tol-sdk 1.8.9__tar.gz → 1.8.11__tar.gz

{tol_sdk-1.8.9/src/tol_sdk.egg-info → tol_sdk-1.8.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.9
+Version: 1.8.11
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.8.9"
+version = "1.8.11"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/src/tol/core/datasource_utils.py

@@ -30,10 +30,13 @@ class DataSourceUtils:
     @classmethod
     def get_datasource_by_datasource_instance(
         cls,
-        datasource_instance: DataObject
+        datasource_instance: DataObject,
+        **kwargs
     ) -> DataSource:
         datasource_config = datasource_instance.data_source_config
-        kwargs = dict(datasource_instance.kwargs) if datasource_instance.kwargs else {}
+        new_kwargs = dict(datasource_instance.kwargs) if datasource_instance.kwargs else {}
+        if kwargs:
+            new_kwargs.update(kwargs)
         if datasource_config:
             relationship_config = cls.get_relationship_config_from_data_source_config(
                 datasource_config
@@ -44,14 +47,14 @@ class DataSourceUtils:
             runtime_fields = cls.get_runtime_fields_from_data_source_config(
                 datasource_config
             )
-            kwargs.update({
+            new_kwargs.update({
                 'relationship_cfg': relationship_config,
                 'attribute_metadata': amd,
                 'runtime_fields': runtime_fields
             })
         return DataSourceUtils.get_datasource_by_name(
             datasource_instance.builtin_name,
-            **kwargs
+            **new_kwargs
         )
 
     @classmethod
@@ -83,7 +86,6 @@ class DataSourceUtils:
         cls,
         datasource_config: DataObject
     ) -> dict:
-        from ..elastic.runtime_fields import RuntimeFields  # Break circular import cycle
         runtime_fields = {}
         f = DataSourceFilter()
         f.and_ = {
@@ -95,6 +97,7 @@ class DataSourceUtils:
             if dsa.object_type not in runtime_fields:
                 runtime_fields[dsa.object_type] = {}
             if 'function' in dsa.runtime_definition:
+                from ..elastic.runtime_fields import RuntimeFields  # Break circular import cycle
                 method = getattr(RuntimeFields, dsa.runtime_definition['function'])
                 runtime_fields[dsa.object_type][dsa.name] = \
                     method(**dsa.runtime_definition.get('function_kwargs', {}))

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/src/tol/goat/client.py

@@ -57,7 +57,7 @@ class GoatApiClient:
         r.raise_for_status()
         return r.json()['results'] if 'results' in r.json() else [], r.json()['status']['hits']
 
-    def __detail_url(self, object_type: str, object_ids: str) -> Tuple[str, Dict]:
+    def __detail_url(self, object_type: str, object_ids: list[str]) -> Tuple[str, Dict]:
         obj_ids_str = ','.join(object_ids)
         return self.__page_url(object_type, 1, len(object_ids), f'tax_name({obj_ids_str})')
 

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/src/tol/goat/goat_datasource.py

@@ -8,8 +8,6 @@ import typing
 from functools import cache
 from typing import Callable, Iterable, List, Optional
 
-from more_itertools import seekable
-
 from .client import GoatApiClient
 from .converter import (
     GoatApiConverter
@@ -113,27 +111,20 @@ class GoatDataSource(
     def get_by_id(
         self,
         object_type: str,
-        object_ids: Iterable[str],
+        object_ids: Iterable[str | int],
         **kwargs,
     ) -> Iterable[Optional[DataObject]]:
         if object_type not in self.supported_types:
             raise DataSourceError(f'{object_type} is not supported')
 
+        object_ids_str = [str(object_id) for object_id in object_ids]
         client = self.__client_factory()
-        goat_response, _ = client.get_detail(object_type, object_ids)
+        goat_response, _ = client.get_detail(object_type, object_ids_str)
         goat_converter = self.__gc_factory()
 
         converted_objects, _ = goat_converter.convert_list(goat_response) \
             if goat_response is not None else ([], 0)
-        seekable_objects = seekable(converted_objects)
-        for id_ in object_ids:
-            seekable_objects.seek(0)
-            for obj in seekable_objects:
-                if obj.id == id_:
-                    yield obj
-                    break
-            else:
-                yield None
+        return self.sort_by_id(converted_objects, object_ids_str)
 
     def get_list_page(
         self,

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/src/tol/sources/portaldb.py

@@ -4,6 +4,7 @@
 
 import os
 
+from .defaults import Defaults
 from ..api_client import (
     ApiDataSource,
     create_api_datasource
@@ -15,9 +16,10 @@ from ..core import (
 
 def portaldb(retries: int = 5, **kwargs) -> ApiDataSource:
     portaldb = create_api_datasource(
-        api_url=os.getenv('PORTAL_URL') + os.getenv('PORTAL_API_PATH') + '/local',
+        api_url=os.getenv('PORTAL_URL', Defaults.PORTAL_URL)
+        + os.getenv('PORTAL_API_PATH', Defaults.PORTAL_API_PATH),
         token=os.getenv('PORTAL_API_KEY'),
-        data_prefix='',
+        data_prefix='/local',
         retries=retries
     )
     core_data_object(portaldb)

tol_sdk-1.8.11/src/tol/sources/sql.py

@@ -0,0 +1,25 @@
+# SPDX-FileCopyrightText: 2023 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from ..core import (
+    core_data_object
+)
+from ..sql import (
+    SqlDataSource,
+    create_sql_datasource
+)
+
+
+# Create a SQL datasource. This is also expecting the models to be passed in
+# so would most likely be used within an app
+def sql(models, db_uri, behind_api, database_factory, **kwargs) -> SqlDataSource:
+    sql_ds = create_sql_datasource(
+        models=models,
+        db_uri=db_uri,
+        behind_api=True,
+        database_factory=database_factory,
+        **kwargs
+    )
+    core_data_object(sql_ds)
+    return sql_ds

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/src/tol/sql/sql_datasource.py

@@ -86,6 +86,7 @@ class SqlDataSource(
         sorter_factory: SorterFactory,
         user_id_getter: Optional[UserIdGetter] = None,
         attribute_metadata: AttributeMetadata = DefaultAttributeMetadata,
+        **kwargs
     ) -> None:
         self.__db = db
         self.__type_tablename_map = type_tablename_map

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/src/tol/validators/taxon_matches_goat.py

@@ -29,7 +29,7 @@ class TaxonMatchesGoatValidator(Validator):
     __goat_datasource: GoatDataSource
     _cached_taxa: dict[str, DataObject]
 
-    def __init__(self, config: Config) -> None:
+    def __init__(self, config: Config, **kwargs) -> None:
         super().__init__()
         self.__config = config
         self.__goat_datasource = goat()

{tol_sdk-1.8.9 → tol_sdk-1.8.11/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.9
+Version: 1.8.11
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.9 → tol_sdk-1.8.11}/src/tol_sdk.egg-info/SOURCES.txt

@@ -298,6 +298,7 @@ src/tol/sources/portal_attributes.py
 src/tol/sources/portaldb.py
 src/tol/sources/prefect.py
 src/tol/sources/sciops.py
+src/tol/sources/sql.py
 src/tol/sources/sts.py
 src/tol/sources/sts_legacy.py
 src/tol/sources/tolid.py