tol-sdk 1.6.36__py3-none-any.whl → 1.7.0__py3-none-any.whl

tol/{sql/loader → 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/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/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/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/api_base/blueprint.py

@@ -35,6 +35,7 @@ from ..core import DataSource, DataSourceError, OperableDataSource
 from ..core.data_source_dict import DataSourceDict
 from ..core.operator import Relational
 from ..core.operator.operator_config import DefaultOperatorConfig, OperatorConfig
+from ..core.requested_fields import ReqFieldsTree
 
 
 class DataBlueprint(Blueprint):
@@ -179,6 +180,7 @@ def _core_blueprint(
     data_source_dict: dict[str, DataSource],
     url_prefix: str,
     auth_inspector: Optional[AuthInspector] = None,
+    include_all_to_ones: bool = True,
 ) -> DataBlueprint:
     """
     Create the core blueprint responsible for managing DataSource endpoints.
@@ -193,6 +195,8 @@ def _core_blueprint(
         url_prefix (str): URL prefix for all data endpoints.
         auth_inspector (Optional[AuthInspector], optional): Authentication
             inspector for request authorisation.
+        include_all_to_ones (bool): Whether to fetch or store all to-one related objects
+            when fetching or serialising DataObjects.
 
     Returns:
         DataBlueprint: A configured blueprint with all data endpoints and error handlers.
@@ -231,18 +235,30 @@ def _core_blueprint(
         hop_limit = None if requested_fields else 1
 
         data_source = data_source_dict[object_type]
+
+        # Build a ReqFieldsTree template for the request
+        req_fields_tree = ReqFieldsTree(
+            object_type,
+            data_source,
+            requested_fields,
+            include_all_to_ones=include_all_to_ones,
+        )
+
         view = DefaultView(
+            requested_tree=req_fields_tree,
             prefix=url_prefix,
-            include_all_to_ones=True,
             hop_limit=hop_limit,
-            requested_fields=requested_fields,
         )
-        return Controller(data_source, view, auth_inspector=auth_inspector)
+        return Controller(data_source, view, req_fields_tree, auth_inspector=auth_inspector)
 
     @data_handler.route('/<object_type>/<path:object_id>', methods=['GET'])  # Allow slashes
     def get_detail(*, object_type: str, object_id: str):
         """Get details of a specific object by ID."""
-        controller = __new_controller(object_type)
+        request_args = ListGetParameters(request.args)
+        controller = __new_controller(
+            object_type,
+            requested_fields=request_args.requested_fields,
+        )
         object_id_unencoded = urllib.parse.unquote(object_id)
         return controller.get_detail(object_type, object_id_unencoded)
 
@@ -325,8 +341,11 @@ def _core_blueprint(
     @data_handler.post('/<object_type>:cursor')
     def get_cursor_page(*, object_type: str):
         """Get a page of results using cursor-based pagination."""
-        controller = __new_controller(object_type)
         request_args = ListGetParameters(request.args)
+        controller = __new_controller(
+            object_type,
+            requested_fields=request_args.requested_fields,
+        )
         search_after = request.json.get('search_after')
         return controller.get_cursor_page(object_type, request_args, search_after)
 
@@ -369,6 +388,7 @@ def data_blueprint(
     url_prefix: str = '/data',
     config_prefix: str = '/_config',
     auth_inspector: Optional[AuthInspector] = None,
+    include_all_to_ones: bool = True,
 ) -> DataBlueprint:
     """
     Create a complete data blueprint with both core and configuration endpoints.
@@ -405,7 +425,10 @@ def data_blueprint(
         config_prefix, data_sources, DefaultOperatorConfig(*data_sources)
     )
     core_bp = _core_blueprint(
-        DataSourceDict(*data_sources), url_prefix, auth_inspector=auth_inspector
+        DataSourceDict(*data_sources),
+        url_prefix,
+        auth_inspector=auth_inspector,
+        include_all_to_ones=include_all_to_ones,
     )
     core_bp.register_blueprint(config_bp)
 

tol/api_base/controller.py

@@ -31,7 +31,7 @@ from ..api_client.exception import (
     UnsupportedOperationError,
 )
 from ..api_client.view import ResponseDict, View
-from ..core import DataObject, OperableDataSource
+from ..core import DataObject, OperableDataSource, ReqFieldsTree
 from ..core.datasource_filter import AndFilter, DataSourceFilter
 from ..core.operator import (
     Aggregator,
@@ -160,6 +160,7 @@ class Controller:
         self,
         data_source: OperableDataSource,
         view: View,
+        requested_tree: ReqFieldsTree | None = None,
         auth_inspector: Optional[AuthInspector] = None,
     ) -> None:
         """
@@ -173,6 +174,7 @@ class Controller:
         """
         self.__data_source = data_source
         self.__view = view
+        self.__requested_tree = requested_tree
         self.__inspector = auth_inspector
 
     @property
@@ -263,13 +265,13 @@ class Controller:
             page_size=query_args.page_size,
             object_filters=self.__combine_filters(query_args.filter, ext_and),
             sort_by=query_args.sort_by,
-            requested_fields=query_args.requested_fields,
+            requested_tree=self.__requested_tree,
         )
-        document_meta = {
+        meta = {
             'total': total,
             'types': self.__data_source.get_attribute_types(object_type),
         }
-        return self.__view.dump_bulk(data_objects, document_meta=document_meta)
+        return self.__view.dump_bulk(data_objects, document_meta=meta)
 
     @validate(Counter, 'get_count', OperatorMethod.COUNT)
     def get_count(
@@ -545,6 +547,7 @@ class Controller:
             query_args.page_size,
             self.__combine_filters(query_args.filter, ext_and),
             search_after,
+            requested_tree=self.__requested_tree,
         )
         meta = {'search_after': new_search_after}
 
@@ -657,7 +660,13 @@ class Controller:
         Raises:
             ObjectNotFoundByIdException: If no object with the given ID exists.
         """
-        data_objects = list(self.__data_source.get_by_id(object_type, [object_id]))
+        data_objects = list(
+            self.__data_source.get_by_id(
+                object_type,
+                [object_id],
+                requested_tree=self.__requested_tree,
+            )
+        )
         if len(data_objects) == 0 or data_objects[0] is None:
             raise ObjectNotFoundByIdException(object_type, object_id)
         return data_objects[0]

tol/api_client/api_datasource.py

@@ -144,7 +144,11 @@ class ApiDataSource(
 
         client = self.__client_factory()
         json_responses = (
-            client.get_detail(object_type, id_)
+            client.get_detail(
+                object_type,
+                id_,
+                requested_fields=requested_fields,
+            )
             for id_ in object_ids
         )
         json_converter = self.__jc_factory()
@@ -184,16 +188,17 @@ class ApiDataSource(
         session: Optional[OperableSession] = None,
         requested_fields: list[str] | None = None,
     ) -> Iterable[DataObject]:
-
         if self.__can_cursor(object_type, object_filters):
             return self._get_list_by_cursor(
                 object_type,
-                object_filters
+                object_filters,
+                requested_fields=requested_fields,
             )
         else:
             return self.__get_list_regular(
                 object_type,
-                object_filters
+                object_filters,
+                requested_fields=requested_fields,
             )
 
     @validate('count')
@@ -266,7 +271,8 @@ class ApiDataSource(
             object_type,
             page_size,
             search_after,
-            filter_string=filter_string
+            filter_string=filter_string,
+            requested_fields=requested_fields,
         )
         return self.__jc_factory().convert_cursor_page(transfer)
 
@@ -429,7 +435,8 @@ class ApiDataSource(
     def __get_list_regular(
         self,
         object_type: str,
-        object_filters: Optional[DataSourceFilter]
+        object_filters: Optional[DataSourceFilter],
+        requested_fields: list[str] | None = None,
     ) -> Iterable[DataObject]:
 
         page = 1
@@ -443,7 +450,8 @@ class ApiDataSource(
                 object_type,
                 page,
                 page_size,
-                filter_string=filter_string
+                filter_string=filter_string,
+                requested_fields=requested_fields,
             )
             (results_page, _) = jc_converter.convert_list(transfer)
 

tol/api_client/client.py

@@ -28,9 +28,13 @@ class JsonApiClient(HttpClient):
         config_prefix: str = '/_config',
         token_header: str = 'token',
         retries: int = 5,
+        status_forcelist: Optional[list[int]] = None,
         merge_collections: bool | None = None,
     ) -> None:
-        super().__init__(token=token, token_header=token_header, retries=retries)
+        kwargs = {'token': token, 'token_header': token_header, 'retries': retries}
+        if status_forcelist is not None:
+            kwargs['status_forcelist'] = status_forcelist
+        super().__init__(**kwargs)
         self.__data_url = f'{api_url}{data_prefix}'
         self.__config_url = f'{self.__data_url}{config_prefix}'
         self.__merge_collections = merge_collections
@@ -77,7 +81,7 @@ class JsonApiClient(HttpClient):
             page_size=page_size,
             filter=filter_string,
             sort_by=sort_string,
-            requested_field=requested_fields
+            requested_fields=requested_fields
         )
         headers = self._merge_headers()
         return self.__fetch_list(
@@ -455,7 +459,9 @@ class JsonApiClient(HttpClient):
         return f'{self.__config_url}/return_mode'
 
     def __no_none_value_dict(self, **kwargs) -> dict[str, Any]:
-        return {
-            k: v for k, v in kwargs.items()
-            if v is not None
-        }
+        str_params = {}
+        for k, v in kwargs.items():
+            if v is None:
+                continue
+            str_params[k] = ','.join([str(x) for x in v]) if isinstance(v, list) else str(v)
+        return str_params

tol/api_client/converter.py

@@ -5,8 +5,8 @@
 from typing import Any, Dict, Optional, Union
 
 from .parser import Parser
-from .view import View
-from ..core import DataObject
+from .view import DefaultView
+from ..core import DataObject, DataSource, ReqFieldsTree
 from ..core.relationship import RelationshipConfig
 
 
@@ -25,7 +25,7 @@ JsonRelationshipConfig = dict[
 ]
 
 
-class JsonApiConverter():
+class JsonApiConverter:
 
     """
     Converts from JSON:API transfers to instances of
@@ -142,26 +142,40 @@ class JsonApiConverter():
         )
 
 
-class DataObjectConverter():
+class DataObjectConverter:
 
     """
     Converts from instances of `DataObject` to
     JSON:API transfers.
     """
 
-    def __init__(self, view: View) -> None:
-        self.__view = view
+    def __init__(
+        self,
+        data_source: DataSource,
+        prefix: str | None = None,
+    ) -> None:
+        self.__data_source = data_source
+        self.__prefix = prefix
+
+    def __build_view(self, object_type):
+        req_fields_tree = ReqFieldsTree(object_type, self.__data_source)
+        return DefaultView(req_fields_tree, self.__prefix)
 
     def convert(self, input_: DataObject) -> JsonApiTransfer:
         """
         Converts a single `DataObject` instance to a JsonApiTransfer
         """
 
-        return self.__view.dump(input_)
+        view = self.__build_view(input_.type)
+        return view.dump(input_)
 
     def convert_list(self, input_: list[DataObject]) -> JsonApiTransfer:
         """
         Converts a `list` of `DataObject` instances to a JsonApiTransfer
         """
 
-        return self.__view.dump_bulk(input_)
+        if not input_:
+            msg = 'Cannot convert empty list'
+            raise ValueError(msg)
+        view = self.__build_view(input_[0].type)
+        return view.dump_bulk(input_)

tol/api_client/factory.py

@@ -17,7 +17,6 @@ from .converter import (
 )
 from .filter import DefaultApiFilter
 from .parser import DefaultParser
-from .view import DefaultView
 from ..core import DataSource
 
 
@@ -66,8 +65,7 @@ class _ConverterFactory:
         Returns an instantiated `DataObjectConverter`.
         """
 
-        view = DefaultView(prefix=self.__prefix)
-        return DataObjectConverter(view)
+        return DataObjectConverter(self.__data_source, prefix=self.__prefix)
 
     def json_converter_factory(self) -> JsonConverterFactory:
         """
@@ -87,6 +85,7 @@ def _get_client_factory(
     token: Optional[str],
     data_prefix: str,
     retries: int,
+    status_forcelist: list[int],
     merge_collections: bool | None,
 ) -> Callable[[], JsonApiClient]:
     """
@@ -99,6 +98,7 @@ def _get_client_factory(
         token=token,
         data_prefix=data_prefix,
         retries=retries,
+        status_forcelist=status_forcelist,
         merge_collections=merge_collections,
     )
 
@@ -113,6 +113,7 @@ def create_api_datasource(
 
     data_prefix: str = '/data',
     retries: int = 5,
+    status_forcelist: Optional[list[int]] = None,
     merge_collections: bool | None = None,
 ) -> ApiDataSource:
     """
@@ -127,6 +128,7 @@ def create_api_datasource(
         token=token,
         data_prefix=data_prefix,
         retries=retries,
+        status_forcelist=status_forcelist,
         merge_collections=merge_collections,
     )
     manager = _ConverterFactory(data_prefix)