tol-sdk 1.7.5b0__tar.gz → 1.7.5b2__tar.gz

{tol_sdk-1.7.5b0/src/tol_sdk.egg-info → tol_sdk-1.7.5b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.7.5b0
+Version: 1.7.5b2
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/pyproject.toml

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

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/ena/client.py

@@ -116,12 +116,13 @@ class EnaApiClient(HttpClient):
         Returns the URL and parameters for a detail query.
         """
         if object_type == 'checklist':
-            ids = ','.join(object_ids)
+            ids = ','.join(str(id_) for id_ in object_ids)
             url = f'{self.__ena_url}/ena/browser/api/xml/{ids}'
             params = {}
             return url, params
         if object_type == 'submittable_taxon':
-            ids = ','.join(object_ids)
+            # This is actually called separately for each taxon id
+            ids = ','.join(str(id_) for id_ in object_ids)
             url = f'{self.__ena_url}/ena/taxonomy/rest/tax-id/{ids}'
             params = {}
             return url, params

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/flows/converters/__init__.py

@@ -34,6 +34,8 @@ from .gap_assembly_to_elastic_assembly_analysis_converter import GapAssemblyToEl
 from .genome_notes_genome_note_to_elastic_genome_note_converter import GenomeNotesGenomeNoteToElasticGenomeNoteConverter  # noqa F401
 from .goat_taxon_to_elastic_species_converter import GoatTaxonToElasticSpeciesConverter  # noqa F401
 from .grit_issue_to_elastic_curation_converter import GritIssueToElasticCurationConverter  # noqa F401
+from .incoming_sample_to_ena_sample_converter import IncomingSampleToEnaSampleConverter # noqa
+from .incoming_sample_to_incoming_sample_with_lists_converter import IncomingSampleToIncomingSampleWithListsConverter  # noqa F401
 from .informatics_tolid_to_elastic_tolid_converter import InformaticsTolidToElasticTolidConverter  # noqa F401
 from .labwhere_location_to_elastic_sample_update_converter import LabwhereLocationToElasticSampleUpdateConverter  # noqa F401
 from .labwhere_location_to_sts_tray_converter import LabwhereLocationToStsTrayConverter  # noqa F401

tol_sdk-1.7.5b2/src/tol/flows/converters/incoming_sample_to_ena_sample_converter.py

@@ -0,0 +1,130 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+# SPDX-License-Identifier: MIT
+
+import re
+from dataclasses import dataclass
+from typing import Iterable
+
+from tol.core import DataObject, DataObjectToDataObjectOrUpdateConverter
+
+
+class IncomingSampleToEnaSampleConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        ena_checklist_id: str
+        project_name: 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]:
+        """
+        converting the samples DataObject into ENA format
+        """
+        s = data_object
+        attributes = {
+            'ENA-CHECKLIST': self.__config.ena_checklist_id,
+            'organism part': self.__replace_underscores(
+                s.attributes.get('ORGANISM_PART')),
+            'lifestage': (
+                'spore-bearing structure'
+                if s.attributes.get('LIFESTAGE') == 'SPORE_BEARING_STRUCTURE'
+                else self.__replace_underscores(
+                    s.attributes.get('LIFESTAGE'))
+            ),
+            'project name':
+                self.__config.project_name,
+            'collected by':
+                self.__replace_underscores(
+                    s.attributes.get('COLLECTED_BY')),
+            'collection date':
+                self.__replace_underscores(
+                    s.attributes.get('DATE_OF_COLLECTION')).lower(),
+            'geographic location (country and/or sea)':
+                self.__collection_country(s).replace('_', ' '),
+            'geographic location (latitude)':
+                self.__replace_underscores(
+                    s.attributes.get('DECIMAL_LATITUDE')).lower(),
+            'geographic location (latitude) units':
+                'DD',
+            'geographic location (longitude)':
+                self.__replace_underscores(
+                    s.attributes.get('DECIMAL_LONGITUDE')).lower(),
+            'geographic location (longitude) units':
+                'DD',
+            'geographic location (region and locality)':
+                self.__collection_region(s).replace('_', ' '),
+            'identified_by':
+                self.__replace_underscores(
+                    s.attributes.get('IDENTIFIED_BY')),
+            'habitat':
+                self.__replace_underscores(
+                    s.attributes.get('HABITAT')),
+            'identifier_affiliation':
+                self.__replace_underscores(
+                    s.attributes.get('IDENTIFIER_AFFILIATION')),
+            'sex':
+                self.__replace_underscores(
+                    s.attributes.get('SEX')),
+            'relationship':
+                self.__replace_underscores(
+                    s.attributes.get('RELATIONSHIP')),
+            'SYMBIONT':
+                'Y' if s.attributes.get('SYMBIONT') == 'SYMBIONT' else 'N',
+            'collecting institution':
+                self.__replace_underscores(
+                    s.attributes.get('COLLECTOR_AFFILIATION'))
+        }
+        if self.__sanitise(s.attributes.get('DEPTH')) != '':
+            attributes['geographic location (depth)'] = s.attributes.get('DEPTH')
+            attributes['geographic location (depth) units'] = 'm'
+        if self.__sanitise(s.attributes.get('ELEVATION')) != '':
+            attributes['geographic location (elevation)'] = s.attributes.get('ELEVATION')
+            attributes['geographic location (elevation) units'] = 'm'
+        if self.__sanitise(s.attributes.get('ORIGINAL_COLLECTION_DATE')) != '':
+            attributes['original collection date'] = s.attributes.get('ORIGINAL_COLLECTION_DATE')
+        if self.__sanitise(s.attributes.get('ORIGINAL_GEOGRAPHIC_LOCATION')) != '':
+            attributes['original geographic location'] = self.__replace_underscores(s.attributes.get('ORIGINAL_GEOGRAPHIC_LOCATION'))  # noqa
+        if s.attributes.get('GAL') is not None:
+            attributes['GAL'] = s.attributes.get('GAL')
+        if s.attributes.get('VOUCHER_ID') is not None:
+            attributes['specimen_voucher'] = s.attributes.get('VOUCHER_ID')
+        if s.attributes.get('SPECIMEN_ID') is not None:
+            attributes['specimen_id'] = s.attributes.get('SPECIMEN_ID')
+        if s.attributes.get('GAL_SAMPLE_ID') is not None:
+            attributes['GAL_sample_id'] = s.attributes.get('GAL_SAMPLE_ID')
+        if s.attributes.get('CULTURE_OR_STRAIN_ID') is not None:
+            attributes['culture_or_strain_id'] = s.attributes.get('CULTURE_OR_STRAIN_ID')
+
+        ret = self._data_object_factory(
+            'sample',
+            s.id,
+            attributes=attributes,
+        )
+        yield ret
+
+    def __collection_country(self, data_object: DataObject):
+        return re.split(
+            r'\s*\|\s*',
+            data_object.attributes.get('COLLECTION_LOCATION'))[0]
+
+    def __collection_region(self, data_object: DataObject):
+        return ' | '.join(re.split(
+            r'\s*\|\s*',
+            data_object.attributes.get('COLLECTION_LOCATION'))[1:])
+
+    def __replace_underscores(self, value):
+        if type(value) != str:
+            return value
+        return self.__sanitise(value, '').replace('_', ' ')
+
+    def __sanitise(self, value, default_value=''):
+        if value is None:
+            return default_value
+        return value

tol_sdk-1.7.5b2/src/tol/flows/converters/incoming_sample_to_incoming_sample_with_lists_converter.py

@@ -0,0 +1,46 @@
+# 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 IncomingSampleToIncomingSampleWithListsConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        fields_to_convert: str
+        separator: 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]:
+        """
+        converting the samples DataObject into ENA format
+        """
+
+        ret = self._data_object_factory(
+            data_object.type,
+            data_object.id,
+            attributes={
+                k: v for k, v in data_object.attributes.items()
+                if k not in self.__config.fields_to_convert
+            } | {
+                field: self.__convert_to_list(data_object.get_field_by_name(field))
+                for field in self.__config.fields_to_convert
+            }
+        )
+        yield ret
+
+    def __convert_to_list(self, value: str | None) -> list[str]:
+        if not value:
+            return []
+        return [item.strip() for item in value.split(self.__config.separator)]

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/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 .ena_checklist import EnaChecklistValidator # noqa
 from .mutually_exclusive import MutuallyExclusiveValidator  # noqa
 from .ena_submittable import EnaSubmittableValidator  # noqa
 from .regex import Regex, RegexValidator  # noqa
@@ -15,6 +16,5 @@ from .sts_fields import StsFieldsValidator  # noqa
 from .tolid import TolidValidator  # noqa
 from .unique_values import UniqueValuesValidator  # noqa
 from .unique_whole_organisms import UniqueWholeOrganismsValidator  # noqa
-# Conditions are used where validators are defined, not just within validators
 from .interfaces import Condition  # noqa
 from .min_one_valid_value import MinOneValidValueValidator   # noqa

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/validators/allowed_values_from_datasource.py

@@ -17,7 +17,6 @@ class AllowedValuesFromDataSourceValidator(Validator):
     """
     @dataclass(slots=True, frozen=True, kw_only=True)
     class Config:
-        allowed_values: List[str | int | float] | None = None
         datasource_instance_id: int
         datasource_object_type: str
         datasource_field_name: str
@@ -30,19 +29,15 @@ class AllowedValuesFromDataSourceValidator(Validator):
     def __init__(
         self,
         config: Config,
+        allowed_values: List[str | int | float] | None = None  # For testing
     ) -> None:
 
         super().__init__()
 
         self.__config = config
-        self.__cached_list = self.__config.allowed_values \
+        self.__cached_list = allowed_values \
             or self.__initialize_list_from_datasource()
 
-        if self.__config.allowed_values is None:
-            self.__cached_list = self.__initialize_list_from_datasource()
-        else:
-            self.__cached_list = self.__config.allowed_values
-
     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)
@@ -59,8 +54,11 @@ class AllowedValuesFromDataSourceValidator(Validator):
         obj: DataObject
     ) -> None:
         field_value = obj.get_field_by_name(self.__config.field_name)
-        if field_value not in self.__cached_list:
-            print(self.__cached_list)
+        if not field_value:
+            return
+        if not isinstance(field_value, list):
+            field_value = [field_value]
+        if any(value not in self.__cached_list for value in field_value):
             multiple_cached_values = len(self.__cached_list) > 1
 
             cached_list_str = ''

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/validators/assert_on_condition.py

@@ -7,7 +7,7 @@ from typing import List
 
 from tol.core import DataObject, Validator
 
-from .interfaces import Condition, ConditionEvaluator
+from .interfaces import Condition, ConditionDict, ConditionEvaluator
 
 
 class AssertOnConditionValidator(Validator, ConditionEvaluator):
@@ -19,8 +19,8 @@ class AssertOnConditionValidator(Validator, ConditionEvaluator):
     """
     @dataclass(slots=True, frozen=True, kw_only=True)
     class Config:
-        condition: Condition
-        assertions: List[Condition]
+        condition: ConditionDict
+        assertions: List[ConditionDict]
 
     __slots__ = ['__config']
     __config: Config
@@ -33,10 +33,10 @@ class AssertOnConditionValidator(Validator, ConditionEvaluator):
     def _validate_data_object(self, obj: DataObject) -> None:
         # Check condition atribute
         # (only perform the assertions if the condition passes)
-        if self._does_condition_pass(self.__config.condition, obj):
+        if self._does_condition_pass(Condition.from_dict(self.__config.condition), obj):
             # Perform each assertion
             for assertion in self.__config.assertions:
-                self.__perform_assertion(obj, assertion)
+                self.__perform_assertion(obj, Condition.from_dict(assertion))
 
     def __perform_assertion(self, obj: DataObject, assertion: Condition) -> None:
         # There's only an error or warning if the assertion condition fails

tol_sdk-1.7.5b2/src/tol/validators/ena_checklist.py

@@ -0,0 +1,73 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+import re
+from dataclasses import dataclass
+
+from tol.core import DataSource
+from tol.core.data_object import DataObject
+from tol.core.validate import Validator
+from tol.sources.ena import ena
+
+
+class EnaChecklistValidator(Validator):
+    """
+    validates the ENA_CHECKLIST for each samples
+    """
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        ena_checklist_id: str
+
+    __slots__ = ['__config']
+    __config: Config
+
+    def __init__(self, config: Config, datasource: DataSource = ena()) -> None:
+        super().__init__()
+        self.__config = config
+        self._datasource = datasource
+
+    def _validate_data_object(self, obj: DataObject) -> None:
+        ena_datasource = self._datasource
+        ena_checklist = ena_datasource.get_one('checklist', self.__config.ena_checklist_id)
+
+        validations = ena_checklist.attributes['checklist']
+        for key in validations:
+            field_name = key
+            if 'field' in validations[key]:
+                field_name = validations[key]['field']
+            if 'mandatory' in validations[key] and key not in obj.attributes:
+                self.add_error(object_id=obj.id, detail='Must be given', field=[field_name])
+                continue
+            if 'mandatory' in validations[key] and obj.attributes[key] is None:
+                self.add_error(object_id=obj.id, detail='Must be given', field=[field_name])
+                continue
+            if 'mandatory' in validations[key] and obj.attributes.get(key) == '':
+                self.add_error(
+                    object_id=obj.id,
+                    detail='Must not be empty', field=[field_name]
+                )
+
+            if 'restricted text' in validations[key] and key in obj.attributes:
+                for condition in validations[key]:
+                    if type(condition) == str and '(' in condition:
+                        regex = condition
+                compiled_re = re.compile(regex)
+                if not compiled_re.search(obj.attributes.get(key)):
+                    self.add_error(
+                        object_id=obj.id,
+                        detail='Must match specific pattern', field=[field_name]
+                    )
+
+            # Check against allowed values
+            if 'text choice' in validations[key] and key in obj.attributes:
+                for condition in validations[key]:
+                    if type(condition) == list:
+                        allowed_values = condition
+                if obj.attributes.get(key).lower() not in \
+                        [x.lower() for x in allowed_values]:
+                    self.add_error(
+                        object_id=obj.id,
+                        detail='Must be in allowed values', field=[field_name]
+                    )

tol_sdk-1.7.5b2/src/tol/validators/interfaces/__init__.py

@@ -0,0 +1,5 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from .condition_evaluator import Condition, ConditionDict, ConditionEvaluator  # noqa

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/validators/interfaces/condition_evaluator.py

@@ -4,11 +4,18 @@
 
 from abc import ABC
 from dataclasses import dataclass
-from typing import Any, Tuple
+from typing import Any, Dict, Tuple, cast
 
 from tol.core import DataObject
 
 
+ConditionDict = Dict[str, str | Any | bool]
+"""
+The dict representation of a Condition. Conditions can be constructed
+from such a dict through Condition.from_dict(condition_dict)
+"""
+
+
 @dataclass(slots=True)
 class Condition:
     field: str
@@ -21,6 +28,40 @@ class Condition:
     def __repr__(self) -> str:
         return f'{self.field} {self.operator} {self.value}'
 
+    @staticmethod
+    def from_dict(condition_dict: ConditionDict) -> 'Condition':
+        """
+        A means of instantiating a Condition from a dictionary.
+        This is a separate method (rather than constructing with kwargs
+        like `Condition(**condition_dict))`) to allow for both precense
+        and type checking for each field.
+        """
+        try:
+            # Extract fields
+            field = condition_dict['field']
+            operator = condition_dict['operator']
+            value = condition_dict['value']
+            is_error = condition_dict.get('is_error', True)
+
+            # Ensure fields are the correct type
+            if not isinstance(field, str) and not isinstance(operator, str):
+                raise Exception(
+                    f'Dictionary {condition_dict} not in valid format '
+                    f'to convert to Condition (type of condition dict incorrect)'
+                )
+
+            return Condition(
+                cast(str, field),
+                cast(str, operator),
+                value,
+                cast(bool, is_error),
+            )
+        except IndexError as e:
+            raise Exception(
+                f'Dictionary {condition_dict} not in valid format '
+                f'to convert to Condition (key "{e.args[0]}" not found)'
+            )
+
 
 class ConditionEvaluator(ABC):
     """

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/validators/mutually_exclusive.py

@@ -7,7 +7,7 @@ from typing import Any, List
 
 from tol.core import DataObject, Validator
 
-from .interfaces import Condition, ConditionEvaluator
+from .interfaces import Condition, ConditionDict, ConditionEvaluator
 
 
 class MutuallyExclusiveValidator(Validator, ConditionEvaluator):
@@ -19,12 +19,16 @@ class MutuallyExclusiveValidator(Validator, ConditionEvaluator):
     """
     @dataclass(slots=True, frozen=True, kw_only=True)
     class Config:
-        first_field_where: Condition
-        second_field_where: Condition
+        first_field_where: ConditionDict
+        second_field_where: ConditionDict
         target_fields: List[str]
         detail: str | None = None
 
         def _get_error_message(self) -> str:
+            # Extract conditions
+            first_condition = Condition.from_dict(self.first_field_where)
+            second_condition = Condition.from_dict(self.second_field_where)
+
             # Use a pre-defined, hard-coded detail message if one was not provided
             if self.detail is None:
                 multiple_target_fields = len(self.target_fields) > 1
@@ -47,8 +51,8 @@ class MutuallyExclusiveValidator(Validator, ConditionEvaluator):
 
                 return (
                     f'The field{possible_plural} {target_fields_str} cannot have the same '
-                    f'value{possible_plural} both when {self.first_field_where} and when '
-                    f'{self.second_field_where}'
+                    f'value{possible_plural} both when {first_condition} and when '
+                    f'{second_condition}'
                 )
             else:
                 return self.detail
@@ -67,7 +71,7 @@ class MutuallyExclusiveValidator(Validator, ConditionEvaluator):
 
     def _validate_data_object(self, obj: DataObject) -> None:
         # Check first field
-        if self._does_condition_pass(self.__config.first_field_where, obj):
+        if self._does_condition_pass(Condition.from_dict(self.__config.first_field_where), obj):
             # Check whether the values of the target fields were found in the second list
             if [
                 obj.get_field_by_name(target_field)
@@ -86,7 +90,7 @@ class MutuallyExclusiveValidator(Validator, ConditionEvaluator):
                 ]
             )
         # Check second field (same as the first condition, but for the second!)
-        elif self._does_condition_pass(self.__config.second_field_where, obj):
+        elif self._does_condition_pass(Condition.from_dict(self.__config.second_field_where), obj):
             # Check whether the values of the target fields were found in the first list
             if [
                 obj.get_field_by_name(target_field)

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/validators/regex.py

@@ -10,6 +10,12 @@ from tol.core import DataObject
 from tol.core.validate import Validator
 
 
+RegexDict = dict[
+    str,
+    str | bool | list[Any],
+]
+
+
 @dataclass(frozen=True, kw_only=True)
 class Regex:
     key: str
@@ -31,7 +37,7 @@ class RegexValidator(Validator):
     """
     @dataclass(slots=True, frozen=True, kw_only=True)
     class Config:
-        regexes: List[Regex]
+        regexes: List[Regex | RegexDict]
 
     __slots__ = ['__config']
     __config: Config
@@ -43,7 +49,7 @@ class RegexValidator(Validator):
 
         super().__init__()
 
-        self.__config = config
+        self.__config = self.__get_config(config)
 
     def _validate_data_object(
         self,
@@ -93,3 +99,18 @@ class RegexValidator(Validator):
                 detail=c.detail,
                 field=c.key,
             )
+
+    def __get_config(
+        self,
+        config: Config,
+    ) -> Config:
+
+        # Ensure config is in Regex format
+        # (as you can either pass in a list of Regex or a RegexDict,
+        # which can be used to initialize a Regex)
+        return self.Config(
+            regexes=[
+                c if isinstance(c, Regex) else Regex(**c)
+                for c in config.regexes
+            ]
+        )

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/validators/regex_by_value.py

@@ -8,7 +8,7 @@ from typing import Dict, List
 from tol.core import DataObject
 from tol.core.validate import Validator
 
-from .regex import Regex
+from .regex import Regex, RegexDict
 
 
 class RegexByValueValidator(Validator):
@@ -20,7 +20,7 @@ class RegexByValueValidator(Validator):
     @dataclass(slots=True, frozen=True, kw_only=True)
     class Config:
         key_column: str
-        regexes: Dict[str, List[Regex]]
+        regexes: Dict[str, List[Regex | RegexDict]]
 
     __slots__ = ['__config']
     config: Config
@@ -32,7 +32,7 @@ class RegexByValueValidator(Validator):
 
         super().__init__()
 
-        self.__config = config
+        self.__config = self.__get_config(config)
 
     def _validate_data_object(
         self,
@@ -78,3 +78,22 @@ class RegexByValueValidator(Validator):
                 detail=c.detail,
                 field=c.key,
             )
+
+    def __get_config(
+        self,
+        config: Config,
+    ) -> Config:
+
+        # Ensure config is in Regex format
+        # (as you can either pass in a list of Regex or a RegexDict,
+        # which can be used to initialize a Regex)
+        return self.Config(
+            key_column=config.key_column,
+            regexes={
+                k: [
+                    c if isinstance(c, Regex) else Regex(**c)
+                    for c in v
+                ]
+                for k, v in config.regexes.items()
+            }
+        )

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol/validators/tolid.py

@@ -90,7 +90,7 @@ class TolidValidator(Validator):
                 f.and_ = {'specimen_id': {'eq': {'value': specimen_id}}}
                 self.__cached_tolids[specimen_id] = list(self.__datasource.get_list(
                     object_type='specimen',
-                    filters=f
+                    object_filters=f
                 ))
 
             if (len(self.__cached_tolids[specimen_id]) == 0):

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.7.5b0
+Version: 1.7.5b2
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.7.5b0 → tol_sdk-1.7.5b2}/src/tol_sdk.egg-info/SOURCES.txt

@@ -185,6 +185,8 @@ src/tol/flows/converters/gap_assembly_to_elastic_assembly_converter.py
 src/tol/flows/converters/genome_notes_genome_note_to_elastic_genome_note_converter.py
 src/tol/flows/converters/goat_taxon_to_elastic_species_converter.py
 src/tol/flows/converters/grit_issue_to_elastic_curation_converter.py
+src/tol/flows/converters/incoming_sample_to_ena_sample_converter.py
+src/tol/flows/converters/incoming_sample_to_incoming_sample_with_lists_converter.py
 src/tol/flows/converters/informatics_tolid_to_elastic_tolid_converter.py
 src/tol/flows/converters/labwhere_location_to_elastic_sample_update_converter.py
 src/tol/flows/converters/labwhere_location_to_sts_tray_converter.py
@@ -328,6 +330,7 @@ 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/ena_checklist.py
 src/tol/validators/ena_submittable.py
 src/tol/validators/min_one_valid_value.py
 src/tol/validators/mutually_exclusive.py

tol_sdk-1.7.5b0/src/tol/validators/interfaces/__init__.py

@@ -1,5 +0,0 @@
-# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
-#
-# SPDX-License-Identifier: MIT
-
-from .condition_evaluator import Condition, ConditionEvaluator  # noqa