tol-sdk 1.7.5b2__tar.gz → 1.7.5b4__tar.gz

{tol_sdk-1.7.5b2/src/tol_sdk.egg-info → tol_sdk-1.7.5b4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.7.5b2
+Version: 1.7.5b4
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.7.5-beta2"
+version = "1.7.5-beta4"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/core/data_object_converter.py

@@ -97,7 +97,8 @@ class SanitisingConverter(DataObjectToDataObjectOrUpdateConverter):
 
     def __init__(
         self,
-        data_object_factory: DataObjectFactory
+        data_object_factory: DataObjectFactory,
+        **kwargs
     ):
         super().__init__(data_object_factory)
 

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/core/operator/detail_getter.py

@@ -82,7 +82,7 @@ class DetailGetter(ABC):
         for id_ in object_ids:
             seekable_objects.seek(0)
             for obj in seekable_objects:
-                if obj.id == id_:
+                if str(obj.id) == str(id_):
                     yield obj
                     break
             else:

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/flows/converters/__init__.py

@@ -55,3 +55,4 @@ from .tolqc_species_to_elastic_species_converter import TolqcSpeciesToElasticSpe
 from .sts_sample_to_casm_benchling_converter import StsSampleToCasmBenchlingConverterFactory # noqa F401
 from .treeofsex_species_to_treeofsexwh_species_converter import TreeofsexSpeciesToTreeofsexwhSpeciesConverter  # noqa F401
 from .treeofsex_upload_to_treeofsex_attribute_converter import TreeofsexUploadToTreeofsexAttributeConverter  # noqa F401
+from .skip_null_fields_converter import SkipNullFieldsConverter  # noqa F401

tol_sdk-1.7.5b4/src/tol/flows/converters/skip_null_fields_converter.py

@@ -0,0 +1,42 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+# SPDX-License-Identifier: MIT
+
+from dataclasses import dataclass
+from typing import Iterable
+
+from tol.core import DataObject, DataObjectToDataObjectOrUpdateConverter
+
+
+class SkipNullFieldsConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        field_names: list[str]
+
+    __slots__ = ['__config']
+    __config: Config
+
+    def __init__(self, data_object_factory, config: Config) -> None:
+        super().__init__(data_object_factory)
+        self.__config = config
+        self._data_object_factory = data_object_factory
+
+    def convert(self, data_object: DataObject) -> Iterable[DataObject]:
+        """
+        removing null fields from the DataObject
+        """
+
+        passes = True
+        for field in self.__config.field_names:
+            value = data_object.get_field_by_name(field)
+            if value is None:
+                passes = False
+                break
+
+        if passes:
+            ret = self._data_object_factory(
+                data_object.type,
+                data_object.id,
+                attributes=data_object.attributes
+            )
+            yield ret

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/sql/auth/models.py

@@ -19,6 +19,7 @@ from sqlalchemy.ext.declarative import declared_attr
 from sqlalchemy.orm import (
     Mapped,
     Session,
+    joinedload,
     mapped_column,
     relationship
 )
@@ -184,7 +185,7 @@ def create_models(
 
         id: Mapped[str] = mapped_column(  # noqa A003
             primary_key=True,
-            name=None if not prefix_with_name else 'state_id'
+            name='state_id' if prefix_with_name else None
         )
 
         created_at: Mapped[datetime] = mapped_column(
@@ -257,13 +258,13 @@ def create_models(
         id: Mapped[int] = mapped_column(  # noqa A003
             primary_key=True,
             autoincrement=True,
-            name=None if not prefix_with_name else 'user_id'
+            name='user_id' if prefix_with_name else None
         )
 
-        _tokens: Mapped[list['Token']] = relationship(
+        _tokens: Mapped[list[Token]] = relationship(
             back_populates='user'
         )
-        _role_bindings: Mapped[list['RoleBinding']] = relationship(
+        _role_bindings: Mapped[list[RoleBinding]] = relationship(
             back_populates='user'
         )
 
@@ -340,7 +341,7 @@ def create_models(
 
     class _TokenPKMixin:
         """
-        Has an integer has a primary key.
+        Has an integer as a primary key.
 
         This is all that is needed in most apps,
         and is the default.
@@ -403,11 +404,19 @@ def create_models(
             token: str
         ) -> Optional[Token]:
 
-            return sess.query(
-                cls
-            ).filter_by(
-                token=token
-            ).one_or_none()
+            return (
+                sess.query(cls)
+                .filter_by(token=token)
+                .options(
+                    # Join through to the Role table when fetching a Token so
+                    # that SQLAlchemy only fires one SELECT query instead of
+                    # four to get `token.user._role_bindings.role.name`
+                    joinedload(cls.user)
+                    .joinedload(User._role_bindings)
+                    .joinedload(RoleBinding.role)
+                )
+                .one_or_none()
+            )
 
         @classmethod
         def get_or_create(
@@ -475,14 +484,14 @@ def create_models(
         id: Mapped[int] = mapped_column(  # noqa A003
             primary_key=True,
             autoincrement=True,
-            name=None if not prefix_with_name else 'role_id'
+            name='role_id' if prefix_with_name else None
         )
 
         name: Mapped[str] = mapped_column(
             unique=True
         )
 
-        _role_bindings: Mapped[list['RoleBinding']] = relationship(
+        _role_bindings: Mapped[list[RoleBinding]] = relationship(
             back_populates='role'
         )
 

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/__init__.py

@@ -6,6 +6,7 @@ from .allowed_keys import AllowedKeysValidator  # noqa
 from .allowed_values import AllowedValuesValidator  # noqa
 from .allowed_values_from_datasource import AllowedValuesFromDataSourceValidator  # noqa
 from .assert_on_condition import AssertOnConditionValidator  # noqa
+from .converter_and_validate import ConverterAndValidateValidator  # noqa
 from .ena_checklist import EnaChecklistValidator # noqa
 from .mutually_exclusive import MutuallyExclusiveValidator  # noqa
 from .ena_submittable import EnaSubmittableValidator  # noqa

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/allowed_keys.py

@@ -26,7 +26,8 @@ class AllowedKeysValidator(Validator):
 
     def __init__(
         self,
-        config: Config
+        config: Config,
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/allowed_values.py

@@ -27,7 +27,8 @@ class AllowedValuesValidator(Validator):
 
     def __init__(
         self,
-        config: Config
+        config: Config,
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/allowed_values_from_datasource.py

@@ -29,7 +29,8 @@ class AllowedValuesFromDataSourceValidator(Validator):
     def __init__(
         self,
         config: Config,
-        allowed_values: List[str | int | float] | None = None  # For testing
+        allowed_values: List[str | int | float] | None = None,  # For testing
+        **kwargs
     ) -> None:
 
         super().__init__()
@@ -40,7 +41,7 @@ class AllowedValuesFromDataSourceValidator(Validator):
 
     def __initialize_list_from_datasource(self) -> List[str | int | float]:
         dsi = portaldb().get_one('data_source_instance', self.__config.datasource_instance_id)
-        ds = DataSourceUtils.get_data_source_by_data_source_instance(dsi)
+        ds = DataSourceUtils.get_datasource_by_datasource_instance(dsi)
         return [
             obj.get_field_by_name(
                 self.__config.datasource_field_name

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/assert_on_condition.py

@@ -25,7 +25,7 @@ class AssertOnConditionValidator(Validator, ConditionEvaluator):
     __slots__ = ['__config']
     __config: Config
 
-    def __init__(self, config: Config) -> None:
+    def __init__(self, config: Config, **kwargs) -> None:
         super().__init__()
 
         self.__config = config

tol_sdk-1.7.5b4/src/tol/validators/converter_and_validate.py

@@ -0,0 +1,93 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+import importlib
+from dataclasses import dataclass
+
+from tol.core import DataObject
+from tol.core.factory import DataObjectFactory
+from tol.core.validate import ValidationResult, Validator
+
+
+class ConverterAndValidateValidator(Validator):
+    """
+    Convert DataObjects, validate the converted ones, and return the original
+    input unchanged. Inner validator results are not merged here.
+
+    {
+        "converters": [{
+            "module": "<path.to.module>",
+            "class_name": "<path.to.ConverterClass>",
+            "config": { ... }
+        }],
+        "validators": [{
+            "module": "<path.to.module>",
+            "class_name": "<path.to.ValidatorClass>",
+            "config": { ... }
+        }]
+    }
+
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        converters: list[dict]
+        validators: list[dict]
+
+    __slots__ = [
+        '__converters',
+        '__validators'
+    ]
+
+    def __init__(
+        self,
+        config: Config,
+        data_object_factory: DataObjectFactory,
+        **kwargs
+    ) -> None:
+        super().__init__()
+        self.__converters = []
+        self.__validators = []
+
+        for conv in config.converters:
+            __module = importlib.import_module(conv.get('module'))
+            converter_class = getattr(__module, conv.get('class_name'))
+
+            converter_conf = converter_class.Config(
+                **conv.get('config')
+            )
+            self.__converters.append(converter_class(
+                data_object_factory=data_object_factory,
+                config=converter_conf,
+            ))
+        for val in config.validators:
+            __module = importlib.import_module(val.get('module'))
+            validator_class = getattr(__module, val.get('class_name'))
+
+            validator_conf = validator_class.Config(
+                **val.get('config')
+            )
+            self.__validators.append(validator_class(
+                data_object_factory=data_object_factory,
+                config=validator_conf,
+            ))
+
+    def _validate_data_object(self, obj: DataObject) -> None:
+        converted_objs = [obj]
+        for converter in self.__converters:
+            converted_objs = converter.convert_iterable(converted_objs)
+        for obj in converted_objs:
+            for validator in self.__validators:
+                validator._validate_data_object(obj)
+
+    @property
+    def results(self) -> list[ValidationResult]:
+        return [result for validator in self.__validators for result in validator.results]
+
+    @property
+    def warnings(self) -> list[ValidationResult]:
+        return [warning for validator in self.__validators for warning in validator.warnings]
+
+    @property
+    def errors(self) -> list[ValidationResult]:
+        return [error for validator in self.__validators for error in validator.errors]

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/ena_checklist.py

@@ -23,7 +23,7 @@ class EnaChecklistValidator(Validator):
     __slots__ = ['__config']
     __config: Config
 
-    def __init__(self, config: Config, datasource: DataSource = ena()) -> None:
+    def __init__(self, config: Config, datasource: DataSource = ena(), **kwargs) -> None:
         super().__init__()
         self.__config = config
         self._datasource = datasource

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/ena_submittable.py

@@ -28,6 +28,7 @@ class EnaSubmittableValidator(Validator):
         self,
         config: Config,
         ena_datasource: DataSource | None = ena(),  # For testing
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/min_one_valid_value.py

@@ -24,6 +24,7 @@ class MinOneValidValueValidator(Validator):
     def __init__(
         self,
         config: Config,
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/mutually_exclusive.py

@@ -62,7 +62,7 @@ class MutuallyExclusiveValidator(Validator, ConditionEvaluator):
     __first_list: List[Any]
     __second_list: List[Any]
 
-    def __init__(self, config: Config) -> None:
+    def __init__(self, config: Config, **kwargs) -> None:
         super().__init__()
 
         self.__config = config

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/regex.py

@@ -26,7 +26,10 @@ class Regex:
 
     def is_allowed(self, __v: Any) -> bool:
         # Check regex
-        return re.search(self.regex, str(__v or ''))
+        return bool(re.search(
+            self.regex,
+            str(__v) if __v is not None else ''
+        ))
 
 
 class RegexValidator(Validator):
@@ -44,7 +47,8 @@ class RegexValidator(Validator):
 
     def __init__(
         self,
-        config: Config
+        config: Config,
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/regex_by_value.py

@@ -27,7 +27,8 @@ class RegexByValueValidator(Validator):
 
     def __init__(
         self,
-        config: Config
+        config: Config,
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/specimens_have_same_taxon.py

@@ -25,7 +25,7 @@ class SpecimensHaveSameTaxonValidator(Validator):
     __config: Config
     __seen: Dict[str, str]
 
-    def __init__(self, config: Config) -> None:
+    def __init__(self, config: Config, **kwargs) -> None:
         super().__init__()
         self.__seen = {}
         self.__config = config

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/sts_fields.py

@@ -28,6 +28,7 @@ class StsFieldsValidator(Validator):
         self,
         config: Config,
         datasource: DataSource = sts(),  # For testing
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/tolid.py

@@ -34,6 +34,7 @@ class TolidValidator(Validator):
         self,
         config: Config,
         datasource=tolid(),
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/unique_values.py

@@ -27,7 +27,8 @@ class UniqueValuesValidator(Validator):
 
     def __init__(
         self,
-        config: Config
+        config: Config,
+        **kwargs
     ) -> None:
 
         super().__init__()

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol/validators/unique_whole_organisms.py

@@ -28,7 +28,7 @@ class UniqueWholeOrganismsValidator(Validator):
     __whole_organisms: List[str]
     __part_organisms: List[str]
 
-    def __init__(self, config: Config) -> None:
+    def __init__(self, config: Config, **kwargs) -> None:
         super().__init__()
         self.__whole_organisms = []
         self.__part_organisms = []

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.7.5b2
+Version: 1.7.5b4
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.7.5b2 → tol_sdk-1.7.5b4}/src/tol_sdk.egg-info/SOURCES.txt

@@ -193,6 +193,7 @@ src/tol/flows/converters/labwhere_location_to_sts_tray_converter.py
 src/tol/flows/converters/mlwh_extraction_to_elastic_extraction_converter.py
 src/tol/flows/converters/mlwh_run_data_to_elastic_run_data_converter.py
 src/tol/flows/converters/mlwh_sequencing_request_to_elastic_sequencing_request_converter.py
+src/tol/flows/converters/skip_null_fields_converter.py
 src/tol/flows/converters/sts_banked_sample_to_elastic_sample_converter.py
 src/tol/flows/converters/sts_manifest_to_elastic_manifest_converter.py
 src/tol/flows/converters/sts_project_to_elastic_sample_update_converter.py
@@ -330,6 +331,7 @@ src/tol/validators/allowed_keys.py
 src/tol/validators/allowed_values.py
 src/tol/validators/allowed_values_from_datasource.py
 src/tol/validators/assert_on_condition.py
+src/tol/validators/converter_and_validate.py
 src/tol/validators/ena_checklist.py
 src/tol/validators/ena_submittable.py
 src/tol/validators/min_one_valid_value.py