tol-sdk 1.8.1__tar.gz → 1.8.4__tar.gz

{tol_sdk-1.8.1/src/tol_sdk.egg-info → tol_sdk-1.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.1
+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-1.8.1 → tol_sdk-1.8.4}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.8.1"
+version = "1.8.4"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [

{tol_sdk-1.8.1 → tol_sdk-1.8.4}/src/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_sdk-1.8.1 → tol_sdk-1.8.4}/src/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_sdk-1.8.1 → tol_sdk-1.8.4}/src/tol/flows/converters/__init__.py

@@ -56,3 +56,4 @@ 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 .auto_detect_manifest_type_converter import AutoDetectManifestTypeConverter # noqa F401

tol_sdk-1.8.4/src/tol/flows/converters/auto_detect_manifest_type_converter.py

@@ -0,0 +1,46 @@
+# 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 AutoDetectManifestTypeConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        rack_or_plate: 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 = {}
+        rack_or_plate_based_manifest = bool(
+            re.fullmatch(r'^[A-P][12]?[0-9]$',
+                         s.attributes.get(self.__config.rack_or_plate))
+        )
+
+        if rack_or_plate_based_manifest:
+            attributes['manifest_type'] = 'PLATE_WELL'
+        else:
+            attributes['manifest_type'] = 'RACK_TUBE'
+
+        ret = self._data_object_factory(
+            data_object.type,
+            s.id,
+            attributes=attributes,
+        )
+        yield ret

{tol_sdk-1.8.1 → tol_sdk-1.8.4}/src/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_sdk-1.8.1 → tol_sdk-1.8.4}/src/tol/sql/pipeline_step/factory.py

@@ -9,7 +9,7 @@ from dataclasses import dataclass
 from datetime import datetime
 from typing import Any, Dict, Iterator, List
 
-from sqlalchemy import ForeignKey, UniqueConstraint
+from sqlalchemy import ForeignKey, Text, UniqueConstraint
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.orm import (
     Mapped,
@@ -64,7 +64,7 @@ def create_pipeline_step_models(
     class Pipeline(base_model_class):
         __tablename__ = 'pipeline'
 
-        id: Mapped[int] = mapped_column( # noqa A003
+        id: Mapped[int] = mapped_column(  # noqa A003
             primary_key=True,
             autoincrement=True
         )
@@ -100,7 +100,7 @@ def create_pipeline_step_models(
             ),
         )
 
-        id: Mapped[int] = mapped_column( # noqa A003
+        id: Mapped[int] = mapped_column(  # noqa A003
             primary_key=True,
             autoincrement=True
         )
@@ -121,6 +121,16 @@ def create_pipeline_step_models(
             nullable=False
         )
 
+        description: Mapped[str | None] = mapped_column(
+            Text,
+            nullable=True
+        )
+
+        is_visible: Mapped[bool] = mapped_column(
+            nullable=False,
+            default=True
+        )
+
         config: Mapped[dict[str, Any]] = mapped_column(
             JSONB,
             nullable=False,
@@ -135,7 +145,7 @@ def create_pipeline_step_models(
     class Upload(base_model_class):
         __tablename__ = 'upload'
 
-        id: Mapped[int] = mapped_column( # noqa A003
+        id: Mapped[int] = mapped_column(  # noqa A003
             primary_key=True,
             autoincrement=True
         )
@@ -173,6 +183,11 @@ def create_pipeline_step_models(
             default=False
         )
 
+        is_ready: Mapped[bool] = mapped_column(
+            nullable=False,
+            default=False
+        )
+
         failure_message: Mapped[str | None] = mapped_column(
             nullable=True,
         )
@@ -182,7 +197,7 @@ def create_pipeline_step_models(
             foreign_keys=[pipeline_id]
         )
 
-        user: Mapped['User'] = relationship( # noqa F821
+        user: Mapped['User'] = relationship(  # noqa F821
             back_populates='user_uploads',
             foreign_keys=[user_id]
         )

{tol_sdk-1.8.1 → tol_sdk-1.8.4}/src/tol/validators/__init__.py

@@ -20,3 +20,7 @@ from .unique_values import UniqueValuesValidator  # noqa
 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_sdk-1.8.4/src/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_sdk-1.8.4/src/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-1.8.4/src/tol/validators/unique_value_check.py

@@ -0,0 +1,41 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from dataclasses import dataclass
+
+from tol.core import Validator
+from tol.core.data_object import DataObject
+
+
+class UniqueValueCheckValidator(Validator):
+    """
+    Validates an incoming stream of `DataObject` instances.
+    For each data object (sample) it checks if the GAL column has only one value
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        field: str
+
+    __slots__ = ['__config', '_cached']
+    __config: Config
+    _cached: str | None
+
+    def __init__(self, config: Config, **kwargs) -> None:
+        super().__init__()
+        self.__config = config
+        self._cached = None
+
+    def _validate_data_object(self, obj: DataObject) -> None:
+        # This function is used to check if the data object has a single value for GAL column
+
+        if not self._cached:
+            self._cached = obj.attributes.get(self.__config.field)
+
+        else:
+            if obj.attributes.get(self.__config.field) != self._cached:
+                self.add_error(
+                    object_id=obj.id,
+                    detail=f'More than one value detected in {self.__config.field}',
+                    field=self.__config.field,
+                )

tol_sdk-1.8.4/src/tol/validators/value_check.py

@@ -0,0 +1,36 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from dataclasses import dataclass
+
+from tol.core import Validator
+from tol.core.data_object import DataObject
+
+
+class ValueCheckValidator(Validator):
+    """
+    Validates an incoming stream of `DataObject` instances.
+    For each data object (sample) it checks if it is a SYMBIONT
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        field: str
+        value: 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 data object is SYMBIONT or not
+
+        if obj.attributes.get(self.__config.field) == self.__config.value:
+            self.add_error(
+                object_id=obj.id,
+                detail=f'{self.__config.value} is detected',
+                field=self.__config.field,
+            )

{tol_sdk-1.8.1 → tol_sdk-1.8.4/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.1
+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-1.8.1 → tol_sdk-1.8.4}/src/tol_sdk.egg-info/SOURCES.txt

@@ -155,6 +155,7 @@ src/tol/flows/logger.py
 src/tol/flows/secrets.py
 src/tol/flows/sequencing_submissions.py
 src/tol/flows/converters/__init__.py
+src/tol/flows/converters/auto_detect_manifest_type_converter.py
 src/tol/flows/converters/benchling_entity_to_benchling_worklist_item_converter_factory.py
 src/tol/flows/converters/benchling_extraction_to_elastic_extraction_converter.py
 src/tol/flows/converters/benchling_extraction_to_elastic_sequencing_request_converter.py
@@ -332,7 +333,9 @@ 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/branching.py
 src/tol/validators/converter_and_validate.py
+src/tol/validators/date_sorting.py
 src/tol/validators/ena_checklist.py
 src/tol/validators/ena_submittable.py
 src/tol/validators/min_one_valid_value.py
@@ -343,8 +346,10 @@ src/tol/validators/specimens_have_same_taxon.py
 src/tol/validators/sts_fields.py
 src/tol/validators/tolid.py
 src/tol/validators/types.py
+src/tol/validators/unique_value_check.py
 src/tol/validators/unique_values.py
 src/tol/validators/unique_whole_organisms.py
+src/tol/validators/value_check.py
 src/tol/validators/interfaces/__init__.py
 src/tol/validators/interfaces/condition_evaluator.py
 src/tol_sdk.egg-info/PKG-INFO