fractal-server 2.17.2__py3-none-any.whl → 2.18.0__py3-none-any.whl

fractal_server/tasks/v2/ssh/reactivate_pixi.py

@@ -5,8 +5,8 @@ from tempfile import TemporaryDirectory
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.models import Profile
 from fractal_server.app.models import Resource
-from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
-from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
+from fractal_server.app.schemas.v2 import TaskGroupActivityAction
+from fractal_server.app.schemas.v2 import TaskGroupActivityStatus
 from fractal_server.logger import reset_logger_handlers
 from fractal_server.logger import set_logger
 from fractal_server.ssh._fabric import SingleUseFractalSSH
@@ -150,7 +150,7 @@ def reactivate_ssh_pixi(
                     logger.info("installing - START")
 
                     # Set status to ONGOING and refresh logs
-                    activity.status = TaskGroupActivityStatusV2.ONGOING
+                    activity.status = TaskGroupActivityStatus.ONGOING
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
@@ -164,7 +164,7 @@ def reactivate_ssh_pixi(
                         script_dir_remote=script_dir_remote,
                         prefix=(
                             f"{int(time.time())}_"
-                            f"{TaskGroupActivityActionV2.REACTIVATE}"
+                            f"{TaskGroupActivityAction.REACTIVATE}"
                         ),
                         logger_name=LOGGER_NAME,
                         fractal_ssh=fractal_ssh,
@@ -247,7 +247,7 @@ def reactivate_ssh_pixi(
                     activity = add_commit_refresh(obj=activity, db=db)
 
                     # Finalize (write metadata to DB)
-                    activity.status = TaskGroupActivityStatusV2.OK
+                    activity.status = TaskGroupActivityStatus.OK
                     activity.timestamp_ended = get_timestamp()
                     activity = add_commit_refresh(obj=activity, db=db)
                     task_group.active = True

fractal_server/tasks/v2/utils_background.py

@@ -6,10 +6,10 @@ from sqlalchemy.orm import Session as DBSyncSession
 
 from fractal_server.app.models.v2 import TaskGroupActivityV2
 from fractal_server.app.models.v2 import TaskGroupV2
-from fractal_server.app.schemas.v2 import TaskCreateV2
-from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
+from fractal_server.app.schemas.v2 import TaskCreate
+from fractal_server.app.schemas.v2 import TaskGroupActivityStatus
 from fractal_server.app.schemas.v2.manifest import ManifestV2
-from fractal_server.app.schemas.v2.task_group import TaskGroupActivityActionV2
+from fractal_server.app.schemas.v2.task_group import TaskGroupActivityAction
 from fractal_server.exceptions import UnreachableBranchError
 from fractal_server.logger import get_logger
 from fractal_server.logger import reset_logger_handlers
@@ -66,11 +66,11 @@ def fail_and_cleanup(
         f"Original error: {str(exception)}"
     )
 
-    task_group_activity.status = TaskGroupActivityStatusV2.FAILED
+    task_group_activity.status = TaskGroupActivityStatus.FAILED
     task_group_activity.timestamp_ended = get_timestamp()
     task_group_activity.log = get_current_log(log_file_path)
     task_group_activity = add_commit_refresh(obj=task_group_activity, db=db)
-    if task_group_activity.action == TaskGroupActivityActionV2.COLLECT:
+    if task_group_activity.action == TaskGroupActivityAction.COLLECT:
         db.delete(task_group)
     db.commit()
     reset_logger_handlers(logger)
@@ -83,7 +83,7 @@ def prepare_tasks_metadata(
     python_bin: Path | None = None,
     project_python_wrapper: Path | None = None,
     package_version: str | None = None,
-) -> list[TaskCreateV2]:
+) -> list[TaskCreate]:
     """
     Based on the package manifest and additional info, prepare the task list.
 
@@ -129,7 +129,7 @@ def prepare_tasks_metadata(
             )
             task_attributes["command_parallel"] = cmd_parallel
         # Create object
-        task_obj = TaskCreateV2(
+        task_obj = TaskCreate(
             **_task.model_dump(
                 exclude={
                     "executable_non_parallel",

fractal_server/tasks/v2/utils_database.py

@@ -3,13 +3,13 @@ from sqlalchemy.orm import Session as DBSyncSession
 
 from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.app.models.v2 import TaskV2
-from fractal_server.app.schemas.v2 import TaskCreateV2
+from fractal_server.app.schemas.v2 import TaskCreate
 
 
 def create_db_tasks_and_update_task_group_sync(
     *,
     task_group_id: int,
-    task_list: list[TaskCreateV2],
+    task_list: list[TaskCreate],
     db: DBSyncSession,
 ) -> TaskGroupV2:
     """
@@ -17,7 +17,7 @@ def create_db_tasks_and_update_task_group_sync(
 
     Args:
         task_group_id: ID of an existing `TaskGroupV2` object.
-        task_list: List of `TaskCreateV2` objects to be inserted into the db.
+        task_list: List of `TaskCreate` objects to be inserted into the db.
         db: Synchronous database session
 
     Returns:
@@ -36,7 +36,7 @@ def create_db_tasks_and_update_task_group_sync(
 async def create_db_tasks_and_update_task_group_async(
     *,
     task_group_id: int,
-    task_list: list[TaskCreateV2],
+    task_list: list[TaskCreate],
     db: AsyncSession,
 ) -> TaskGroupV2:
     """
@@ -44,7 +44,7 @@ async def create_db_tasks_and_update_task_group_async(
 
     Args:
         task_group_id: ID of an existing `TaskGroupV2` object.
-        task_list: List of `TaskCreateV2` objects to be inserted into the db.
+        task_list: List of `TaskCreate` objects to be inserted into the db.
         db: Synchronous database session
 
     Returns:

fractal_server/types/__init__.py

@@ -10,6 +10,9 @@ from fractal_server.urls import normalize_url
 
 from .validators import val_absolute_path
 from .validators import val_http_url
+from .validators import val_no_dotdot_in_path
+from .validators import val_non_absolute_path
+from .validators import val_os_path_normpath
 from .validators import val_unique_list
 from .validators import valdict_keys
 from .validators import validate_attribute_filters
@@ -27,11 +30,22 @@ A non-empty string, with no leading/trailing whitespaces.
 AbsolutePathStr = Annotated[
     NonEmptyStr,
     AfterValidator(val_absolute_path),
+    AfterValidator(val_no_dotdot_in_path),
+    AfterValidator(val_os_path_normpath),
 ]
 """
 String representing an absolute path.
+
+Validation fails if the path is not absolute or if it contains a
+parent-directory reference "/../".
 """
 
+RelativePathStr = Annotated[
+    NonEmptyStr,
+    AfterValidator(val_no_dotdot_in_path),
+    AfterValidator(val_os_path_normpath),
+    AfterValidator(val_non_absolute_path),
+]
 
 HttpUrlStr = Annotated[
     NonEmptyStr,
@@ -44,19 +58,27 @@ String representing an URL.
 
 ZarrUrlStr = Annotated[
     NonEmptyStr,
+    AfterValidator(val_no_dotdot_in_path),
     AfterValidator(normalize_url),
 ]
 """
 String representing a zarr URL/path.
+
+Validation fails if the path is not absolute or if it contains a
+parent-directory reference "/../".
 """
 
 
 ZarrDirStr = Annotated[
     NonEmptyStr,
+    AfterValidator(val_no_dotdot_in_path),
     AfterValidator(normalize_url),
 ]
 """
 String representing a `zarr_dir` path.
+
+Validation fails if the path is not absolute or if it contains a
+parent-directory reference "/../".
 """
 
 DictStrAny = Annotated[

fractal_server/types/validators/__init__.py

@@ -1,6 +1,9 @@
 from ._common_validators import val_absolute_path  # noqa F401
+from ._common_validators import val_no_dotdot_in_path  # noqa F401
+from ._common_validators import val_os_path_normpath  # noqa F401
 from ._common_validators import val_http_url  # noqa F401
 from ._common_validators import val_unique_list  # noqa F401
 from ._common_validators import valdict_keys  # noqa F401
+from ._common_validators import val_non_absolute_path  # noqa F401
 from ._filter_validators import validate_attribute_filters  # noqa F401
 from ._workflow_task_arguments_validators import validate_wft_args  # noqa F401

fractal_server/types/validators/_common_validators.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 from typing import Any
 
 from pydantic import HttpUrl
@@ -29,6 +30,37 @@ def val_absolute_path(path: str) -> str:
     return path
 
 
+def val_non_absolute_path(path: str) -> str:
+    """
+    Check that a string attribute is not an absolute path
+    """
+    if os.path.isabs(path):
+        raise ValueError(
+            f"String must not be an absolute path (given '{path}')."
+        )
+    return path
+
+
+def val_no_dotdot_in_path(path: str) -> str:
+    """
+    Check that a string attribute has no '/../' in it
+    """
+    if ".." in Path(path).parts:
+        raise ValueError("String must not contain '/../'.")
+    return path
+
+
+def val_os_path_normpath(path: str) -> str:
+    """
+    Apply `os.path.normpath` to `path`.
+
+    Note: we keep this separate from `fractal_server.urls.normalize_url`,
+    because this function only applies to on-disk paths, while `normalize_url`
+    may apply to s3 URLs as well.
+    """
+    return os.path.normpath(path)
+
+
 def val_unique_list(must_be_unique: list) -> list:
     if len(set(must_be_unique)) != len(must_be_unique):
         raise ValueError("List has repetitions")

{fractal_server-2.17.2.dist-info → fractal_server-2.18.0.dist-info}/METADATA

@@ -1,16 +1,17 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.2
+Version: 2.18.0
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE
 Author: Tommaso Comparin
 Author-email: tommaso.comparin@exact-lab.it
-Requires-Python: >=3.11,<3.14
+Requires-Python: >=3.11,<3.15
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
 Requires-Dist: fabric (>=3.2.2,<3.3.0)
 Requires-Dist: fastapi (>=0.120.0,<0.121.0)