tol-sdk 1.8.4__py3-none-any.whl → 1.8.6__py3-none-any.whl

tol/dummy/parser.py

@@ -0,0 +1,70 @@
+# SPDX-FileCopyrightText: 2024 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from __future__ import annotations
+
+import typing
+from abc import ABC, abstractmethod
+from typing import Any, Iterable
+
+from dateutil.parser import parse as dateutil_parse
+
+from ..core import DataObject
+
+if typing.TYPE_CHECKING:
+    from ..core import DataSource
+
+
+DummyResource = dict[str, Any]
+DummyDoc = dict[str, list[DummyResource]]
+
+
+class Parser(ABC):
+
+    def parse_iterable(
+        self,
+        transfers: Iterable[DummyResource]
+    ) -> Iterable[DataObject]:
+        """
+        Parses an `Iterable` of Dummy transfer resources
+        """
+
+        return (
+            self.parse(t) for t in transfers
+        )
+
+    @abstractmethod
+    def parse(self, transfer: DummyResource) -> DataObject:
+        """
+        Parses an individual Dummy transfer resource to a
+        `DataObject` instance
+        """
+
+
+class DefaultParser(Parser):
+
+    def __init__(self, data_source_dict: dict[str, DataSource]) -> None:
+        self.__dict = data_source_dict
+
+    def parse(self, transfer: DummyResource) -> DataObject:
+        ds = self.__dict[transfer.get('type')]
+        return ds.data_object_factory(
+            transfer.get('type'),
+            id_=transfer.get('id'),
+            attributes={
+                k: (
+                    dateutil_parse(v)
+                    if k in ['date'] and v is not None
+                    else v
+                )
+                for k, v in transfer.items()
+                if k not in ['id', 'type', 'category']
+            },
+            to_one={
+                'category': ds.data_object_factory(
+                    'category',
+                    transfer.get('category')
+                ) if 'category' in transfer else None
+            }
+        )

tol/flows/converters/__init__.py

@@ -56,4 +56,8 @@ from .sts_sample_to_casm_benchling_converter import StsSampleToCasmBenchlingConv
 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
+from .default_field_value_if_missing_converter import DefaultFieldValueIfMissingConverter  # noqa F401
+from .prefix_field_converter import PrefixFieldConverter  # noqa F401
+from .combine_fields_converter import CombineFieldsConverter  # noqa F401
 from .auto_detect_manifest_type_converter import AutoDetectManifestTypeConverter # noqa F401
+from .time_string_to_time import TimeStringToTimeConverter # noqa F401

tol/flows/converters/combine_fields_converter.py

@@ -0,0 +1,45 @@
+# 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 CombineFieldsConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        field1: str
+        field2: str
+        dest_field: str
+        lowercase_field1: bool
+
+    __slots__ = ('__config',)
+    __config: Config
+
+    def __init__(self, data_object_factory, config: Config) -> None:
+        super().__init__(data_object_factory)
+        self.__config = config
+
+    def convert(self, data_object: DataObject) -> Iterable[DataObject]:
+        """
+        Concatenates the values of two fields and stores the result in a new field.
+        The first field's value may be lowercased if specified in the configuration.
+        The destination field name is given by the configuration.
+        """
+
+        val1 = data_object.get_field_by_name(self.__config.field1)
+        val2 = data_object.get_field_by_name(self.__config.field2)
+        attributes = dict(data_object.attributes)
+
+        if val1 is not None and val2 is not None:
+            part1 = str(val1).lower() if self.__config.lowercase_field1 else str(val1)
+            attributes[self.__config.dest_field] = f'{part1}{val2}'
+
+        yield self._data_object_factory(
+            data_object.type,
+            data_object.id,
+            attributes=attributes,
+        )

tol/flows/converters/default_field_value_if_missing_converter.py

@@ -0,0 +1,43 @@
+# 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 DefaultFieldValueIfMissingConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        field_name: str
+        default_value: str
+
+    __slots__ = ['__config']
+    __config: Config
+
+    def __init__(self, data_object_factory, config: Config) -> None:
+        super().__init__(data_object_factory)
+        self.__config = config
+
+    def convert(self, data_object: DataObject) -> Iterable[DataObject]:
+        """
+        Adds a default value for a configured field if missing, empty, or None
+        """
+
+        attributes_obj = data_object.attributes
+        if hasattr(attributes_obj, 'get_field_by_name'):
+            current_value = attributes_obj.get_field_by_name(self.__config.field_name)
+        else:
+            current_value = attributes_obj.get(self.__config.field_name)
+        attributes = dict(attributes_obj)
+        if not current_value:
+            attributes[self.__config.field_name] = self.__config.default_value
+
+        ret = self._data_object_factory(
+            data_object.type,
+            data_object.id,
+            attributes=attributes
+        )
+        yield ret

tol/flows/converters/prefix_field_converter.py

@@ -0,0 +1,49 @@
+# 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 PrefixFieldConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        field_name: str
+        prefix: 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]:
+        """
+        Ensures the configured field value
+        starts with the configured prefix. If the field is None, it is
+        left as-is.
+        """
+
+        value = data_object.get_field_by_name(
+            self.__config.field_name
+        )
+
+        if value is not None:
+            value_str = str(value)
+            if not value_str.startswith(self.__config.prefix):
+                value = f'{self.__config.prefix}{value_str}'
+
+        ret = self._data_object_factory(
+            data_object.type,
+            data_object.id,
+            attributes={
+                **data_object.attributes,
+                self.__config.field_name: value
+            }
+        )
+        yield ret

tol/flows/converters/time_string_to_time.py

@@ -0,0 +1,35 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+import re
+from datetime import time
+
+from tol.core import DataObject
+
+
+class Converter:
+    def convert(self, obj):
+        raise NotImplementedError()
+
+
+class TimeStringToTimeConverter(Converter):
+    """
+    Converts string fields representing time in HH:MM (24-hour) format to Python time objects.
+    If the string is not in HH:MM, tries to append ':00' and parse as HH:MM:SS.
+    """
+    def __init__(self, field: str):
+        self.field = field
+
+    def convert(self, obj: DataObject) -> DataObject:
+        value = obj.attributes.get(self.field)
+        if isinstance(value, str):
+            match = re.match(r'^(\d{1,2}):(\d{2})(?::(\d{2}))?$', value)
+            if match:
+                h, m = int(match.group(1)), int(match.group(2))
+                s = int(match.group(3)) if match.group(3) else 0
+                try:
+                    obj.attributes[self.field] = time(h, m, s)
+                except ValueError:
+                    pass
+        return obj

tol/sources/dummy.py

@@ -0,0 +1,17 @@
+# SPDX-FileCopyrightText: 2024 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from ..core import (
+    core_data_object
+)
+from ..dummy import (
+    DummyDataSource,
+    create_dummy_datasource
+)
+
+
+def dummy(**kwargs) -> DummyDataSource:
+    dummy = create_dummy_datasource()
+    core_data_object(dummy)
+    return dummy

tol/sql/auth/blueprint.py

@@ -8,7 +8,6 @@ from datetime import datetime, timedelta
 from typing import Any, Callable, Optional
 from urllib.parse import urlencode
 
-import requests
 from requests.auth import HTTPBasicAuth
 
 from .models import ModelClass, ModelTuple, create_models
@@ -228,9 +227,14 @@ class DbAuthManager(AuthManager):
         Raises:
             requests.HTTPError: If the user info request fails
         """
+
+        client = HttpClient()
+
+        session = client.get_session()
+
         headers = {'Authorization': f'Bearer {token}'}
 
-        r = requests.get(self.__config.user_info_url, headers=headers)
+        r = session.get(self.__config.user_info_url, headers=headers)
         r.raise_for_status()
 
         json_return = r.json()
@@ -401,13 +405,16 @@ class DbAuthManager(AuthManager):
         Raises:
             requests.HTTPError: If the token request fails
         """
-        r = requests.post(
+        client = HttpClient()
+
+        session = client.get_session()
+        r = session.post(
             self.__config.token_url,
-            auth=self.__basic_auth(),
             data=self.__token_post_data(code),
+            auth=self.__basic_auth()
         )
-        r.raise_for_status()
 
+        r.raise_for_status()
         return r.json()
 
     def __basic_auth(self) -> HTTPBasicAuth:

tol/sql/sql_datasource.py

@@ -42,6 +42,7 @@ from ..core.operator import (
     Upserter,
 )
 from ..core.relationship import RelationshipConfig
+from ..core.requested_fields import requested_fields_to_tree
 
 if typing.TYPE_CHECKING:
     from ..core.session import OperableSession
@@ -56,26 +57,6 @@ FilterFactory = Callable[[DataSourceFilter], DatabaseFilter]
 SorterFactory = Callable[[Optional[str]], DatabaseSorter]
 
 
-def requested_fields_to_tree(func):
-    """
-    Allows `requested_fields` keyword arguments to be supplied to methods if a
-    `requested_tree` object has not been given.
-    """
-
-    def wrapper(self, tablename, *args, **kwargs):
-        if 'requested_fields' in kwargs:
-            if 'requested_tree' in kwargs:
-                msg = 'Both requested_fields and requested_tree arguments given'
-                raise TypeError(msg)
-            flds = kwargs.pop('requested_fields')
-            kwargs['requested_tree'] = ReqFieldsTree(
-                tablename, self, requested_fields=flds
-            )
-        return func(self, tablename, *args, **kwargs)
-
-    return wrapper
-
-
 class SqlDataSource(
     Counter,
     Cursor,

tol/sql/standard/factory.py

@@ -485,6 +485,8 @@ def create_standard_models(
             foreign_keys=[data_source_config_id]
         )
 
+        source_order: Mapped[list[str]] = mapped_column(JSONB, nullable=True)
+
     class DataSourceConfigSummary(base_model_class):
         __tablename__ = 'data_source_config_summary'
 

tol/validators/ena_checklist.py

@@ -12,6 +12,11 @@ from tol.sources.ena import ena
 
 
 class EnaChecklistValidator(Validator):
+    ENA_TO_INTERNAL_FIELD_MAP = {
+        'geographic location (longitude)': 'DECIMAL_LONGITUDE',
+        'geographic location (latitude)': 'DECIMAL_LATITUDE',
+    }
+
     """
     validates the ENA_CHECKLIST for each samples
     """
@@ -37,16 +42,18 @@ class EnaChecklistValidator(Validator):
             field_name = key
             if 'field' in validation:
                 field_name = validation['field']
+            internal_field = self.ENA_TO_INTERNAL_FIELD_MAP.get(field_name, field_name)
+
             if 'mandatory' in validation and key not in obj.attributes:
-                self.add_error(object_id=obj.id, detail='Must be given', field=[field_name])
+                self.add_error(object_id=obj.id, detail='Must be given', field=[internal_field])
                 continue
             if 'mandatory' in validation and obj.attributes[key] is None:
-                self.add_error(object_id=obj.id, detail='Must be given', field=[field_name])
+                self.add_error(object_id=obj.id, detail='Must be given', field=[internal_field])
                 continue
             if 'mandatory' in validation and obj.attributes.get(key) == '':
                 self.add_error(
                     object_id=obj.id,
-                    detail='Must not be empty', field=[field_name]
+                    detail='Must not be empty', field=[internal_field]
                 )
 
             if 'restricted text' in validation and key in obj.attributes:
@@ -55,12 +62,25 @@ class EnaChecklistValidator(Validator):
                         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]
-                    )
+                    if internal_field in ('DECIMAL_LONGITUDE', 'DECIMAL_LATITUDE'):
+                        self.add_error(
+                            object_id=obj.id,
+                            detail=(
+                                f'Value for {internal_field} must be a valid decimal in the'
+                                f' format required by ENA (e.g. 12.3456). '
+                                f'See ENA checklist for accepted format.',
+                            ),
+                            field=[internal_field]
+                        )
+                    else:
+                        self.add_error(
+                            object_id=obj.id,
+                            detail=(
+                                f'Value for {internal_field} must match the required pattern.'
+                            ),
+                            field=[internal_field]
+                        )
 
-            # Check against allowed values
             if 'text choice' in validation and key in obj.attributes:
                 for condition in validation:
                     if isinstance(condition, list):
@@ -69,5 +89,5 @@ class EnaChecklistValidator(Validator):
                         [x.lower() for x in allowed_values]:
                     self.add_error(
                         object_id=obj.id,
-                        detail='Must be in allowed values', field=[field_name]
+                        detail='Must be in allowed values', field=[internal_field]
                     )

tol/validators/specimens_have_same_taxon.py

@@ -53,7 +53,7 @@ class SpecimensHaveSameTaxonValidator(Validator):
             if specimen_id in self.__seen and taxon_id != self.__seen[specimen_id]:
                 self.add_error(
                     object_id=obj.id,
-                    detail='A non-symbiont must have a matching Specimen ID and Taxon ID',
+                    detail='All samples from the same specimen_ID must have the same TAXON_ID.',
                     field=self.__config.specimen_id_field,
                 )
             if specimen_id not in self.__seen:

tol/validators/types.py

@@ -55,12 +55,19 @@ class TypesValidator(Validator):
                     continue
                 type_class = type_map.get(expected_type)
                 if type_class and not isinstance(actual_value, type_class):
-                    self.__add_result(
-                        obj,
-                        key,
-                        detail=f'Field {key} value "{actual_value}" is not of type '
-                               f'"{expected_type}"',
-                    )
+                    if expected_type == 'time':
+                        self.__add_result(
+                            obj,
+                            key,
+                            detail='Only HH:MM format is accepted.',
+                        )
+                    else:
+                        self.__add_result(
+                            obj,
+                            key,
+                            detail=f'Field {key} value "{actual_value}" is not of type '
+                                   f'"{expected_type}"',
+                        )
                 if type_class and isinstance(actual_value, type_class):
                     # Special case for bool since isinstance(True, int) is True
                     if expected_type == 'int' and isinstance(actual_value, bool):

tol/validators/value_check.py

@@ -26,11 +26,12 @@ class ValueCheckValidator(Validator):
         self.__config = config
 
     def _validate_data_object(self, obj: DataObject) -> None:
-        # This function is used to check if the data object is SYMBIONT or not
-
-        if obj.attributes.get(self.__config.field) == self.__config.value:
+        if obj.attributes.get(self.__config.field) != self.__config.value:
             self.add_error(
                 object_id=obj.id,
-                detail=f'{self.__config.value} is detected',
+                detail=(
+                    f"Expected '{self.__config.value}' for field "
+                    f"'{self.__config.field}', but got '{obj.attributes.get(self.__config.field)}'"
+                ),
                 field=self.__config.field,
             )

{tol_sdk-1.8.4.dist-info → tol_sdk-1.8.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.4
+Version: 1.8.6
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.4.dist-info → tol_sdk-1.8.6.dist-info}/RECORD

@@ -10,7 +10,7 @@ tol/api_base/blueprint.py,sha256=AHCvBUwvXbXtKuRv_MmQNtMrXnVEtdNVZMh-_CMsYY0,193
 tol/api_base/controller.py,sha256=5Fp2FobjXXPlongu1j7adGJKlSVufW0_jpk_wZIMRa4,26818
 tol/api_base/data_upload.py,sha256=z8Kp4BWQ6q06vT9ZwS8cgedWuGxBwZLkT6xpHk1K008,2939
 tol/api_base/pipeline_steps.py,sha256=Y3rcqQh1w4F0tCxMLGI3H8W3pbl54OWLrUYbBR44Y4A,5850
-tol/api_base/system.py,sha256=c47sbcNaCd3teiJLO-Zwg1cUNvfCvRO4GmKzAMNxZrw,1219
+tol/api_base/system.py,sha256=NLvG1eQnIgOa5H_NYufVn87NZtpazpmITPFJqm5KMZI,1822
 tol/api_base/auth/__init__.py,sha256=LNbVtQDlzKWzLoCmxAPSIAcM6mlVMnn0Aj9HFUudseo,460
 tol/api_base/auth/asserts.py,sha256=3kHP2yW6HZxevIgeO8Rl3iKovi8WHZcguVbPSFUjawQ,2765
 tol/api_base/auth/blueprint.py,sha256=-Bv5FNnyr73NpdRlqjkq3h4J5-29BrM01bxfBPPHUV8,2209
@@ -31,15 +31,15 @@ tol/api_base/misc/list_get_parameters.py,sha256=6DtUgfKPTok3utKPOxceJdwV_ZnJ5nis
 tol/api_base/misc/relation_url.py,sha256=qfo-okp8Gv9-PEDghMfGZ2pHdYbHRhohvA9v3Govtlo,1127
 tol/api_base/misc/stats_parameters.py,sha256=IVpHqUeGQyjuih59jwqT-fIQMCBeESi2T9b4r9i4J28,1721
 tol/api_client/__init__.py,sha256=58SAywuMrIUCBAY9us_d_RLTMnaUTYWWts0LRQC5wLo,187
-tol/api_client/api_datasource.py,sha256=9CPNsujgnp__EwkZGwu9ZTmOxSwOldfLraOEQ7GBLng,14490
-tol/api_client/client.py,sha256=hNqoyGPSiKSiT2DeHi13agrDBlXIWm7wtNjrMRCUuQg,13977
+tol/api_client/api_datasource.py,sha256=AYvaOqsrTuBu8CTRSmm9Fo-VHReJAQjpZUSZc63dLXQ,15161
+tol/api_client/client.py,sha256=H4X5_Jj-JmnaeAN85ghCWGtQUhYprOZqJXNmCJq_Vz0,14216
 tol/api_client/converter.py,sha256=g32fjqga4mC923n95HmQImPuawMfeb9rQcl3ZxUWP2s,4463
 tol/api_client/exception.py,sha256=MkvJaIyRVCzQ2rKOYnCOcT747mpOeQwGJJl3Kkb1BsQ,3999
-tol/api_client/factory.py,sha256=WGHA5wio4XS8OHqG07DLSVjehOeAsVoVCc5phAIq4H8,3737
+tol/api_client/factory.py,sha256=PHRMpCJwBcgaEU_9x_9hNM__RI0udTN7Q7xzAxfVcNk,3492
 tol/api_client/filter.py,sha256=D49RIai5Yj4CiQvIkgaEIXdw_oSU7CD5cn9SdXWRYXU,1474
 tol/api_client/parser.py,sha256=88Q2RlPwn9JJsSIukC2_yxfaM2AaXjsGuDOESqY7se4,8351
 tol/api_client/validate.py,sha256=9wFZotTJ4fI21BdO5AuMZok0rDQ4s8zM_WojLdVvA0A,3071
-tol/api_client/view.py,sha256=DvhRTA957Fn5vVPByV7e8ngvJaD9DSa5SaJ48ONWQlU,8753
+tol/api_client/view.py,sha256=LGojaC0vCPkjemV8A83b3T_uDVQ002nQYgAZN7JapIU,8763
 tol/barcodes/__init__.py,sha256=k9KoBO0xJyxg1kanLrN0E3HuVSbbpfSInGEsWX-8UsY,214
 tol/barcodes/main.py,sha256=QxueF2AdrclIaQuu7W4lb4eF5tU_l-p3UMsDFIYgCfo,6213
 tol/benchling/__init__.py,sha256=9VIL6PBxvZRaBrN1j2Di75MdEY261kEHs_D-lUutIlg,229
@@ -100,7 +100,7 @@ tol/core/datasource_utils.py,sha256=18mwvFmtJL73_mxtFb56rKXZCGCtZFoEb8sWFKn3Yf0,
 tol/core/factory.py,sha256=pLLu8l-yK8QaLTt52izMhKZ2VlFHqRQlUHwMaLL6DI4,9156
 tol/core/http_client.py,sha256=QyZarplEHVYIrqEfrySeHbawfbnBU4nN62TLt41x4tY,2242
 tol/core/relationship.py,sha256=etdyCjLbfi2tgkaqzE6cntpNtTzgT_jOPGeNKmPu5yc,4624
-tol/core/requested_fields.py,sha256=QFNky8QmT1Cmfn42EYPciwbCueJ0DVQNKkP0Vz-_7Jk,6715
+tol/core/requested_fields.py,sha256=-UXBnalzK1Fd-6zaYbZxlvlQOqIndOW0Zjvr4Z5UgaQ,7397
 tol/core/session.py,sha256=6AohamIEfB8oV3Z414ishKqmlTgVfUaGYWzvxLgZgM4,3803
 tol/core/validate.py,sha256=kFRPhgYyeZisGbSXR7S1pmD8jvz_aZ7RX40bT-gD_iA,4083
 tol/core/operator/__init__.py,sha256=ircyLdj45IlaL5k0cDzWHjEr-_66BAx7YRbuEvWF30k,1826
@@ -124,6 +124,12 @@ tol/core/operator/statter.py,sha256=qCyJ6AOeyvDy5t0tQEJr6-p-5Rw6vVwlQ-PXTmHXn8c,
 tol/core/operator/summariser.py,sha256=l7kmcvI_s9TkLGQf9XModrMziqvxKH6jdyo-mROUUxU,5823
 tol/core/operator/updater.py,sha256=uLx02Mw77c6sHCw76pdJIArlGbk6N7HDv4FUf0C542w,1055
 tol/core/operator/upserter.py,sha256=0sAx13I-_YiXnzGC7t8N23BZFiil9FxT9S0WJ8Z6EKk,2603
+tol/dummy/__init__.py,sha256=A7mBVh-j6rmSZ_Chk3FodUCSb42vreeP4pG0GKz0ZCM,193
+tol/dummy/client.py,sha256=tU5Oj-XWuvo2G6JYUyHvC6Oc5TZ--tbWsMf8-DA0pss,2516
+tol/dummy/converter.py,sha256=WU4y3VyYDhJLERqBqROKmEK0glwWlGPeF9XoDYtQY50,1068
+tol/dummy/dummy_datasource.py,sha256=wgbO2qycdApAARL3y_9WsiUftyMCxoVuQktNzBAjAp8,2862
+tol/dummy/factory.py,sha256=Jf5Oo5D_FlQMthIMLEF2kROxpJIoXiB7qG8DsCJdGn8,2105
+tol/dummy/parser.py,sha256=xQRTLRdMdwolkQ1KXkS5RxTDiKwrLWwLd3lpXIAGCew,1793
 tol/elastic/__init__.py,sha256=5zOZ83jkup26AHrTEhLw4Pve548uN3gnzC6fe_mtm-Q,166
 tol/elastic/elastic_datasource.py,sha256=XPMr5sn64qPMe9H6Rf6xd-6TgMagVJzaZ2J1wZfRvwM,42041
 tol/elastic/runtime_fields.py,sha256=08N8JnbF1U2znSK9mpuCoyQjxiCShuxsggljptfCVoE,4479
@@ -149,7 +155,7 @@ tol/flows/__init__.py,sha256=M7iSvnBJs6fJ8M38cW0bYQa9WW0TN8FHAMjIHPDNAJ4,166
 tol/flows/logger.py,sha256=rWXbaknGcPEZRFvC1CiB1qkhFRZsQk435w7VyJ3cpyw,170
 tol/flows/secrets.py,sha256=1mlbsxaahzYRfVAx3XdztHOmUCtDMSJDzHysdbaCtj0,352
 tol/flows/sequencing_submissions.py,sha256=ukz_y5be-BCBN2y3JPQ2EK6b3jwOCh-187j-jnw3EUY,11027
-tol/flows/converters/__init__.py,sha256=QgbwWIbMKI8LWZBwYVrHARKi03ISLDS3yzpHNPRLXdk,6324
+tol/flows/converters/__init__.py,sha256=m2q04EXBdG5SZ3ieMsm_ork9eUuj-g8z6ulMOlVHs4U,6641
 tol/flows/converters/auto_detect_manifest_type_converter.py,sha256=uHakTmVHMbm2kFQOWaAv8ynD9ueh7p-kq6wmfEGnmEw,1361
 tol/flows/converters/benchling_entity_to_benchling_worklist_item_converter_factory.py,sha256=PN27fcvN4JLBnLrtPPAot1cWjAwPQHVcIDoMfPDeKzU,1210
 tol/flows/converters/benchling_extraction_to_elastic_extraction_converter.py,sha256=S8pbmIeKlcXrLPRJHYBUGP0-Q7jTOV2QQk2TeA2naWo,1966
@@ -165,6 +171,8 @@ tol/flows/converters/bioscan_qc_specimen_to_elastic_sample_update_converter.py,s
 tol/flows/converters/bioscan_qc_uksi_entry_to_elastic_sample_update_converter.py,sha256=F_81d9XweccUWPppIzuq1rHVEaIctwoFBmWf9g9jWtw,650
 tol/flows/converters/bold_bin_to_elastic_sample_update_converter.py,sha256=viQNm-3PGCTf8zUHax3H1PpZSfW2P9HCocVL8h9O74o,579
 tol/flows/converters/bold_sample_to_elastic_sample_update_converter.py,sha256=eehTzW37x4IINKtMdXDrgSk-Iptx1k8_IR1WDNX1JtA,585
+tol/flows/converters/combine_fields_converter.py,sha256=S_Bm4dix18kgmfPF6TEUTp05Wv53hJPR2MjtGjn8BrI,1528
+tol/flows/converters/default_field_value_if_missing_converter.py,sha256=81xKskti_cpAEIs7A1arG9nlaIvrl1TkQj6URvFI3o0,1397
 tol/flows/converters/elastic_object_to_portaldb_object_converter.py,sha256=YVUTYMvsLwDfq33WQbyIDl2d3D5jEcMxhqnGhx3HtQ4,1600
 tol/flows/converters/elastic_sample_to_benchling_tissue_converter.py,sha256=zsybAg8ZyRI_ibTpkvSy7Zn2lNzUYmhc9SNMQQFj1HE,1103
 tol/flows/converters/elastic_sample_to_benchling_tissue_update_converter.py,sha256=2Y_Kn8Z5_Sksgah9p4Q3Gy4Em3KOAG-rnzmy4_jtod0,3726
@@ -190,6 +198,7 @@ tol/flows/converters/labwhere_location_to_sts_tray_converter.py,sha256=dSBP5Hfdv
 tol/flows/converters/mlwh_extraction_to_elastic_extraction_converter.py,sha256=047eU_3Zb3ZlJ8utrk3o_VW7jifv5VO0WxgmFg-QkaE,1195
 tol/flows/converters/mlwh_run_data_to_elastic_run_data_converter.py,sha256=f0I_N8DH_9Kom4Fpl_O7hKTUPPiURWeyhxWN3XFLmLk,1313
 tol/flows/converters/mlwh_sequencing_request_to_elastic_sequencing_request_converter.py,sha256=zXYkq37qsvHEY7O1zh2vOoMBdt8hE7T1SuFIOR2DQrM,1209
+tol/flows/converters/prefix_field_converter.py,sha256=MHYvreOygcEOZdqF067MrDmWQWiLcp_c0w5-juK4oY4,1435
 tol/flows/converters/skip_null_fields_converter.py,sha256=IlLrX31XWpQ58indW-hk9eApMunu2HGFhMConYDmxtU,1226
 tol/flows/converters/sts_banked_sample_to_elastic_sample_converter.py,sha256=HK_3Q60E6CKCT8YSWbZXu0Wqs2mmBLYhcD0OEwXM4Qs,688
 tol/flows/converters/sts_manifest_to_elastic_manifest_converter.py,sha256=Ko3ulOFXXYaZB1YUiwu_HPlP5oPZeI65hViAZ05cioQ,1806
@@ -198,6 +207,7 @@ tol/flows/converters/sts_sample_project_to_elastic_sample_converter.py,sha256=YE
 tol/flows/converters/sts_sample_to_casm_benchling_converter.py,sha256=Zo577u2v5_Fela2uQVtZsGZmHq4bLecTCC4Ewvq61Xo,39414
 tol/flows/converters/sts_sampleset_to_elastic_sampleset_converter.py,sha256=PUP0Qjy9wTmqp5GHNEd9fukqtWdoMvDfs4rJisfLzcc,3197
 tol/flows/converters/sts_species_to_elastic_species_converter.py,sha256=ELZ_ML8vPlLkfXrx0B_wxUWiPyxkI8UXgSPQZCKknXU,1164
+tol/flows/converters/time_string_to_time.py,sha256=myo9K9pRMT6GtT5vXf3c0UDK5n8bMVbvW7ewhSPkecU,1062
 tol/flows/converters/tolid_specimen_to_elastic_tolid_converter.py,sha256=4Ird6ATYjsjSFZ1AGsxpuWdQ6QtQTvKJ-rF-_TCC_rg,1072
 tol/flows/converters/tolqc_data_to_elastic_run_data_converter.py,sha256=f9PYnsswikskvXpnSlrfYN7wXfyn8iXQpg996ZsQHbw,3799
 tol/flows/converters/tolqc_sample_to_elastic_sequencing_request_converter.py,sha256=MzPcO75Z_3-6nsWC8X0kmmmxJTurV_HOZhseC-tWdFo,1397
@@ -267,6 +277,7 @@ tol/sources/bioscan_qc.py,sha256=XpU7gufFOcjtUEgW65nNGATrpt6utWhON-kCogDhEaM,171
 tol/sources/bold.py,sha256=vbJGRaO-xJj7-mNcaUEPC_YTNTlb1_442YP3sGvCbu4,674
 tol/sources/copo.py,sha256=L03fFT3x1xWe3IpbijoVnKDGlncVQPmKhuGcAjdAuYg,485
 tol/sources/defaults.py,sha256=wnxLSqZzxgQYwSJCshzfjJ0gzw7Au7Ag75aC3C9IzeA,1463
+tol/sources/dummy.py,sha256=p2eZWpsKd2bv_uZW0sBGCgpr0Sye_35g1VEeWOlNZlc,328
 tol/sources/elastic.py,sha256=LNl0MKT8jZta2aCB9Jjl4lJkC9b8Qd4TjgmyqLgQxWw,1058
 tol/sources/ena.py,sha256=BnCq_tGAOQ3Ij0afcArjFaMjYG1MqGRJUrGZhnpvxYY,615
 tol/sources/gap.py,sha256=h3dwi-Y19kT6vRsU-GHtZBgD-piaHR4r4wqU7qBIGww,1544
@@ -302,16 +313,16 @@ 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=jLPQSolGtKRKezjVnMrlj8YO6bLepyiFARMbDYEXuN8,16219
+tol/sql/sql_datasource.py,sha256=RnPkfg4TSHaxfJG77eBrNgBAKexJaypc-fvfFzssdac,15598
 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
-tol/sql/auth/blueprint.py,sha256=3M55fYi_H1PgFaFxYSW8pgOwgFwdl1lN6VRbEt1r8N8,26008
+tol/sql/auth/blueprint.py,sha256=1B4RqYKxOfoBhrNY6qrsPO1kHSfaUfKyoAzjPSCZGs4,26131
 tol/sql/auth/models.py,sha256=U4CsKMMyzGMg6hj4tp_iRenr3_Q--64WJmHWvxQ2--Q,12297
 tol/sql/pipeline_step/__init__.py,sha256=O7u4RrLfuoB0mwLcPxFoUrdTBZGB_4bE1vWCn5ho-qw,147
 tol/sql/pipeline_step/factory.py,sha256=FaO61WLST4GQdAWuCIGqAvpVBvzkfBOgZWgHEZy2OXo,5483
 tol/sql/standard/__init__.py,sha256=2NbLXFk0rneGZosZ2ESIRcT0WMK0KncmPWaLPqvX-i4,142
-tol/sql/standard/factory.py,sha256=yY8iWmZRMvUqphwnzBeOIQtKGgxsU6AcA7YTz53UYvc,20010
+tol/sql/standard/factory.py,sha256=zCCbPBpPwoTNKacqSjWXFY8ROGzHx8IaL7TsrGUeelM,20089
 tol/status/__init__.py,sha256=sBo-j1wCmberl89uryVCBEJk8ohbfsYhaNpIp_brR9Y,146
 tol/status/status_datasource.py,sha256=UYU2vB561XRWY8y2dY96qHiWXy15xaHxsbGCVCIUnqs,1916
 tol/sts/__init__.py,sha256=1nb_lBWDwxJo3hutxSid2rqMIpfZ4GHxDS6cfj-FKv4,187
@@ -331,25 +342,25 @@ tol/validators/assert_on_condition.py,sha256=eBGgSVfIQ6e45SheM-ZDg7daXJjyZxRVS5L
 tol/validators/branching.py,sha256=7YFjHNjrrTmy4hZ3E7JKDT6MEsBMhrc3P3p3ykv4wKI,5720
 tol/validators/converter_and_validate.py,sha256=O1uYdrU4YDZ8eZjb7Koots4-8fMVOkJFXESg-LVw2o8,2992
 tol/validators/date_sorting.py,sha256=NzYsBfhgeG4NYlYjVUYgcGGwEHns5hESqeaPvXUxjUI,1918
-tol/validators/ena_checklist.py,sha256=M10VAFGpaxnm7rWO4jmFhTWkYRlCmU0Ox2IUEDFGKbo,2812
+tol/validators/ena_checklist.py,sha256=2IfgzdgpumTPPwzoycIpfFFnkTSRlEjpZ8RQYQpBoXY,3771
 tol/validators/ena_submittable.py,sha256=CujF9t4mA4N3Wm_5rA5MRp401aW19kbioOZpfWVXg6I,1965
 tol/validators/min_one_valid_value.py,sha256=gZUHtfRA-Lvpw0d1FJoAA31cRJpLbbxAJCC9DCt5lCY,1442
 tol/validators/mutually_exclusive.py,sha256=6blZK-2IY4Eq79fHKKrm-pxsQ6B5DNH5ldtxOFVCPhU,4492
 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=m2LLRIZMdhPj1fzyioDJOraI6UHXgy1l963xhezgk7E,2177
+tol/validators/specimens_have_same_taxon.py,sha256=BaJcZ38ZprPcuGTIorSxxC9uGN0_lj6HS6B54EObcuY,2183
 tol/validators/sts_fields.py,sha256=aYbzy15btEg4-ocDT1qrspe7-atoWRrOJ_KmuPU6J14,8936
 tol/validators/tolid.py,sha256=yODebLYbKtlem3IpVcv8XImvq90r-AK68asH9JEawqo,3897
-tol/validators/types.py,sha256=KDBNqx5isJG5XI1l2V9Wmi9135ZwDace3MU6Qij3J6E,2612
+tol/validators/types.py,sha256=jMVpckRp8RS93f7usf58YH_K-5rKWgZIYs7bO9dHhQc,2914
 tol/validators/unique_value_check.py,sha256=sFvDooYkKeORvULGEOTsgIcxlbe0AXDWxY3Gbr3j0KI,1282
 tol/validators/unique_values.py,sha256=o5IrfUNLEmlEp8kpInTtFnTq-FqiHSC9TItKdf-LI1o,3114
 tol/validators/unique_whole_organisms.py,sha256=RdqA1GzIf3LTdrmNGGdxv0aW2udDY2P9EaqZb40hhik,5735
-tol/validators/value_check.py,sha256=lxfhfL8BCIs_B838CQ5znJ6KFD7ms_fSVCS9QuVearE,1052
+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-1.8.4.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
-tol_sdk-1.8.4.dist-info/METADATA,sha256=g4uV0VKLkExU3Zc1waAU3ukQbtb6wRhzkaZgX-BoT5Y,3142
-tol_sdk-1.8.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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-tol_sdk-1.8.4.dist-info/RECORD,,
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