tol-sdk 1.8.6__tar.gz → 1.8.8__tar.gz

{tol_sdk-1.8.6/src/tol_sdk.egg-info → tol_sdk-1.8.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.6
+Version: 1.8.8
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.8.6"
+version = "1.8.8"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/api_client/api_datasource.py

@@ -134,28 +134,17 @@ class ApiDataSource(
             for k, v in transfer.items()
         }
 
+    @requested_fields_to_tree
     @validate('detailGet')
     def get_by_id(
         self,
         object_type: str,
         object_ids: Iterable[str],
         session: Optional[OperableSession] = None,
-        requested_fields: list[str] | None = None,
         requested_tree: ReqFieldsTree | None = None,
     ) -> Iterable[Optional[DataObject]]:
 
         client = self.__client_factory()
-        # This would be better handled in the decorator but there is a slight
-        # difference in handling here with the requested_tree when requested_fields is None
-        requested_tree = (
-            ReqFieldsTree(
-                object_type,
-                self,
-                requested_fields=requested_fields,
-            )
-            if object_type
-            else None
-        )
 
         json_responses = (
             client.get_detail(
@@ -182,7 +171,6 @@ class ApiDataSource(
         object_filters: Optional[DataSourceFilter] = None,
         sort_by: Optional[str] = None,
         session: Optional[OperableSession] = None,
-        requested_fields: list[str] | None = None,
         requested_tree: ReqFieldsTree | None = None,
     ) -> tuple[Iterable[DataObject], int]:
 
@@ -204,7 +192,6 @@ class ApiDataSource(
         object_type: str,
         object_filters: Optional[DataSourceFilter] = None,
         session: Optional[OperableSession] = None,
-        requested_fields: list[str] | None = None,
         requested_tree: ReqFieldsTree | None = None,
     ) -> Iterable[DataObject]:
         if self.__can_cursor(object_type, object_filters):

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/api_client/client.py

@@ -54,11 +54,13 @@ class JsonApiClient(HttpClient):
         url = self.__detail_url(object_type, object_id)
         headers = self._merge_headers()
 
+        params = {}
+        if requested_tree:
+            params['requested_fields'] = requested_tree.to_paths()
+
         return self.__fetch_detail(
             url,
-            params={
-                'requested_fields': requested_tree.to_paths() if requested_tree else None,
-            },
+            params=params,
             headers=headers,
         )
 

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/api_client/factory.py

@@ -64,6 +64,14 @@ class _ConverterFactory:
         """
         Returns an instantiated `JsonApiConverter`.
         """
+
+        # If we're going to parse a JSON:API data object (i.e. we have been
+        # passed an `object_type`), we need to add a ReqFieldsTree so that
+        # DataSources with default loading of to-one objects correctly
+        # process the to-ones from the `included` array.
+        if object_type and not requested_tree:
+            requested_tree = ReqFieldsTree(object_type, self.__data_source)
+
         parser = DefaultParser(self.__ds_dict, requested_tree)
         return JsonApiConverter(parser)
 

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/benchling/benchling_warehouse_datasource.py

@@ -45,6 +45,7 @@ class BenchlingWarehouseDataSource(DataSource, ListGetter):
             'sample': 'sts_id',
             'sequencing_request': 'sanger_sample_id',
             'extraction': 'extraction_id',
+            'extraction_container': 'fluidx_container_id',
             'tissue_prep': 'eln_tissue_prep_id'
         }
 
@@ -70,7 +71,7 @@ class BenchlingWarehouseDataSource(DataSource, ListGetter):
             yield self.data_object_factory(
                 object_type,
                 id_=obj[id_col],
-                attributes=obj
+                attributes={k: v for k, v in obj.items() if k != id_col}
             )
 
     def get_list(
@@ -82,7 +83,9 @@ class BenchlingWarehouseDataSource(DataSource, ListGetter):
         file_suffix = ''
         if object_filters is not None:
             if isinstance(object_filters.and_, dict):
-                for field_name in ['sequencing_platform', 'extraction_type']:
+                for field_name in [
+                    'sequencing_platform', 'extraction_type', 'extraction.extraction_type'
+                ]:
                     if field_name in object_filters.and_:
                         # For an in_list, treat as multiple eq
                         if 'in_list' in object_filters.and_[field_name]:
@@ -101,7 +104,7 @@ class BenchlingWarehouseDataSource(DataSource, ListGetter):
                                 ) for val in object_filters.and_[field_name]['in_list']['value']
                             )
                         elif 'eq' in object_filters.and_[field_name]:
-                            file_suffix = '_' + field_name + '_' \
+                            file_suffix = '_' + field_name.replace('.', '_') + '_' \
                                           + object_filters.and_[field_name]['eq']['value']
             else:
                 raise DataSourceError('Filtering only on sequencing platform and extraction '

tol_sdk-1.8.6/src/tol/benchling/sql/extraction_containers_dna.sql → tol_sdk-1.8.8/src/tol/benchling/sql/extraction_container_extraction_extraction_type_dna.sql

@@ -9,28 +9,29 @@ Output: Table with columns:
 
 1) taxon_id: [character] Tissue metadata. Origin: STS
 2) eln_tissue_id: [character] Benchling ID for the tissue the extraction is derived from.
-3) eln_tissue_prep_id: [character] Benchling ID for the tissue prep the extraction is derived from.
-4) extraction_id: [character] DNA extraction entity ID (Benchling).
-5) programme_id: [character] ToLID. Origin: BWH.
-6) specimen_id: [character] Specimen ID. Origin: STS.
-7) creation_date: [date] Date the container was created.
-8) fluidx_container_id: [character] Primary key for the FluidX container.
-9) fluidx_id: [character] FluidX barcode.
-10) tube_type: [character] Type of tube/container.
-11) volume_ul: [numeric] Volume in microliters (0 if archived as 'Retired' or 'Expended').
-12) location: [character] Storage location name.
-13) rack: [character] Box/rack barcode.
-14) archive_purpose: [character] Reason for archiving the DNA extraction.
-15) nanodrop_concentration_ngul: [numeric] Latest Nanodrop concentration (ng/µL).
-16) dna_260_280_ratio: [numeric] Latest Nanodrop 260/280 ratio.
-17) dna_260_230_ratio: [numeric] Latest Nanodrop 260/230 ratio.
-18) qubit_concentration_ngul: [numeric] Latest Qubit concentration (ng/µL).
-19) yield_ng: [numeric] Latest yield (ng).
-20) femto_date_code: [character] Latest Femto date code.
-21) femto_description: [character] Latest Femto profile description.
-22) gqn_index: [numeric] Latest GQN index from Femto.
-23) next_step: [character] Latest decision making next step.
-24) extraction_qc_result: [character] Latest extraction QC result.
+3) tissue_sts_id: [character] STS ID for the tissue the extraction is derived from.
+4) eln_tissue_prep_id: [character] Benchling ID for the tissue prep the extraction is derived from.
+5) extraction_id: [character] DNA extraction entity ID (Benchling).
+6) programme_id: [character] ToLID. Origin: BWH.
+7) specimen_id: [character] Specimen ID. Origin: STS.
+8) creation_date: [date] Date the container was created.
+9) fluidx_container_id: [character] Primary key for the FluidX container.
+10) fluidx_id: [character] FluidX barcode.
+11) tube_type: [character] Type of tube/container.
+12) volume_ul: [numeric] Volume in microliters (0 if archived as 'Retired' or 'Expended').
+13) location: [character] Storage location name.
+14) rack: [character] Box/rack barcode.
+15) archive_purpose: [character] Reason for archiving the DNA extraction.
+16) nanodrop_concentration_ngul: [numeric] Latest Nanodrop concentration (ng/µL).
+17) dna_260_280_ratio: [numeric] Latest Nanodrop 260/280 ratio.
+18) dna_260_230_ratio: [numeric] Latest Nanodrop 260/230 ratio.
+19) qubit_concentration_ngul: [numeric] Latest Qubit concentration (ng/µL).
+20) yield_ng: [numeric] Latest yield (ng).
+21) femto_date_code: [character] Latest Femto date code.
+22) femto_description: [character] Latest Femto profile description.
+23) gqn_index: [numeric] Latest GQN index from Femto.
+24) next_step: [character] Latest decision making next step.
+25) extraction_qc_result: [character] Latest extraction QC result.
 
 NOTES:
 1) Only extractions from the 'ToL Core Lab' project and relevant folders are included.
@@ -109,6 +110,7 @@ latest_decision_making AS (
 SELECT DISTINCT
     t.taxon_id,
     t.id AS eln_tissue_id,
+    t.sts_id AS tissue_sts_id,
     tp.id AS eln_tissue_prep_id,
     dna.id AS extraction_id,
     t.programme_id,
@@ -170,4 +172,4 @@ LEFT JOIN entry$raw AS ent
 WHERE proj.name = 'ToL Core Lab'
     AND  (f.name IN ('Routine Throughput', 'DNA', 'Core Lab Entities', 'Benchling MS Project Move') OR f.name IS NULL)
     AND (con.archive_purpose$ != ('Made in error') OR con.archive_purpose$ IS NULL)
-    AND ent.name NOT LIKE '%Nuclei isolation and tagmentation%'
+    AND COALESCE(ent.name, '') NOT LIKE '%Nuclei isolation and tagmentation%'

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/benchling/sql/sequencing_request_sequencing_platform_pacbio.sql

@@ -24,7 +24,7 @@ Output: Table with cols:
 4) eln_file_registry_id: [character] id in Benchling Registry. Origin: BWH
 5) extraction_id: [character] Original DNA extract entity name. For pooled samples, the first DNA extract pooled. Origin: BWH
 6) submission_sample_name: [character] Entity name. Origin: BWH
-7) fluidx_id: [character] Container barcode of the DNA fluidx tube. Origin: BWH
+7) fluidx_container_id: [character] Container id of the DNA fluidx tube. Origin: BWH
 8) programme_id: [character] ToLID. Origin: BWH
 9) specimen_id: [character] Specimen ID. Origin: STS
 10) tube_name: [character] Name of the submission tube/container.
@@ -73,7 +73,7 @@ pacbio_submissions_container_routine AS (
 		subsam.file_registry_id$ AS eln_file_registry_id,
 		subsam.original_dna_extract AS extraction_id,
 		subsam.name$ AS submission_sample_name,
-		c_dna.barcode AS fluidx_id,
+		c_dna.id AS fluidx_container_id,
 		t.programme_id, 
 		t.specimen_id, 
 		con.name AS tube_name,
@@ -145,7 +145,7 @@ pacbio_submissions_container_pooled AS (
 		subsam.file_registry_id$ AS eln_file_registry_id,
 		subsam.pooled_sample  AS extraction_id,
 		subsam.name$ AS eln_submission_sample_name,
-		c_pool.barcode AS fluidx_id,
+		c_pool.id AS fluidx_container_id,
 		t.programme_id, 
 		t.specimen_id,
 		con.name AS tube_name,
@@ -219,7 +219,7 @@ pacbio_submissions_container_legacy_deprecated AS (
 		subsam.file_registry_id$ AS eln_file_registry_id,
 		subsam.original_dna_extract AS extraction_id,
 		subsam.name$ AS submission_sample_name,
-		c_dna.barcode AS fluidx_id,
+		c_dna.id AS fluidx_container_id,
 		t.programme_id,
 		t.specimen_id,
 		con.name AS tube_name,
@@ -283,7 +283,7 @@ pacbio_submissions_plate_automated_manifest AS (
 		subsam.file_registry_id$ AS eln_file_registry_id,
 		subsam.originaL_dna_extract AS extraction_id,
 		subsam.name$ AS submission_sample_name,
-		c_dna.barcode AS fluidx_id,
+		c_dna.id AS fluidx_container_id,
 		t.programme_id,
 		t.specimen_id,
 		con.name AS tube_name,
@@ -350,7 +350,7 @@ pacbio_submissions_plate_automated_manifest_pooled AS (
 		subsam.file_registry_id$ AS eln_file_registry_id,
 		subsam.pooled_sample AS extraction_id,
 		subsam.name$ AS submission_sample_name,
-		c_pool.barcode AS fluidx_id,
+		c_pool.id AS fluidx_container_id,
 		t.programme_id,
 		t.specimen_id,
 		con.name AS tube_name,
@@ -415,7 +415,7 @@ pacbio_submissions_plate_routine AS (
 		subsam.file_registry_id$ AS eln_file_registry_id,
 		subsam.original_dna_extract AS extraction_id,
 		subsam.name$ AS submission_sample_name,
-		c_dna.barcode AS fluidx_id,
+		c_dna.id AS fluidx_container_id,
 		t.programme_id,
 		t.specimen_id,
 		c_subsam.name AS tube_name,
@@ -485,7 +485,7 @@ pacbio_submissions_plate_routine_pooled AS (
 		subsam.file_registry_id$ AS eln_file_registry_id,
 		subsam.pooled_sample AS extraction_id,
 		subsam.name$ AS submission_sample_name,
-		c_pool.barcode AS fluidx_id,
+		c_pool.id AS fluidx_container_id,
 		t.programme_id,
 		t.specimen_id,
 		c_subsam.name AS tube_name,

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/core/factory.py

@@ -189,7 +189,7 @@ def core_data_object(
                 if object_from_datasource is not None:
                     self.__type = object_from_datasource.type
                     self.__attributes = object_from_datasource.attributes
-                    self.__to_one_objects = object_from_datasource.to_one_objects
+                    self.__to_one_objects = object_from_datasource._to_one_objects
                     break
 
         @property

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/core/requested_fields.py

@@ -17,17 +17,17 @@ def requested_fields_to_tree(func):
     `requested_tree` object has not been given.
     """
 
-    def wrapper(self, tablename, *args, **kwargs):
+    def wrapper(self, object_type, *args, **kwargs):
         if 'requested_fields' in kwargs:
             if 'requested_tree' in kwargs:
                 msg = 'Both requested_fields and requested_tree arguments given'
                 raise TypeError(msg)
             flds = kwargs.pop('requested_fields')
-            kwargs['requested_tree'] = ReqFieldsTree(
-                tablename, self, requested_fields=flds
-            )
-        return func(self, tablename, *args, **kwargs)
-
+            if flds and object_type:
+                kwargs['requested_tree'] = ReqFieldsTree(
+                    object_type, self, requested_fields=flds
+                )
+        return func(self, object_type, *args, **kwargs)
     return wrapper
 
 

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/flows/converters/__init__.py

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 
+from .benchling_extraction_container_to_elastic_extraction_container_converter import BenchlingExtractionContainerToElasticExtractionContainerConverter  # noqa F401
 from .benchling_extraction_to_elastic_extraction_converter import BenchlingExtractionToElasticExtractionConverter  # noqa F401
 from .benchling_extraction_to_elastic_sequencing_request_converter import BenchlingExtractionToElasticSequencingRequestConverter  # noqa F401
 from .benchling_sequencing_request_to_elastic_sequencing_request_converter import (  # noqa F401

tol_sdk-1.8.8/src/tol/flows/converters/benchling_extraction_container_to_elastic_extraction_container_converter.py

@@ -0,0 +1,53 @@
+# SPDX-FileCopyrightText: 2026 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from typing import Iterable
+
+from ...core import (
+    DataObject,
+    DataObjectToDataObjectOrUpdateConverter
+)
+
+
+class BenchlingExtractionContainerToElasticExtractionContainerConverter(
+        DataObjectToDataObjectOrUpdateConverter):
+    def convert(self, data_object: DataObject) -> Iterable[DataObject]:
+        if data_object.tissue_sts_id is not None:
+            ret = self._data_object_factory(
+                'extraction_container',
+                data_object.id,
+                attributes={
+                    **{k: v
+                       for k, v in data_object.attributes.items()
+                       if k not in ['tissue_sts_id', 'specimen_id', 'taxon_id',
+                                    'programme_id', 'eln_tissue_prep_id', 'extraction_id']}
+                },
+                to_one={
+                    'sample': self._data_object_factory(
+                        'sample',
+                        data_object.tissue_sts_id
+                    ) if data_object.tissue_sts_id is not None else None,
+                    'species': self._data_object_factory(
+                        'species',
+                        data_object.taxon_id
+                    ) if data_object.taxon_id is not None else None,
+                    'specimen': self._data_object_factory(
+                        'specimen',
+                        data_object.specimen_id
+                    ) if data_object.specimen_id is not None else None,
+                    'tolid': self._data_object_factory(
+                        'tolid',
+                        data_object.programme_id
+                    ) if data_object.programme_id is not None else None,
+                    'tissue_prep': self._data_object_factory(
+                        'tissue_prep',
+                        data_object.eln_tissue_prep_id
+                    ) if data_object.eln_tissue_prep_id is not None else None,
+                    'extraction': self._data_object_factory(
+                        'extraction',
+                        data_object.extraction_id
+                    ) if data_object.extraction_id is not None else None,
+                }
+            )
+            yield ret

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/flows/converters/benchling_sequencing_request_to_elastic_sequencing_request_converter.py

@@ -15,12 +15,18 @@ class BenchlingSequencingRequestToElasticSequencingRequestConverter(
     def convert(self, data_object: DataObject) -> Iterable[DataObject]:
         if data_object.sts_id is not None:
             extraction = None
+            extraction_container = None
             tissue_prep = None
             if 'extraction_id' in data_object.attributes:
                 extraction = self._data_object_factory(
                     'extraction',
                     data_object.extraction_id
                 )
+            if 'fluidx_container_id' in data_object.attributes:
+                extraction_container = self._data_object_factory(
+                    'extraction_container',
+                    data_object.fluidx_container_id
+                )
             if 'tissue_prep_id' in data_object.attributes:
                 tissue_prep = self._data_object_factory(
                     'tissue_prep',
@@ -34,7 +40,7 @@ class BenchlingSequencingRequestToElasticSequencingRequestConverter(
                        for k, v in data_object.attributes.items()
                        if k not in ['sanger_sample_id', 'sts_id',
                                     'specimen_id', 'taxon_id', 'extraction_id',
-                                    'programme_id', 'tissue_prep_id']}
+                                    'programme_id', 'tissue_prep_id', 'fluidx_container_id']}
                 },
                 to_one={
                     'sample': self._data_object_factory(
@@ -54,6 +60,7 @@ class BenchlingSequencingRequestToElasticSequencingRequestConverter(
                         data_object.programme_id
                     ) if data_object.programme_id is not None else None,
                     'extraction': extraction,
+                    'extraction_container': extraction_container,
                     'tissue_prep': tissue_prep,
                 })
             yield ret

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/flows/converters/elastic_sequencing_request_to_elastic_run_data_update_converter.py

@@ -29,5 +29,13 @@ class ElasticSequencingRequestToElasticRunDataUpdateConverter(
                     'extraction',
                     extraction.id
                 )
+        if 'benchling_extraction_container' in data_object.to_one_relationships:
+            extraction_container = \
+                data_object.to_one_relationships['benchling_extraction_container']
+            if extraction_container is not None:
+                to_ones['benchling_extraction_container'] = self._data_object_factory(
+                    'extraction_container',
+                    extraction_container.id
+                )
         yield (None, to_ones | {
             'mlwh_sequencing_request.id': data_object.id})  # The candidate key

tol_sdk-1.8.8/src/tol/flows/converters/time_string_to_time.py

@@ -0,0 +1,44 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+import re
+from dataclasses import dataclass
+from datetime import time
+from typing import Iterable
+
+from tol.core import DataObject, DataObjectToDataObjectOrUpdateConverter
+
+
+class TimeStringToTimeConverter(DataObjectToDataObjectOrUpdateConverter):
+
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        field_names: list[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]:
+        """
+        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.
+        """
+
+        for field_name in self.__config.field_names:
+            value = data_object.attributes.get(field_name)
+            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:
+                        data_object.attributes[field_name] = time(h, m, s)
+                    except ValueError:
+                        pass
+        yield data_object

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/validators/allowed_values_from_datasource.py

@@ -46,7 +46,7 @@ class AllowedValuesFromDataSourceValidator(Validator):
             obj.get_field_by_name(
                 self.__config.datasource_field_name
             ) for obj in ds.get_list(
-                object_type=self.__config.datasource_object_type
+                self.__config.datasource_object_type
             )
         ]
 

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol/validators/tolid.py

@@ -90,7 +90,7 @@ class TolidValidator(Validator):
                 f = DataSourceFilter()
                 f.and_ = {'specimen_id': {'eq': {'value': specimen_id}}}
                 self.__cached_tolids[specimen_id] = list(self.__datasource.get_list(
-                    object_type='specimen',
+                    'specimen',
                     object_filters=f
                 ))
 

{tol_sdk-1.8.6 → tol_sdk-1.8.8/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.6
+Version: 1.8.8
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.6 → tol_sdk-1.8.8}/src/tol_sdk.egg-info/SOURCES.txt

@@ -52,7 +52,7 @@ src/tol/benchling/benchling_converter.py
 src/tol/benchling/benchling_datasource.py
 src/tol/benchling/benchling_warehouse_datasource.py
 src/tol/benchling/sql/__init__.py
-src/tol/benchling/sql/extraction_containers_dna.sql
+src/tol/benchling/sql/extraction_container_extraction_extraction_type_dna.sql
 src/tol/benchling/sql/extraction_extraction_type_dna.sql
 src/tol/benchling/sql/extraction_extraction_type_lres.sql
 src/tol/benchling/sql/extraction_extraction_type_pooled_dna.sql
@@ -163,6 +163,7 @@ 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_container_to_elastic_extraction_container_converter.py
 src/tol/flows/converters/benchling_extraction_to_elastic_extraction_converter.py
 src/tol/flows/converters/benchling_extraction_to_elastic_sequencing_request_converter.py
 src/tol/flows/converters/benchling_sample_casm_to_sts_sample_converter.py

tol_sdk-1.8.6/src/tol/flows/converters/time_string_to_time.py

@@ -1,35 +0,0 @@
-# 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