tol-sdk 1.8.1__tar.gz → 1.8.3__tar.gz

{tol_sdk-1.8.1/src/tol_sdk.egg-info → tol_sdk-1.8.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.1
+Version: 1.8.3
 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-1.8.3}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.8.1"
+version = "1.8.3"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [

{tol_sdk-1.8.1 → tol_sdk-1.8.3}/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-1.8.3/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-1.8.3}/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-1.8.3}/src/tol/validators/__init__.py

@@ -20,3 +20,5 @@ 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 .unique_value_check import UniqueValueCheckValidator  # noqa

tol_sdk-1.8.3/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-1.8.3/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-1.8.3/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.1
+Version: 1.8.3
 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-1.8.3}/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
@@ -343,8 +344,10 @@ 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