tol-sdk 1.6.24__tar.gz → 1.8.4__tar.gz

{tol_sdk-1.6.24/src/tol_sdk.egg-info → tol_sdk-1.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.6.24
+Version: 1.8.4
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT
@@ -15,6 +15,7 @@ License-File: LICENSE
 Requires-Dist: cachetools==5.3.3
 Requires-Dist: case-converter==1.1.0
 Requires-Dist: Click==8.1.7
+Requires-Dist: dacite==1.9.2
 Requires-Dist: more-itertools==10.2.0
 Requires-Dist: python_dateutil>=2.8.1
 Requires-Dist: python-dotenv>=1.0.1
@@ -36,7 +37,7 @@ Requires-Dist: atlassian-python-api==3.41.14; extra == "jira"
 Provides-Extra: json
 Requires-Dist: minio==7.2.15; extra == "json"
 Provides-Extra: mysql
-Requires-Dist: mysql-connector-python; extra == "mysql"
+Requires-Dist: mysql-connector-python==9.5.0; extra == "mysql"
 Provides-Extra: postgresql
 Requires-Dist: SQLAlchemy==2.0.35; extra == "postgresql"
 Requires-Dist: psycopg2-binary==2.9.9; extra == "postgresql"
@@ -49,6 +50,8 @@ Requires-Dist: openpyxl>=3.0.10; extra == "sheets"
 Requires-Dist: XlsxWriter==3.1.9; extra == "sheets"
 Requires-Dist: xlrd==2.0.1; extra == "sheets"
 Requires-Dist: gspread>=5.12.0; extra == "sheets"
+Provides-Extra: s3
+Requires-Dist: minio==7.2.15; extra == "s3"
 Provides-Extra: all
 Requires-Dist: tol-sdk[api-base]; extra == "all"
 Requires-Dist: tol-sdk[benchling]; extra == "all"
@@ -60,6 +63,10 @@ Requires-Dist: tol-sdk[mysql]; extra == "all"
 Requires-Dist: tol-sdk[postgresql]; extra == "all"
 Requires-Dist: tol-sdk[prefect]; extra == "all"
 Requires-Dist: tol-sdk[sheets]; extra == "all"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
 Dynamic: license-file
 
 <!--
@@ -71,4 +78,5 @@ SPDX-License-Identifier: MIT
 # ToL SDK
 
 A Python SDK for ToL services. Full documentation is available:
+https://tol.pages.internal.sanger.ac.uk/platforms/tol-sdk/
 https://ssg-confluence.internal.sanger.ac.uk/display/TOL/ToL+SDK

{tol_sdk-1.6.24 → tol_sdk-1.8.4}/README.md

@@ -7,4 +7,5 @@ SPDX-License-Identifier: MIT
 # ToL SDK
 
 A Python SDK for ToL services. Full documentation is available:
+https://tol.pages.internal.sanger.ac.uk/platforms/tol-sdk/
 https://ssg-confluence.internal.sanger.ac.uk/display/TOL/ToL+SDK

{tol_sdk-1.6.24 → tol_sdk-1.8.4}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.6.24"
+version = "1.8.4"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [
@@ -26,6 +26,7 @@ dependencies = [
   "cachetools == 5.3.3",
   "case-converter == 1.1.0",
   "Click == 8.1.7",
+  "dacite == 1.9.2",
   "more-itertools == 10.2.0",
   "python_dateutil >= 2.8.1",
   "python-dotenv >= 1.0.1",
@@ -42,7 +43,7 @@ elastic = ["elasticsearch == 7.17.9"]
 irods = ["python-irodsclient == 3.1.0"]
 jira = ["atlassian-python-api==3.41.14"]
 json = ["minio == 7.2.15"]
-mysql = ["mysql-connector-python"]
+mysql = ["mysql-connector-python==9.5.0"]
 postgresql = ["SQLAlchemy == 2.0.35", "psycopg2-binary == 2.9.9"]
 prefect = ["prefect == 2.20.18", "griffe < 1.0.0"]
 sheets = [
@@ -52,6 +53,7 @@ sheets = [
     "xlrd == 2.0.1",
     "gspread >= 5.12.0"
 ]
+s3 = ["minio == 7.2.15"]
 all = [
     "tol-sdk[api-base]",
     "tol-sdk[benchling]",
@@ -64,6 +66,11 @@ all = [
     "tol-sdk[prefect]",
     "tol-sdk[sheets]"
 ]
+docs = [
+    "sphinx",
+    "sphinx_rtd_theme",
+    "sphinx-autobuild"
+]
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -73,4 +80,7 @@ where = ["src"]
 "tol.benchling.sql" = ["*.sql"]
 
 [project.scripts]
-tol = "tol.cli:cli"
+tol = "tol.cli:cli"
+
+[tool.black]
+line-length = 99

{tol_sdk-1.6.24/src/tol/sql/loader → tol_sdk-1.8.4/src/tol/actions}/__init__.py

@@ -2,5 +2,5 @@
 #
 # SPDX-License-Identifier: MIT
 
-
-from .factory import create_loader_models  # noqa F401
+from .action import Action  # noqa
+from .upsert_action import UpsertAction  # noqa

tol_sdk-1.8.4/src/tol/actions/action.py

@@ -0,0 +1,31 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from __future__ import annotations
+
+from abc import ABC, abstractmethod
+from typing import Any
+
+from ..core import DataSource
+
+
+class Action(ABC):
+    """
+    The central class for running local actions.
+    """
+
+    @abstractmethod
+    def run(
+        self,
+        datasource: DataSource,
+        ids: list[str],
+        object_type: str,
+        params: dict[str, Any] | None = None
+    ) -> tuple[dict[str, bool], int]:
+        """
+        Run the action on the given IDs and return status in
+        format ({'success': True}, 200).
+        """
+
+        pass

tol_sdk-1.8.4/src/tol/actions/upsert_action.py

@@ -0,0 +1,56 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from __future__ import annotations
+
+from typing import Any
+
+from .action import Action
+from ..core import DataSource
+
+
+class UpsertAction(Action):
+    """
+    The central class for running local actions.
+    """
+
+    def __init__(self):
+        super().__init__()
+
+    def run(
+        self,
+        datasource: DataSource,
+        ids: list[str],
+        object_type: str,
+        params: dict[str, Any] | None = None
+    ) -> tuple[dict[str, bool], int]:
+
+        data_objects = self.__convert_to_data_objects(
+            datasource=datasource,
+            ids=ids,
+            object_type=object_type,
+            params=params
+        )
+
+        try:
+            datasource.upsert_batch(object_type=object_type, objects=data_objects)
+            return {'success': True}, 200
+        except Exception as e:
+            return {'error': str(e)}, 500
+
+    def __convert_to_data_objects(
+        self,
+        datasource: DataSource,
+        ids: list[str],
+        object_type: str,
+        params: dict[str, Any] | None = None
+    ) -> Any:
+        CoreDataObject = datasource.data_object_factory # noqa N806
+
+        for id_ in ids:
+            yield CoreDataObject(
+                type_=object_type,
+                id_=id_,
+                attributes=params
+            )

{tol_sdk-1.6.24 → tol_sdk-1.8.4}/src/tol/api_base/__init__.py

@@ -7,5 +7,6 @@ from .blueprint import (  # noqa
     custom_blueprint,
     data_blueprint
 )
+from .data_upload import data_upload_blueprint  # noqa
 from .pipeline_steps import pipeline_steps_blueprint # noqa
 from .system import system_blueprint  # noqa

{tol_sdk-1.6.24 → tol_sdk-1.8.4}/src/tol/api_base/action.py

@@ -4,6 +4,7 @@
 
 from __future__ import annotations
 
+import importlib
 import typing
 from datetime import datetime
 from typing import Any
@@ -151,31 +152,79 @@ def action_blueprint(
             else {}
         )
 
-        flow_params = {
-            'extra_params': {
+        if action.flow_name:
+            flow_params = {
+                'extra_params': {
+                    **params,
+                    **action_params,
+                },
+                'user_id': user_id,
+                'object_type': object_type,
+                'ids': ids
+            }
+
+            flow_run_id, flow_run_name = __insert_flow_run(
+                action,
+                flow_params,
+                user_id
+            )
+
+            user_action_params = {
                 **params,
                 **action_params,
-            },
-            'user_id': user_id,
-            'object_type': object_type,
-            'ids': ids
-        }
-
-        flow_run_id, flow_run_name = __insert_flow_run(
-            action,
-            flow_params,
-            user_id
-        )
+                'ids': ids,
+                'flow_run_id': flow_run_id,
+                'flow_run_name': flow_run_name
+            }
 
-        user = sql_ds.get_one('user', user_id)
+        elif action.class_name:
+            # Try to import the class from tol.actions first, then fall back to main.actions
+            action_class = None
+            try:
+                tol_actions_module = importlib.import_module('tol.actions')
+                if hasattr(tol_actions_module, action.class_name):
+                    action_class = getattr(tol_actions_module, action.class_name)
+
+                if action_class is None:
+                    main_actions_module = importlib.import_module('main.actions')
+                    if hasattr(main_actions_module, action.class_name):
+                        action_class = getattr(main_actions_module, action.class_name)
+
+            except ImportError:
+                raise DataSourceError(
+                    'Action Class Import Error',
+                    'Class not found in tol.actions or main.actions',
+                    500
+                )
+
+            if action_class is None:
+                raise DataSourceError(
+                    'Action Class Not Found',
+                    f'Action class "{action.class_name}" not found in tol.actions or main.actions',
+                    404
+                )
+
+            class_params = {**action_params, **params}
+
+            action_instance = action_class()
+            status = action_instance.run(ids=ids, params=class_params,
+                                         object_type=object_type, datasource=sql_ds)
+
+            user_action_params = {
+                **params,
+                **action_params,
+                'ids': ids,
+                'status': status
+            }
 
-        user_action_params = {
-            **params,
-            **action_params,
-            'ids': ids,
-            'flow_run_id': flow_run_id,
-            'flow_run_name': flow_run_name
-        }
+        else:
+            raise DataSourceError(
+                'Invalid Action',
+                'No Actions are defined',
+                400
+            )
+
+        user = sql_ds.get_one('user', user_id)
 
         user_action = sql_ds.data_object_factory(
             'user_action',

{tol_sdk-1.6.24 → tol_sdk-1.8.4}/src/tol/api_base/auth/abc/__init__.py

@@ -3,3 +3,4 @@
 # SPDX-License-Identifier: MIT
 
 from .auth import AuthManager  # noqa F401
+from .authorisation import AuthorisationManager  # noqa F401

tol_sdk-1.8.4/src/tol/api_base/auth/abc/authorisation.py

@@ -0,0 +1,51 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+from abc import ABC, abstractmethod
+from typing import Any
+
+
+class AuthorisationManager(ABC):
+    """
+    Abstract base class for managing user authorisations and memberships.
+
+    This class defines the interface for authorisation managers that need to
+    retrieve user membership information for access control purposes. Concrete
+    implementations should handle the specific logic for querying user memberships
+    from various authorisation systems (e.g., LDAP, database, external services).
+
+    The class follows the ABC (Abstract Base Class) pattern to ensure that all
+    concrete implementations provide the required methods for authorisation
+    management.
+    """
+
+    @abstractmethod
+    def get_user_memberships(self, user: Any) -> list[str]:
+        """
+        Retrieve the list of group memberships for a given user.
+
+        This method should be implemented by concrete subclasses to fetch
+        the user's membership information from the appropriate authorisation
+        source. The memberships are typically used to determine what resources
+        or actions the user is authorised to access.
+
+        Args:
+            user (Any): The user object or identifier for which to retrieve
+                       memberships. The type is flexible to accommodate
+                       different user representation formats (e.g., user ID,
+                       user object, username string, etc.).
+
+        Returns:
+            list[str]: A list of group names or membership identifiers that
+                      the user belongs to. Returns an empty list if the user
+                      has no memberships or if the user is not found.
+
+        Raises:
+            NotImplementedError: If called on the abstract base class directly
+                               rather than on a concrete implementation.
+
+        Note:
+            Concrete implementations may raise additional exceptions specific
+            to their authorisation backend (e.g., connection errors, authentication
+            failures, etc.).
+        """

{tol_sdk-1.6.24 → tol_sdk-1.8.4}/src/tol/api_base/auth/asserts.py

@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 from functools import wraps
+from inspect import BoundArguments
 from typing import Any, Callable, Optional, Protocol
 
 from .error import ForbiddenError
@@ -21,12 +22,11 @@ class AuthInspector(Protocol):
     lock down access to a user's objects by their ID).
     """
 
-    # TODO support segementation within `object_type` - e.g. by programme/project
-
     def __call__(
         self,
         object_type: str,
-        method: OperatorMethod
+        method: OperatorMethod,
+        bound_args: BoundArguments
     ) -> Optional[AndFilter]:
         ...
 
@@ -104,7 +104,8 @@ def basic_auth_inspector(
 
     def auth_inspector(
         __object_type: str,
-        method: OperatorMethod
+        method: OperatorMethod,
+        bound_args: BoundArguments | None,
     ) -> None:
 
         if method in NO_AUTH: