tol-sdk 1.8.9__py3-none-any.whl → 1.8.11__py3-none-any.whl

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/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/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/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/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/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/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.dist-info → tol_sdk-1.8.11.dist-info}/METADATA

@@ -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.dist-info → tol_sdk-1.8.11.dist-info}/RECORD

@@ -96,7 +96,7 @@ tol/core/data_source_dict.py,sha256=d-hSmoWTwG6IOc0cQTLap1EBslsxYIWGUd3ScSoeH_Q,
 tol/core/datasource.py,sha256=e9GaeDPfO_Gs7cgQhmNxCiSDlRNf64reegzFebcMNkA,6303
 tol/core/datasource_error.py,sha256=TqfqaPANG0gishadhA7myCmTO1Fg9u7hVZOvsY6BdAo,1660
 tol/core/datasource_filter.py,sha256=RY2S9kTx0XwdrFRSE2n2GohB9__fKGzFVsZrkN5hzQk,726
-tol/core/datasource_utils.py,sha256=18mwvFmtJL73_mxtFb56rKXZCGCtZFoEb8sWFKn3Yf0,6232
+tol/core/datasource_utils.py,sha256=6J72RS49IO2quCaFUXBl4DnjZBlXx-aW3Zy9iuzyeQ8,6327
 tol/core/factory.py,sha256=qbLvp5mLTcHbxOjopqtnK-wbZrlskgXjRIREszZjSyE,9157
 tol/core/http_client.py,sha256=QyZarplEHVYIrqEfrySeHbawfbnBU4nN62TLt41x4tY,2242
 tol/core/relationship.py,sha256=etdyCjLbfi2tgkaqzE6cntpNtTzgT_jOPGeNKmPu5yc,4624
@@ -218,11 +218,11 @@ tol/flows/converters/treeofsex_upload_to_treeofsex_attribute_converter.py,sha256
 tol/gap/__init__.py,sha256=aI9h4IEKAd_qCqJayj0fpUDgAYQxy0d8xyBtiABP0xY,134
 tol/gap/gap_datasource.py,sha256=SfBfJh1-2W5Kb5ABNRX7FBJVR8VuD096UQgZ2SKjI6A,3527
 tol/goat/__init__.py,sha256=6e_Wss7QPo5LY0YhlZz9iXsFAD5txMhSlhT5APWqr6Q,190
-tol/goat/client.py,sha256=_bjPkftZf6jMhJZErVOSbnf6ytIpSw9CbTEY21YM3Tg,3680
+tol/goat/client.py,sha256=q8nqpqlkVplPqpN6EfnzkMXbOE_GJEZU4ImJKcrl6ko,3686
 tol/goat/converter.py,sha256=jHUWoJxZOHKp63S45FZA5DbU0rdvoKDkF0hUtedqnvE,1114
 tol/goat/factory.py,sha256=-SOz8VIb_Nljvx7VrLWAg-1CXel9w7wVKQnz9vyZSQo,2639
 tol/goat/filter.py,sha256=J-Fj8O7MSp1O1pIQGMhcMuIQycjYAEx_0ecXYZ9WSqI,3013
-tol/goat/goat_datasource.py,sha256=XEEjMwWxGV92vk1hkOEwYLhRjt2de77PZNMAT2scMdI,6107
+tol/goat/goat_datasource.py,sha256=rADBYKiyteM8cW0RbG6s7vR5xnxF36NJ_Ogkou2VBZQ,5917
 tol/goat/parser.py,sha256=552e0p4rFXBnL7FpJ4AAf2kpnPYsh2PfzmZ95-YOSX8,4039
 tol/google_sheets/__init__.py,sha256=SDrDFfqkLFll0Y6MNFh2yuyyeIfDtFwK1XSnEpsLNgg,133
 tol/google_sheets/google_sheet_datasource.py,sha256=UPhcOZv5IJ2s91M_2wPcL00hl5Bou6qCLNWMjXdNNiQ,6501
@@ -290,9 +290,10 @@ tol/sources/labwhere.py,sha256=gbfpPNKEZEfvw9DXGshg1w4Kdo_tpjWoxndDza6Oa6E,541
 tol/sources/mlwh.py,sha256=wPs2yuU1A8v57jaDQbeIThraDqVtzzhm5DAa0qekApM,324
 tol/sources/portal.py,sha256=1mhX1c4fjbRoHJ86RuBgyXFbDJrVIV55pGwvnuOxVuA,761
 tol/sources/portal_attributes.py,sha256=j_ZIZ8RHpgbRzOdHSOnzhAM9xA0HcwiAxuVgybVtDrg,1926
-tol/sources/portaldb.py,sha256=A-eD_tpJ1cqyDEsnN_fEE67Zkl-WQnRcVlfodZzMcVw,545
+tol/sources/portaldb.py,sha256=fZNIUk5mZ3RuQiknZQlPxOK6Vdz_pzqz1-w_dW0L2yE,626
 tol/sources/prefect.py,sha256=16PrC_KfvxrsDzAcq7UvEBo4c6_n38NC23vHQeiljck,1046
 tol/sources/sciops.py,sha256=qbdoNEo-BfWGw16sjANV7dxFRVMDJQlvaSZgofE8604,1129
+tol/sources/sql.py,sha256=mP5hyNNoxi8yKY1Z-6G5EZ1VW24BW_3q5Hp-w5VpPmE,623
 tol/sources/sts.py,sha256=vd65QAYIM1lltHajqJPOrGg10ZCI7OUB2dbWNAlrAn8,749
 tol/sources/sts_legacy.py,sha256=jWDM1_Jicxhay9UEOGh4lzeO0TIxuH8sa34TCn-GDWQ,440
 tol/sources/tolid.py,sha256=ERSB5L_u7c4NtGYTzdGXWjiGiL58QJNC_0ij1MQMMEQ,663
@@ -314,7 +315,7 @@ tol/sql/relationship.py,sha256=EClMgVx_If5nZV9MV99TQk7Wr7uACWetwQdWAliM5XI,2891
 tol/sql/session.py,sha256=VmqTegr4L2X2zvaOJCpwSrkVRx8fc1RVL0drkL2MXu8,806
 tol/sql/sort.py,sha256=ENrjHGgj4fZtXKmkdlkv1HRi1X14SVlcl-tp8Pu7G0k,2553
 tol/sql/sql_converter.py,sha256=taD5FRwadvw2bBaUGrCIiUs0-ATAbBnRYI1M7xe3yEc,4618
-tol/sql/sql_datasource.py,sha256=RnPkfg4TSHaxfJG77eBrNgBAKexJaypc-fvfFzssdac,15598
+tol/sql/sql_datasource.py,sha256=2FUwGTIN5Dw2cNAEb9fWGsZ0PVdjhdjn8WajA_9LT_Y,15615
 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
@@ -351,7 +352,7 @@ tol/validators/regex.py,sha256=dLAi_vQt9_DsT6wQZmbYC7X5-Wp15l0leUE6XkPaItg,2602
 tol/validators/regex_by_value.py,sha256=XM5EnT4vgD17rfpR3bUE9I56IemSw26BI9MZtMakd4E,2582
 tol/validators/specimens_have_same_taxon.py,sha256=BaJcZ38ZprPcuGTIorSxxC9uGN0_lj6HS6B54EObcuY,2183
 tol/validators/sts_fields.py,sha256=aYbzy15btEg4-ocDT1qrspe7-atoWRrOJ_KmuPU6J14,8936
-tol/validators/taxon_matches_goat.py,sha256=-5UJus3WZOc_ji5Kmat43nI6Auhr924BVi-igEnFP6Q,3482
+tol/validators/taxon_matches_goat.py,sha256=lYZ0qwPver9wXJm2ekv_6KcC49MugVXD9t1IAxPGG2Q,3492
 tol/validators/tolid.py,sha256=VOb6lNFz11H_0KaWX8_nvsw8xJEa6KrjB0p-5lkcqog,3885
 tol/validators/types.py,sha256=jMVpckRp8RS93f7usf58YH_K-5rKWgZIYs7bO9dHhQc,2914
 tol/validators/unique_value_check.py,sha256=sFvDooYkKeORvULGEOTsgIcxlbe0AXDWxY3Gbr3j0KI,1282
@@ -360,9 +361,9 @@ tol/validators/unique_whole_organisms.py,sha256=RdqA1GzIf3LTdrmNGGdxv0aW2udDY2P9
 tol/validators/value_check.py,sha256=DdNx_B1gns01zgBg5N6Bwia46Aukw6MAteM-M37Kv1k,1122
 tol/validators/interfaces/__init__.py,sha256=jtOxnwnwqV_29xjmmMcS_kvlt-pQiWwQYJn2YRP07_w,172
 tol/validators/interfaces/condition_evaluator.py,sha256=nj8Cb8hi47OBy6OVNfeLhF-Pjwtr8MiOSymYL6hfVes,3766
-tol_sdk-1.8.9.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
-tol_sdk-1.8.9.dist-info/METADATA,sha256=MgDxVlsVbpKw9s2vFEdeeTUYpv9hdL48ETxeGTbGF-Y,3142
-tol_sdk-1.8.9.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-tol_sdk-1.8.9.dist-info/entry_points.txt,sha256=jH3HfTwxjzog7E3lq8CKpUWGIRY9FSXbyL6CpUmv6D0,36
-tol_sdk-1.8.9.dist-info/top_level.txt,sha256=PwKMQLphyZNvagBoriVbl8uwHXQl8IC1niawVG0iXMM,10
-tol_sdk-1.8.9.dist-info/RECORD,,
+tol_sdk-1.8.11.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
+tol_sdk-1.8.11.dist-info/METADATA,sha256=qwTqwgW3IHEgw2e6nNAwg6uXKrYh4Doo3ZkLVlWFaT8,3143
+tol_sdk-1.8.11.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+tol_sdk-1.8.11.dist-info/entry_points.txt,sha256=jH3HfTwxjzog7E3lq8CKpUWGIRY9FSXbyL6CpUmv6D0,36
+tol_sdk-1.8.11.dist-info/top_level.txt,sha256=PwKMQLphyZNvagBoriVbl8uwHXQl8IC1niawVG0iXMM,10
+tol_sdk-1.8.11.dist-info/RECORD,,