tol-sdk 1.8.2__py3-none-any.whl → 1.8.3__py3-none-any.whl

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/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/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,
@@ -121,6 +121,11 @@ 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

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/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/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-1.8.2.dist-info → tol_sdk-1.8.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.2
+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-1.8.2.dist-info → tol_sdk-1.8.3.dist-info}/RECORD

@@ -149,7 +149,8 @@ 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=ZSF9i-32mVsV4-rNYjA6TrIEPrgku5svCF8lz6HEqf8,6231
+tol/flows/converters/__init__.py,sha256=QgbwWIbMKI8LWZBwYVrHARKi03ISLDS3yzpHNPRLXdk,6324
+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
 tol/flows/converters/benchling_extraction_to_elastic_sequencing_request_converter.py,sha256=2RiyRvGRSWzpUwEI4p-s0afshJpFUUxPqv2z-nyDSVg,1992
@@ -308,7 +309,7 @@ tol/sql/auth/__init__.py,sha256=e3JuwugXmXobklqZ1Mt1w03qPgb1WdUaJVM7oblzHyk,202
 tol/sql/auth/blueprint.py,sha256=u0vT_TC9IMKrg08QFa9W29_83mT0y0jzLj3DvXy1BBw,25906
 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=oGjL0pDpsGjofjEwM-zLP22x57iu0tPGTYQVr27Yxu4,5365
+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/status/__init__.py,sha256=sBo-j1wCmberl89uryVCBEJk8ohbfsYhaNpIp_brR9Y,146
@@ -322,7 +323,7 @@ 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=QI5ykFzsTLsIQXcL4vF_aaVGdSr2l0X0Qkssbnxumss,1176
+tol/validators/__init__.py,sha256=vRuNMVhUlRPinTZQ-TBtmfIAW40vcE4dez6RI89sgoI,1295
 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
@@ -338,13 +339,15 @@ tol/validators/specimens_have_same_taxon.py,sha256=m2LLRIZMdhPj1fzyioDJOraI6UHXg
 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/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/interfaces/__init__.py,sha256=jtOxnwnwqV_29xjmmMcS_kvlt-pQiWwQYJn2YRP07_w,172
 tol/validators/interfaces/condition_evaluator.py,sha256=nj8Cb8hi47OBy6OVNfeLhF-Pjwtr8MiOSymYL6hfVes,3766
-tol_sdk-1.8.2.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
-tol_sdk-1.8.2.dist-info/METADATA,sha256=bbRRrGT96nJrprgKu0hJTeQYM584GsjdE3sxo31mtMg,3142
-tol_sdk-1.8.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-tol_sdk-1.8.2.dist-info/entry_points.txt,sha256=jH3HfTwxjzog7E3lq8CKpUWGIRY9FSXbyL6CpUmv6D0,36
-tol_sdk-1.8.2.dist-info/top_level.txt,sha256=PwKMQLphyZNvagBoriVbl8uwHXQl8IC1niawVG0iXMM,10
-tol_sdk-1.8.2.dist-info/RECORD,,
+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,,