tol-sdk 1.8.3__py3-none-any.whl → 1.8.5__py3-none-any.whl

tol/api_client/client.py

@@ -206,7 +206,7 @@ class JsonApiClient(HttpClient):
         )
 
         headers = self._merge_headers()
-        session = self._get_session()
+        session = self.get_session()
         r = session.post(
             url,
             headers=headers,
@@ -228,7 +228,7 @@ class JsonApiClient(HttpClient):
 
         url = self.__insert_url(object_type)
         headers = self._merge_headers()
-        session = self._get_session()
+        session = self.get_session()
         r = session.post(url, headers=headers, json=transfer)
         self.__assert_no_error(r)
         return r.json()

tol/api_client/view.py

@@ -197,7 +197,7 @@ class DefaultView(View):
             sub_tree = tree.get_sub_tree(rel)
             if sub_tree and rel in data_object._to_many_objects:
                 many_obj = data_object._to_many_objects.get(rel)
-                to_many[rel] = [self.__dump_stub(x, rel) for x in many_obj]
+                to_many[rel] = {'data': [self.__dump_stub(x, rel) for x in many_obj]}
                 for obj in many_obj:
                     included.add_dump(self.__dump_object(obj, included, sub_tree))
             elif quoted_id:

tol/core/http_client.py

@@ -55,7 +55,7 @@ class HttpClient:
             **__empty_if_none(self.__token)
         }
 
-    def _get_session(self) -> requests.Session:
+    def get_session(self) -> requests.Session:
 
         cert_path = os.path.join(
             os.path.dirname(__file__),
@@ -74,7 +74,7 @@ class HttpClient:
         """
         Attempts a call to the endpoint 5 times, with a delay of 1 second
         """
-        session = self._get_session()
+        session = self.get_session()
 
         retry_strategy = Retry(
             total=self.__retries,

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/sql/auth/blueprint.py

@@ -22,6 +22,7 @@ from ...api_base.auth import (
 )
 from ...api_base.auth.abc import AuthorisationManager
 from ...api_base.misc import AuthContext
+from ...core import HttpClient
 
 
 class DbAuthManager(AuthManager):
@@ -194,7 +195,12 @@ class DbAuthManager(AuthManager):
         Raises:
             requests.HTTPError: If the revocation request fails
         """
-        r = requests.post(
+
+        client = HttpClient()
+
+        session = client.get_session()
+
+        r = session.post(
             self.__config.revoke_url,
             data={
                 'token': token,

tol/validators/__init__.py

@@ -21,4 +21,6 @@ from .unique_whole_organisms import UniqueWholeOrganismsValidator  # noqa
 from .interfaces import Condition  # noqa
 from .min_one_valid_value import MinOneValidValueValidator   # noqa
 from .value_check import ValueCheckValidator  # noqa
+from .branching import BranchingValidator  # noqa
 from .unique_value_check import UniqueValueCheckValidator  # noqa
+from .date_sorting import DateSortingValidator # noqa

tol/validators/branching.py

@@ -0,0 +1,160 @@
+# SPDX-FileCopyrightText: 2026 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+import importlib
+from dataclasses import dataclass
+from typing import Dict, List, cast
+
+from tol.core import DataObject
+from tol.core.validate import ValidationResult, Validator
+
+from .interfaces import Condition, ConditionDict, ConditionEvaluator
+
+
+Subvalidation = Dict[str, ConditionDict | str | Dict]
+
+
+class BranchingValidator(Validator, ConditionEvaluator):
+    """
+    This validator is configured with a list of conditions.
+    If a condition passes, the corresponding sub-validator will be run.
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        """
+        ```
+        validations=[
+            {
+                'condition': {
+                    'field': 'column_name',
+                    'operator': '==',
+                    'value': 'expected_value',
+                },
+                'module': '<path.to.module>',
+                'class_name': '<path.to.ValidatorClass>',
+                'config_details': { ... },
+            },
+            {
+                ...
+            }
+        ]
+        ```
+        """
+        validations: List[Subvalidation]
+
+    __slots__ = ['__config', '_cached_validators']
+    __config: Config
+    _cached_validators: Dict[int, Validator]
+    """
+    Stores all sub-validators that have already been seen so that they can be used again.
+    Their keys are their indexes in the `validations` list in the validator config
+    """
+
+    def __init__(
+        self,
+        config: Config,
+        **kwargs
+    ) -> None:
+        super().__init__()
+
+        del kwargs
+        self.__config = config
+        self._cached_validators = {}
+
+    def _validate_data_object(
+        self,
+        obj: DataObject
+    ) -> None:
+        for subvalidator_index, subvalidation in enumerate(self.__config.validations):
+            # Do not run this sub-validation if its condition does not pass
+            condition_dict = cast(ConditionDict, subvalidation['condition'])
+            if not self._does_condition_pass(Condition.from_dict(condition_dict), obj):
+                continue
+
+            # Obtain validator, either from cache or anew
+            validator: Validator
+            if subvalidator_index in self._cached_validators:
+                # Use existing validator to perform subvalidation
+                validator = self._cached_validators[subvalidator_index]
+            else:
+                # Create a new validator and use that for the subvalidation
+                validator = self.__instantiate_validator(subvalidation)
+
+                # Add the new validator to the store of cached validators
+                self._cached_validators[subvalidator_index] = validator
+
+            # Validate data object
+            validator._validate_data_object(obj)
+
+            # At this point, I initially added `break` so that once a condition passed, the rest
+            # did not need to be checked. However, I decided against it because it is more flexible
+            # to have the opportunity to allow multiple conditions to pass, and thus execute
+            # multiple subvalidations, on the same `DataObject` in the same iteration
+
+    def __instantiate_validator(self, subvalidation: Subvalidation) -> Validator:
+        # Before attempting to extract items from the subvalidation, ensure all of the required
+        # keys are there and that they contain values of the correct types.
+        # This allows the dictionary to be safely queried thereafter
+        try:
+            # Accessing with square brackets will also check whether the key exists or not
+            if not isinstance(subvalidation['module'], str):
+                raise TypeError('module')
+            elif not isinstance(subvalidation['class_name'], str):
+                raise TypeError('class_name')
+        except (KeyError, TypeError) as e:
+            # Make errors more specific to validators
+            if isinstance(e, KeyError):
+                raise KeyError(
+                    f'Invalid config in BranchingValidator: `{e.args[0]}` not found'
+                )
+            else:
+                raise TypeError(
+                    f'Invalid config in BranchingValidator: '
+                    f'`{e.args[0]}` contains an erroneous value type'
+                )
+
+        # Dynamically retrieve the validator class
+        validator_module = importlib.import_module(subvalidation['module'])
+        validator_class = getattr(validator_module, subvalidation['class_name'])
+
+        # Construct and return the new validator
+        validator_config = validator_class.Config(
+            subvalidation['config_details']
+        )
+        return validator_class(
+            config=validator_config,
+        )
+
+    @property
+    def results(self) -> List[ValidationResult]:
+        """
+        Fetches results from all sub-validators, collated into a single list
+        """
+        return [
+            result
+            for validator in self._cached_validators.values()
+            for result in validator.results
+        ]
+
+    @property
+    def warnings(self) -> List[ValidationResult]:
+        """
+        Fetches warnings from all sub-validators, collated into a single list
+        """
+        return [
+            warning
+            for validator in self._cached_validators.values()
+            for warning in validator.warnings
+        ]
+
+    @property
+    def errors(self) -> List[ValidationResult]:
+        """
+        Fetches errors from all sub-validators, collated into a single list
+        """
+        return [
+            error
+            for validator in self._cached_validators.values()
+            for error in validator.errors
+        ]

tol/validators/date_sorting.py

@@ -0,0 +1,58 @@
+# SPDX-FileCopyrightText: 2026 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from dataclasses import dataclass
+from datetime import date, datetime
+
+from tol.core import Validator
+from tol.core.data_object import DataObject
+
+
+class DateSortingValidator(Validator):
+    """
+    Validates an incoming stream of `DataObject` instances.
+    For each data object (sample) check the collection date
+    is not preceding the plating date
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        dates: list[str]
+
+    __slots__ = ['__config']
+    __config: Config
+
+    def __init__(self, config: Config, **kwargs) -> None:
+        super().__init__()
+        self.__config = config
+
+    def _validate_data_object(self, obj: DataObject) -> None:
+        # This function is used to check if the dates obtained
+        # are in the standard format and the date of collection
+        # is not preceding the date of plating
+
+        previous_date = None
+
+        for date_field in self.__config.dates:
+            date_value = obj.get_field_by_name(date_field)
+
+            # Validate that the value is a date or datetime object
+            if not isinstance(date_value, (date, datetime)):
+                self.add_error(
+                    object_id=obj.id,
+                    detail=f'{date_field} of {date_value} is not in the right date format',
+                    field=self.__config.dates,
+                )
+                return
+
+            # Check if dates are in ascending order
+            if previous_date is not None and date_value < previous_date:
+                self.add_error(
+                    object_id=obj.id,
+                    detail=f'Date {date_field} ({date_value})'
+                    f'is before previous date ({previous_date})',
+                    field=self.__config.dates,
+                )
+                return
+
+            previous_date = date_value

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-1.8.3.dist-info → tol_sdk-1.8.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.3
+Version: 1.8.5
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.3.dist-info → tol_sdk-1.8.5.dist-info}/RECORD

@@ -32,14 +32,14 @@ tol/api_base/misc/relation_url.py,sha256=qfo-okp8Gv9-PEDghMfGZ2pHdYbHRhohvA9v3Go
 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=gcnX4iCZtjnCC6qylizXxLe3l6xLhME6LEJH0UeW7V4,13979
+tol/api_client/client.py,sha256=hNqoyGPSiKSiT2DeHi13agrDBlXIWm7wtNjrMRCUuQg,13977
 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/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
@@ -98,7 +98,7 @@ tol/core/datasource_error.py,sha256=TqfqaPANG0gishadhA7myCmTO1Fg9u7hVZOvsY6BdAo,
 tol/core/datasource_filter.py,sha256=RY2S9kTx0XwdrFRSE2n2GohB9__fKGzFVsZrkN5hzQk,726
 tol/core/datasource_utils.py,sha256=18mwvFmtJL73_mxtFb56rKXZCGCtZFoEb8sWFKn3Yf0,6232
 tol/core/factory.py,sha256=pLLu8l-yK8QaLTt52izMhKZ2VlFHqRQlUHwMaLL6DI4,9156
-tol/core/http_client.py,sha256=05Wa_ySmpm_lC8OkxqXkq6jer0t693GexpaKNQBHufI,2244
+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/session.py,sha256=6AohamIEfB8oV3Z414ishKqmlTgVfUaGYWzvxLgZgM4,3803
@@ -198,6 +198,7 @@ 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
@@ -306,7 +307,7 @@ tol/sql/sql_datasource.py,sha256=jLPQSolGtKRKezjVnMrlj8YO6bLepyiFARMbDYEXuN8,162
 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=u0vT_TC9IMKrg08QFa9W29_83mT0y0jzLj3DvXy1BBw,25906
+tol/sql/auth/blueprint.py,sha256=3M55fYi_H1PgFaFxYSW8pgOwgFwdl1lN6VRbEt1r8N8,26008
 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
@@ -323,31 +324,33 @@ tol/treeval/treeval_datasource.py,sha256=GzY6JwH67b5QdV-UVdCFJfgGAIuZ96J2nl53YxZ
 tol/utils/__init__.py,sha256=764-Na1OaNGUDWpMIu51ZtXG7n_nB5MccUFK6LmkWRI,138
 tol/utils/csv.py,sha256=mihww25fSn72c4h-RFeqD_pFIG6KHZP4v1_C0rx81ws,421
 tol/utils/s3.py,sha256=aoYCwJ-qcMqFrpxmViFqPa0O1jgp0phtztO3-0CSNjw,491
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