tol-sdk 1.6.36__py3-none-any.whl → 1.6.37__py3-none-any.whl

tol/actions/__init__.py

@@ -0,0 +1,6 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+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/sql/sql_datasource.py

@@ -202,32 +202,35 @@ class SqlDataSource(
         )
         sorter = self.__sorter_factory(sort_by)
         in_session = self.__get_sqla_session(session)
-        total_count = self.__db.count(
-            tablename,
-            in_session,
-            filters=database_filter
-        )
-        models = self.__get_list_page_models(
-            tablename,
-            database_filter,
-            page_number,
-            page_size,
-            sorter,
-            in_session,
-            requested_relationships=self.__format_requested_relationships(
-                object_type,
-                requested_fields
-            ),
-        )
-        converter = self.__get_converter(
-            requested_fields=requested_fields
-        )
-        return_list = list(
-            converter.convert_iterable(models)
-        )
-        if session is None:
+        try:
+            total_count = self.__db.count(
+                tablename,
+                in_session,
+                filters=database_filter
+            )
+            models = self.__get_list_page_models(
+                tablename,
+                database_filter,
+                page_number,
+                page_size,
+                sorter,
+                in_session,
+                requested_relationships=self.__format_requested_relationships(
+                    object_type,
+                    requested_fields
+                ),
+            )
+            converter = self.__get_converter(
+                requested_fields=requested_fields
+            )
+            return_list = list(
+                converter.convert_iterable(models)
+            )
+            if session is None:
+                in_session.close()
+            return return_list, total_count
+        except KeyError:
             in_session.close()
-        return return_list, total_count
 
     def get_list(
         self,

{tol_sdk-1.6.36.dist-info → tol_sdk-1.6.37.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.6.36
+Version: 1.6.37
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.6.36.dist-info → tol_sdk-1.6.37.dist-info}/RECORD

@@ -1,8 +1,11 @@
 certs/cacert.pem,sha256=VBU2YEgoq_W2VrRC9IYcMoZuRzO96nwmcHBep2xt_l0,199181
 tol/__init__.py,sha256=0WL4ZHy0Kpa-QZUXJDSu0af690J4gotyQN5wqbk6Zf0,85
 tol/markdown.py,sha256=X-ooYUYLkkVS8DyBHYib8d2QBBNMPlBP5_ZQz8-mAYc,570
+tol/actions/__init__.py,sha256=xOj2kvRYv2GWQLqrpL_xhwZUZDwtOBnxb5CZ9qmP-pk,169
+tol/actions/action.py,sha256=HlfUsfVGd2vuNAwD_01yo1i32nh6UNrt_ytcY2ladgM,651
+tol/actions/upsert_action.py,sha256=DnSz1LhHibF0WcK6Qht5eLIGi3PPXc6GSRsd8Y2dZBE,1366
 tol/api_base/__init__.py,sha256=xv9kkAyb1Q5vhKgq6f-JpY7lIAla51U-gIpA5U1OfkA,312
-tol/api_base/action.py,sha256=GYjc9ZIqcqJ8DhLWV83cB55R_6SQRoCESlUDL7-EMLc,4676
+tol/api_base/action.py,sha256=l3MzD3jSDdYiZs-HCT4YEsXkp34X26k6yWugXrRB2XU,6575
 tol/api_base/blueprint.py,sha256=k7so2is91-oHO41a3o0dhkXg4_xfmwQX9AaGzMZhzTY,18286
 tol/api_base/controller.py,sha256=nAN7RvGFq7_fMibVTR4iGf4QXPuEYGmxfjyxihfMHqE,26556
 tol/api_base/pipeline_steps.py,sha256=lz888M2cF-5z-EkGK_sWfZf1otnYRmgnNuC0WUqI-po,5667
@@ -292,7 +295,7 @@ tol/sql/relationship.py,sha256=8biXecUuJ6KKGjgB9fIIEKyDvcHjdG76iotb-x8LG8Q,2890
 tol/sql/session.py,sha256=VmqTegr4L2X2zvaOJCpwSrkVRx8fc1RVL0drkL2MXu8,806
 tol/sql/sort.py,sha256=ENrjHGgj4fZtXKmkdlkv1HRi1X14SVlcl-tp8Pu7G0k,2553
 tol/sql/sql_converter.py,sha256=WtqdAT9PPuwBn8q3ZO-e_uAqBUP0cYU2seowBGUVT0Q,5282
-tol/sql/sql_datasource.py,sha256=68L7xF3PiEMXE5fxC0fndOkxkOoc4EinVPPcQmtGyLY,17274
+tol/sql/sql_datasource.py,sha256=xP6-ZTEfF6BXLvGs_18tea7vRJGoT_Eg1lh7XTEutWQ,17447
 tol/sql/action/__init__.py,sha256=T1zAsCza_lvsNtXF1ecSLt9OFGup8tGnIs68YylBmXI,142
 tol/sql/action/factory.py,sha256=HkareJp_57ud0_Bdd9Kwz3_Rnq2l211sGJgftohFAHg,3589
 tol/sql/auth/__init__.py,sha256=e3JuwugXmXobklqZ1Mt1w03qPgb1WdUaJVM7oblzHyk,202
@@ -321,9 +324,9 @@ tol/validators/__init__.py,sha256=XXwCt8JPQ5-w2kN1bVjJPLXbS9F4s1nJUnY9jaKdmVk,27
 tol/validators/allowed_keys.py,sha256=BJMomJtaQdxsdGsueDtLewv75TlwdIXiQipLGFcJ7_c,1331
 tol/validators/allowed_values.py,sha256=yJ5SdiUlV7PSKORtsBJ9hYSqwvlx_esbFmFL_Gxh-p4,2262
 tol/validators/unique_values.py,sha256=stI-1i006WEbERcjSMapRggJkEF-RFDzw2uUtXBAE_M,1885
-tol_sdk-1.6.36.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
-tol_sdk-1.6.36.dist-info/METADATA,sha256=G3rnsFcEIx7d74X6o1q4ukuUlc4CySHpo__cDNYA8sg,3073
-tol_sdk-1.6.36.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tol_sdk-1.6.36.dist-info/entry_points.txt,sha256=jH3HfTwxjzog7E3lq8CKpUWGIRY9FSXbyL6CpUmv6D0,36
-tol_sdk-1.6.36.dist-info/top_level.txt,sha256=PwKMQLphyZNvagBoriVbl8uwHXQl8IC1niawVG0iXMM,10
-tol_sdk-1.6.36.dist-info/RECORD,,
+tol_sdk-1.6.37.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
+tol_sdk-1.6.37.dist-info/METADATA,sha256=2C34dKqCV06qMbCP73eObpby_rO-56dD9QMgSTrQHzU,3073
+tol_sdk-1.6.37.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+tol_sdk-1.6.37.dist-info/entry_points.txt,sha256=jH3HfTwxjzog7E3lq8CKpUWGIRY9FSXbyL6CpUmv6D0,36
+tol_sdk-1.6.37.dist-info/top_level.txt,sha256=PwKMQLphyZNvagBoriVbl8uwHXQl8IC1niawVG0iXMM,10
+tol_sdk-1.6.37.dist-info/RECORD,,