task_list: list[TaskCreateV2],
+    db: DBSyncSession,
+) -> list[TaskV2]:
+    """
+    Insert tasks into database
+    """
+
+    task_db_list = [
+        TaskV2(**t.dict(), type=_get_task_type(t)) for t in task_list
+    ]
+    db.add_all(task_db_list)
+    db.commit()
+    for t in task_db_list:
+        db.refresh(t)
+    db.close()
+    return task_db_list
+
+
+async def background_collect_pip(
+    state_id: int,
+    venv_path: Path,
+    task_pkg: _TaskCollectPip,
+) -> None:
+    """
+    Install package and collect tasks
+
+    Install a python package and collect the tasks it provides according to
+    the manifest.
+
+    In case of error, copy the log into the state and delete the package
+    directory.
+    """
+    logger_name = task_pkg.package.replace("/", "_")
+    logger = set_logger(
+        logger_name=logger_name,
+        log_file_path=get_log_path(venv_path),
+    )
+    logger.debug("Start background task collection")
+    for key, value in task_pkg.dict(exclude={"package_manifest"}).items():
+        logger.debug(f"{key}: {value}")
+
+    with next(get_sync_db()) as db:
+        state: CollectionStateV2 = db.get(CollectionStateV2, state_id)
+        data = TaskCollectStatusV2(**state.data)
+        data.info = None
+
+        try:
+            # install
+            logger.debug("Task-collection status: installing")
+            data.status = "installing"
+
+            state.data = data.sanitised_dict()
+            db.merge(state)
+            db.commit()
+            task_list = await create_package_environment_pip(
+                venv_path=venv_path,
+                task_pkg=task_pkg,
+                logger_name=logger_name,
+            )
+
+            # collect
+            logger.debug("Task-collection status: collecting")
+            data.status = "collecting"
+            state.data = data.sanitised_dict()
+            db.merge(state)
+            db.commit()
+            tasks = await _insert_tasks(task_list=task_list, db=db)
+
+            # finalise
+            logger.debug("Task-collection status: finalising")
+            collection_path = get_collection_path(venv_path)
+            data.task_list = [
+                TaskReadV2(**task.model_dump()) for task in tasks
+            ]
+            with collection_path.open("w") as f:
+                json.dump(data.sanitised_dict(), f, indent=2)
+
+            # Update DB
+            data.status = "OK"
+            data.log = get_collection_log(venv_path)
+            state.data = data.sanitised_dict()
+            db.merge(state)
+            db.commit()
+
+            # Write last logs to file
+            logger.debug("Task-collection status: OK")
+            logger.info("Background task collection completed successfully")
+            close_logger(logger)
+            db.close()
+
+        except Exception as e:
+            # Write last logs to file
+            logger.debug("Task-collection status: fail")
+            logger.info(f"Background collection failed. Original error: {e}")
+            close_logger(logger)
+
+            # Update db
+            data.status = "fail"
+            data.info = f"Original error: {e}"
+            data.log = get_collection_log(venv_path)
+            state.data = data.sanitised_dict()
+            db.merge(state)
+            db.commit()
+            db.close()
+
+            # Delete corrupted package dir
+            logger.info(f"Now deleting temporary folder {venv_path}")
+            shell_rmtree(venv_path)

fractal_server/tasks/v2/get_collection_data.py

@@ -0,0 +1,14 @@
+import json
+from pathlib import Path
+
+from fractal_server.app.schemas.v2 import TaskCollectStatusV2
+from fractal_server.tasks.utils import get_absolute_venv_path
+from fractal_server.tasks.utils import get_collection_path
+
+
+def get_collection_data(venv_path: Path) -> TaskCollectStatusV2:
+    package_path = get_absolute_venv_path(venv_path)
+    collection_path = get_collection_path(package_path)
+    with collection_path.open() as f:
+        data = json.load(f)
+    return TaskCollectStatusV2(**data)

fractal_server/urls.py

@@ -0,0 +1,13 @@
+from os.path import normpath
+
+
+def normalize_url(url: str) -> str:
+    if url.startswith("/"):
+        return normpath(url)
+    elif url.startswith("s3"):
+        # It would be better to have a NotImplementedError
+        # but Pydantic Validation + FastAPI require
+        # ValueError, TypeError or AssertionError
+        raise ValueError("S3 handling not implemented yet")
+    else:
+        raise ValueError("URLs must begin with '/' or 's3'.")

{fractal_server-1.4.10.dist-info → fractal_server-2.0.0.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 1.4.10
+Version: 2.0.0
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
-Author: Jacopo Nespolo
-Author-email: jacopo.nespolo@exact-lab.it
+Author: Tommaso Comparin
+Author-email: tommaso.comparin@exact-lab.it
 Requires-Python: >=3.9,<4.0
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
@@ -16,21 +16,21 @@ Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: gunicorn
 Provides-Extra: postgres
 Requires-Dist: aiosqlite (>=0.19.0,<0.20.0)
-Requires-Dist: alembic (>=1.9.1,<2.0.0)
+Requires-Dist: alembic (>=1.13.1,<2.0.0)
 Requires-Dist: asyncpg (>=0.29.0,<0.30.0) ; extra == "postgres"
 Requires-Dist: bcrypt (==4.0.1)
-Requires-Dist: cloudpickle (>=2.2.1,<2.3.0)
+Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)
 Requires-Dist: clusterfutures (>=0.5,<0.6)
-Requires-Dist: fastapi (>=0.109.0,<0.110.0)
+Requires-Dist: fastapi (>=0.110.0,<0.111.0)
 Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
-Requires-Dist: gunicorn (>=21.2.0,<22.0.0) ; extra == "gunicorn"
+Requires-Dist: gunicorn (>=21.2,<23.0) ; extra == "gunicorn"
 Requires-Dist: packaging (>=23.2,<24.0)
 Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
 Requires-Dist: pydantic (>=1.10.8,<2)
-Requires-Dist: python-dotenv (>=0.21.0,<0.22.0)
+Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
-Requires-Dist: sqlmodel (>=0.0.14,<0.0.15)
-Requires-Dist: uvicorn (>=0.27.0,<0.28.0)
+Requires-Dist: sqlmodel (>=0.0.16,<0.0.17)
+Requires-Dist: uvicorn (>=0.29.0,<0.30.0)
 Project-URL: Changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md
 Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server
 Project-URL: Repository, https://github.com/fractal-analytics-platform/fractal-server

fractal_server-2.0.0.dist-info/RECORD

@@ -0,0 +1,169 @@
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+fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
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+fractal_server/app/models/__init__.py,sha256=FRRDJkx7LgPaUqSp8IV7qevu_VE2dt0-fQtQruHFaVo,267
+fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
+fractal_server/app/models/security.py,sha256=UG9wCVA5GRSyHrYEFhH8lIF1hXykxsr9LSi8_dFToMY,3378
+fractal_server/app/models/v1/__init__.py,sha256=qUlUGnWFaIm3aBXfUuLdhcW9f_s1VzAEuypr31zvHGo,458
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