tol-sdk 1.8.3__py3-none-any.whl → 1.8.4__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/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/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_sdk-1.8.3.dist-info → tol_sdk-1.8.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.3
+Version: 1.8.4
 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-1.8.4.dist-info}/RECORD

@@ -32,7 +32,7 @@ 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
@@ -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
@@ -306,7 +306,7 @@ 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
@@ -323,12 +323,14 @@ 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
-tol/validators/__init__.py,sha256=vRuNMVhUlRPinTZQ-TBtmfIAW40vcE4dez6RI89sgoI,1295
+tol/validators/__init__.py,sha256=_ETv6oGQ2bTH_6-foYFy9T5wP5OG3cl96zEjvrIS7zk,1399
 tol/validators/allowed_keys.py,sha256=RJcHBiguL84B8hjSRaXLNES21yZqaKFwJNp2Tz9zvh0,1506
 tol/validators/allowed_values.py,sha256=-Yy3Sqo1WYacGKlot_dn3M2o7Oj5MXOioJrJmrWCCxs,1536
 tol/validators/allowed_values_from_datasource.py,sha256=ICFO6FcYXDN7M2Cv1OwpyN38CdhmY7oU-njzIatA3-w,3185
 tol/validators/assert_on_condition.py,sha256=eBGgSVfIQ6e45SheM-ZDg7daXJjyZxRVS5L8AWvbXag,2027
+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_submittable.py,sha256=CujF9t4mA4N3Wm_5rA5MRp401aW19kbioOZpfWVXg6I,1965
 tol/validators/min_one_valid_value.py,sha256=gZUHtfRA-Lvpw0d1FJoAA31cRJpLbbxAJCC9DCt5lCY,1442
@@ -345,9 +347,9 @@ tol/validators/unique_whole_organisms.py,sha256=RdqA1GzIf3LTdrmNGGdxv0aW2udDY2P9
 tol/validators/value_check.py,sha256=lxfhfL8BCIs_B838CQ5znJ6KFD7ms_fSVCS9QuVearE,1052
 tol/validators/interfaces/__init__.py,sha256=jtOxnwnwqV_29xjmmMcS_kvlt-pQiWwQYJn2YRP07_w,172
 tol/validators/interfaces/condition_evaluator.py,sha256=nj8Cb8hi47OBy6OVNfeLhF-Pjwtr8MiOSymYL6hfVes,3766
-tol_sdk-1.8.3.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
-tol_sdk-1.8.3.dist-info/METADATA,sha256=xD9AOIVwrZlC5Vgb3rPRM9eT5HdJ0FmCsJDRmxfdvw8,3142
-tol_sdk-1.8.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tol_sdk-1.8.3.dist-info/entry_points.txt,sha256=jH3HfTwxjzog7E3lq8CKpUWGIRY9FSXbyL6CpUmv6D0,36
-tol_sdk-1.8.3.dist-info/top_level.txt,sha256=PwKMQLphyZNvagBoriVbl8uwHXQl8IC1niawVG0iXMM,10
-tol_sdk-1.8.3.dist-info/RECORD,,
+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
+tol_sdk-1.8.4.dist-info/entry_points.txt,sha256=jH3HfTwxjzog7E3lq8CKpUWGIRY9FSXbyL6CpUmv6D0,36
+tol_sdk-1.8.4.dist-info/top_level.txt,sha256=PwKMQLphyZNvagBoriVbl8uwHXQl8IC1niawVG0iXMM,10
+tol_sdk-1.8.4.dist-info/RECORD,,