tol-sdk 1.8.0__tar.gz → 1.8.2__tar.gz

{tol_sdk-1.8.0/src/tol_sdk.egg-info → tol_sdk-1.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.0
+Version: 1.8.2
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.0 → tol_sdk-1.8.2}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.8.0"
+version = "1.8.2"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [

tol_sdk-1.8.0/src/tol/benchling/sql/extraction_extraction_type_dna.sql → tol_sdk-1.8.2/src/tol/benchling/sql/extraction_containers_dna.sql

@@ -1,48 +1,43 @@
 /* 
-## SQL Query: DNA extractions Benchling Warehouse (BWH)
+## SQL Query: DNA Extraction Containers (Benchling Warehouse)
 
-This SQL query retrieves all the information of DNA extractions performed by the ToL Core Laboratory. 
+This SQL query retrieves detailed information about DNA extraction containers managed by the ToL Core Laboratory, including metadata, container details, and the latest QC measurements.
 
-The table produced also contains the eln_dna_extract_id and eln_file_registry_id which uniquely idenfied each dna extract entity in Benchling Warehouse (BWH). 
+The resulting table includes identifiers for tissues, tissue preps, extractions, containers, and locations, as well as the most recent QC results (Nanodrop, Qubit, Femto, Yield, and Decision Making).
 
-The eln_dna_extract_id should be used as the foreign key to the DNA extract entity the submission is derived from.
+Output: Table with columns:
 
-Output: Table with cols: 
+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.
 
-1) sts_id: [integer] Tissue metadata. Origin: STS
-2) taxon_id: [character] Tissue metadata. Origin: STS
-3) eln_tissue_id: [character] Benchling id for the tissue the extractions is derived from.
-4) eln_tissue_prep_id: [character] Benchling id for the tissue prep the extractions is derived from.
-5) eln_file_registry_id: [character] id in Benchling Registry.
-6) extraction_id: [character] Primary key. 
-7) programme_id: [character] ToLID. Origin: BWH
-8) specimen_id: [character] Specimen ID. Origin: STS
-9) completion_date: [date] Extraction date. This field coalesces created_at$ and created_on fields. Created_on is for bnt legacy data.
-10) extraction_name: [character] Entity name. 
-11) fluidx_id: [character] Fluidx ID.
-12) volume_ul: [double] volume of DNA available in the fluidx tube.
-13) location: [character] Physical locationo of the DNA extraction. Freezer shelf.
-14) rack: [character] Physical locationo of the DNA extraction. Rack barcode.
-15) bnt_id: [character] Batches and Tracking legacy id.
-16) manual_vs_automatic: [character].
-17) extraction_protocol: [character] DNA extraction protocol as recorded at the time of extraction
-18) tube_type: [character] Type of tube. Marked NULL or voucher.
-19) extraction_type: [character] dna.
-20) name: [character] Folder name.
-21) archive_purpose: [character] Reason for archiving the DNA extraction.
-22) nanodrop_concentration_ngul: [double] Concentration of DNA as measured by Nanodrop.
-23) dna_260_280_ratio: [double] Ratio of absorbance at 260:280nm as measured by spectrophotometer.
-24) dna_260_230_ratio: [double] Ratio of absorbance at 260:230nm as measured by spectrophotometer.
-25) qubit_concentration_ngul: [double] Concentration of DNA as measured by Qubit.
-26) yield_ng: [double] DNA yield after extraction.
-27) femto_date_code: [character] Femto date code.
-28) femto_description:[character] Categorical description of the femto pulse profile. 
-29) gqn_index: [character] Genomic Quality Number (GQN) index, calculated by the Femto software.
-30) extraction_qc_result: [character] QC result: Yes = Extraction passed; No = Extraction failed. 
-
-NOTES: 
-1) Data types were casted explicitly to conserved the data type stored in BWH.
-2) To add the Fluidx ID of the original DNA extract a few filters were applied to delete Vouchers, tubes archived because they were made in error, and invalid container names.
+NOTES:
+1) Only extractions from the 'ToL Core Lab' project and relevant folders are included.
+2) Containers archived as 'Made in error' or with names matching '%Nuclei isolation and tagmentation%' are excluded.
+3) Latest QC results are joined from their respective measurement tables.
+4) Volume is set to 0 for archived/expended extractions.
+5) Data types are preserved as in the Benchling Warehouse.
 
 */
 
@@ -112,30 +107,23 @@ latest_decision_making AS (
 )
 
 SELECT DISTINCT
-    t.sts_id,
     t.taxon_id,
     t.id AS eln_tissue_id,
     tp.id AS eln_tissue_prep_id,
-    dna.file_registry_id$ AS eln_file_registry_id,
     dna.id AS extraction_id,
     t.programme_id,
     t.specimen_id,
-    COALESCE(DATE(dna.created_on), DATE(dna.created_at$)) AS completion_date, -- Homogenising BnT and Benchling dates
-    dna.name$ AS extraction_name,
+    DATE(con.created_at) AS creation_date,
+    con.id AS fluidx_container_id, -- primary key
     con.barcode AS fluidx_id,
-    con.id AS fluidx_container_id,
+    tube.type AS tube_type,
     CASE
         WHEN con.archive_purpose$ IN ('Retired', 'Expended') THEN 0 -- Retired or expended DNA extractions have a weight of 0
         ELSE con.volume_si * 1000000
     END AS volume_ul,
     loc.name AS location,
     box.barcode AS rack,
-    dna.bt_id AS bnt_id,
-	dna.manual_vs_automatic AS manual_vs_automatic,
-    dna.extraction_protocol,
-    tube.type AS tube_type,
-    'dna'::varchar AS extraction_type,
-    f.name, dna.archive_purpose$,
+    con.archive_purpose$ AS archive_purpose,
     latest_nanodrop_conc.nanodrop_concentration_ngul,
     latest_nanodrop_conc.dna_260_280_ratio,
     latest_nanodrop_conc.dna_260_230_ratio,
@@ -147,20 +135,20 @@ SELECT DISTINCT
     latest_decision_making.next_step,
     latest_decision_making.extraction_qc_result
 FROM dna_extract$raw AS dna
-LEFT JOIN container_content$raw AS cc
+INNER JOIN container_content$raw AS cc -- Start of container/tube join
      ON cc.entity_id = dna.id
 LEFT JOIN container$raw AS con
      ON con.id = cc.container_id
+LEFT JOIN tube$raw AS tube
+     ON cc.container_id = tube.id -- End of container/tube join
+LEFT JOIN box$raw AS box -- Location chunk
+    ON con.box_id = box.id
+LEFT JOIN location$raw AS loc
+    ON loc.id = box.location_id -- End of location chunk
 LEFT JOIN tissue_prep$raw AS tp
      ON tp.id = dna.tissue_prep
 LEFT JOIN tissue$raw AS t
      ON t.id = tp.tissue
-LEFT JOIN tube$raw AS tube
-     ON cc.container_id = tube.id
-LEFT JOIN folder$raw AS f
-     ON dna.folder_id$ = f.id
-LEFT JOIN project$raw AS proj
-    ON dna.project_id$ = proj.id
 LEFT JOIN latest_nanodrop_conc -- Results chunk
     ON dna.id = latest_nanodrop_conc.sample_id
 LEFT JOIN latest_qubit_conc
@@ -171,13 +159,15 @@ LEFT JOIN latest_femto
     ON dna.id = latest_femto.sample_id
 LEFT JOIN latest_decision_making
     ON dna.id = latest_decision_making.sample_id -- End Results chunk
-LEFT JOIN box$raw AS box -- Location chunk
-    ON con.box_id = box.id
-LEFT JOIN location$raw AS loc
-    ON loc.id = box.location_id -- End of location chunk
+LEFT JOIN folder$raw AS f
+     ON dna.folder_id$ = f.id
+LEFT JOIN project$raw AS proj
+    ON dna.project_id$ = proj.id
+LEFT JOIN registration_origin$raw AS reg
+	ON reg.entity_id = dna.id
+LEFT JOIN entry$raw AS ent
+	ON reg.origin_entry_id = ent.id
 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 (dna.archive_purpose$ != ('Made in error') OR dna.archive_purpose$ IS NULL)
     AND (con.archive_purpose$ != ('Made in error') OR con.archive_purpose$ IS NULL)
-    AND con.barcode NOT LIKE 'CON%'
-ORDER BY completion_date DESC
+    AND ent.name NOT LIKE '%Nuclei isolation and tagmentation%'

tol_sdk-1.8.2/src/tol/benchling/sql/extraction_extraction_type_dna.sql

@@ -0,0 +1,68 @@
+/* 
+## SQL Query: DNA extractions Benchling Warehouse (BWH)
+
+This SQL query retrieves all the information of DNA extractions performed by the ToL Core Laboratory. 
+
+The table produced also contains the eln_dna_extract_id and eln_file_registry_id which uniquely idenfied each dna extract entity in Benchling Warehouse (BWH). 
+
+The eln_dna_extract_id should be used as the foreign key to the DNA extract entity the submission is derived from.
+
+Output: Table with cols: 
+
+1) sts_id: [integer] Tissue metadata. Origin: STS
+2) taxon_id: [character] Tissue metadata. Origin: STS
+3) eln_tissue_id: [character] Benchling 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) eln_file_registry_id: [character] id in Benchling Registry.
+6) extraction_id: [character] Primary key. 
+7) programme_id: [character] ToLID. Origin: BWH
+8) specimen_id: [character] Specimen ID. Origin: STS
+9) completion_date: [date] Extraction date. This field coalesces created_at$ and created_on fields. Created_on is for bnt legacy data.
+10) extraction_name: [character] Entity name.
+11) bnt_id: [character] Batches and Tracking legacy id.
+12) manual_vs_automatic: [character] Extraction method indicator.
+13) extraction_protocol: [character] DNA extraction protocol as recorded at the time of extraction.
+14) extraction_type: [character] Type of extraction, set to 'dna'.
+15) folder_name: [character] Folder name.
+16) archive_purpose: [character] Reason for archiving the DNA extraction.
+
+NOTES: 
+1) Data types were casted explicitly to conserved the data type stored in BWH.
+2) To add the Fluidx ID of the original DNA extract a few filters were applied to delete Vouchers, tubes archived because they were made in error, and invalid container names.
+
+*/
+
+SELECT DISTINCT
+    t.sts_id,
+    t.taxon_id,
+    t.id AS eln_tissue_id,
+    tp.id AS eln_tissue_prep_id,
+    dna.file_registry_id$ AS eln_file_registry_id,
+    dna.id AS extraction_id,
+    t.programme_id,
+    t.specimen_id,
+    COALESCE(DATE(dna.created_on), DATE(dna.created_at$)) AS completion_date, -- Homogenising BnT and Benchling dates
+    dna.name$ AS extraction_name,
+    dna.bt_id AS bnt_id,
+    dna.manual_vs_automatic AS manual_vs_automatic,
+    dna.extraction_protocol,
+    'dna'::varchar AS extraction_type,
+    f.name AS folder_name
+FROM dna_extract$raw AS dna
+LEFT JOIN tissue_prep$raw AS tp
+     ON tp.id = dna.tissue_prep
+LEFT JOIN tissue$raw AS t
+     ON t.id = tp.tissue
+LEFT JOIN folder$raw AS f
+     ON dna.folder_id$ = f.id
+LEFT JOIN project$raw AS proj
+    ON dna.project_id$ = proj.id
+LEFT JOIN registration_origin$raw AS reg
+	ON reg.entity_id = dna.id
+LEFT JOIN entry$raw AS ent
+	ON reg.origin_entry_id = ent.id
+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 (dna.archive_purpose$ != ('Made in error') OR dna.archive_purpose$ IS NULL)
+    AND ent.name NOT LIKE '%Nuclei isolation and tagmentation%'
+ORDER BY completion_date DESC

{tol_sdk-1.8.0 → tol_sdk-1.8.2}/src/tol/benchling/sql/extraction_extraction_type_lres.sql

@@ -28,8 +28,8 @@ SELECT DISTINCT
 	tp.name$ AS eln_tissue_prep_name,
 	ssid.sanger_sample_id,
 	ssid.sanger_sample_id AS extraction_id,
-	c.barcode AS fluidx_id,
-	c.id AS fluidx_container_id,
+	sub_con.barcode AS fluidx_id,
+	sub_con.id AS fluidx_container_id,
 	DATE(tpsub.submitted_submission_date) AS completion_date,
 	'lres'::varchar AS extraction_type
 FROM tissue_prep$raw AS tp
@@ -41,8 +41,16 @@ LEFT JOIN container$raw AS c
 	ON cc.container_id = c.id
 LEFT JOIN tissue_prep_submission_workflow_output$raw AS tpsub
 	ON c.id = tpsub.sample_tube_id
+LEFT JOIN container$raw AS sub_con
+	ON tpsub.sample_tube_id = sub_con.id
 LEFT JOIN storage$raw AS stor 
 	ON c.location_id = stor.id
 LEFT JOIN sanger_sample_id$raw AS ssid 
 	ON c.id = ssid.sample_tube
-WHERE stor.name$ = 'SciOps ToL Lab'
+LEFT JOIN project$raw AS proj
+	ON tp.project_id$ = proj.id
+LEFT JOIN folder$raw AS f 
+	ON tp.folder_id$ = f.id
+WHERE sub_con.id IS NOT NULL
+	AND proj.name = 'ToL Core Lab'
+	AND f.name = 'Sample Prep'

{tol_sdk-1.8.0 → tol_sdk-1.8.2}/src/tol/excel/excel_datasource.py

@@ -119,6 +119,10 @@ class ExcelDataSource(
         if isinstance(__v, pd.Timestamp):
             __v = datetime.fromtimestamp(__v.timestamp())
 
+        # If float and is whole number, convert to int
+        if isinstance(__v, float) and __v.is_integer():
+            __v = int(__v)
+
         if __k not in self.__mappings:
             return __v
 

{tol_sdk-1.8.0 → tol_sdk-1.8.2}/src/tol/sql/pipeline_step/factory.py

@@ -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 +121,11 @@ def create_pipeline_step_models(
             nullable=False
         )
 
+        is_visible: Mapped[bool] = mapped_column(
+            nullable=False,
+            default=True
+        )
+
         config: Mapped[dict[str, Any]] = mapped_column(
             JSONB,
             nullable=False,
@@ -135,7 +140,7 @@ 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 +178,11 @@ 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 +192,7 @@ 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-1.8.2/src/tol/validators/sts_fields.py

@@ -0,0 +1,229 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from dataclasses import dataclass
+from datetime import datetime, timedelta
+from typing import List
+
+from tol.core import DataObject, DataSource
+from tol.core.validate import Validator
+from tol.sources.sts import sts
+
+
+class StsFieldsValidator(Validator):
+    """
+    Validates that a stream of `DataObject` instances
+    contains fields that observe the validations in STS
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        project_code: str
+
+    __slots__ = ['__config', '__datasource', '__fields']
+    __config: Config
+    __datasource: DataSource
+    __fields: List[str | int | float]
+
+    def __init__(
+        self,
+        config: Config,
+        datasource: DataSource = sts(),  # For testing
+        **kwargs
+    ) -> None:
+
+        super().__init__()
+
+        self.__config = config
+        self.__datasource = datasource
+        self.__fields = self.__initialize_fields_from_datasource()
+
+    def __initialize_fields_from_datasource(self) -> List[str | int | float]:
+        return {
+            field.get('data_input_key'): field
+            for field in self.__datasource.get_one(
+                'project', self.__config.project_code
+            ).template.get('data_fields', [])
+            if field.get('in_manifest')
+        }
+
+    def _validate_data_object(
+        self,
+        obj: DataObject
+    ) -> None:
+        for field in self.__fields.values():
+            # Ignore inactive fields
+            if field.get('status') == 'Inactive':
+                continue
+            # Get the value from the data object
+            field_value = obj.get_field_by_name(field.get('data_input_key'))
+            if isinstance(field_value, list):
+                field_value = ' | '.join(str(v) for v in field_value)
+
+            # mandatory_input fields must be present
+            if field.get('mandatory_input') and field.get('data_input_key') not in obj.attributes:
+                self.add_error(
+                    object_id=obj.id,
+                    detail=f'Field {field.get("data_input_key")} is required '
+                           f'for project {self.__config.project_code}',
+                    field=field.get('data_input_key'),
+                )
+                continue
+
+            # Skip further validations if validation is not mandatory
+            if not field.get('mandatory_validation'):
+                continue
+
+            # Mandatory validation fields must have a value
+            if field_value is None or field_value == '':
+                self.add_error(
+                    object_id=obj.id,
+                    detail=f'Field {field.get("data_input_key")} is required to have a value '
+                           f'for project {self.__config.project_code}',
+                    field=field.get('data_input_key'),
+                )
+                continue
+
+            # Allowed values
+            if field.get('allowed_values'):
+                allowed_values = [
+                    value.get('value') for value in field.get('allowed_values', [])
+                ]
+                if field_value not in allowed_values:
+                    self.add_error(
+                        object_id=obj.id,
+                        detail=f'Field {field.get("data_input_key")} value '
+                               f'"{field_value}" not found in allowed values '
+                               f'{allowed_values} for project '
+                               f'{self.__config.project_code}',
+                        field=field.get('data_input_key'),
+                    )
+
+            if field.get('type') in ['String', 'TextArea']:
+                self.__validate_string(obj, field, field_value)
+
+            if field.get('type') in ['Integer', 'Decimal', 'Percentage']:
+                self.__validate_number(obj, field, field_value)
+
+            if field.get('type') in ['Boolean']:
+                self.__validate_boolean(obj, field, field_value)
+
+            if field.get('type') in ['Date']:
+                self.__validate_date(obj, field, field_value)
+
+    def __validate_string(
+        self,
+        obj: DataObject,
+        field: dict,
+        field_value: str | int | float | None
+    ) -> None:
+        # Check type is a string
+        # if not isinstance(field_value, str):
+        #     self.add_error(
+        #         object_id=obj.id,
+        #         detail=f'Field {field.get("data_input_key")} value '
+        #                 f'"{field_value}" is not a string for project '
+        #                 f'{self.__config.project_code}',
+        #         field=field.get('data_input_key'),
+        #     )
+        #     return
+
+        # Min/Max validations for string
+        if field.get('min') and len(field_value) < field.get('min'):
+            self.add_error(
+                object_id=obj.id,
+                detail=f'Field {field.get("data_input_key")} value '
+                       f'"{field_value}" is shorter than minimum length '
+                       f'"{field.get("min")}" for project '
+                       f'{self.__config.project_code}',
+                field=field.get('data_input_key'),
+            )
+        if field.get('max') and len(field_value) > field.get('max'):
+            self.add_error(
+                object_id=obj.id,
+                detail=f'Field {field.get("data_input_key")} value '
+                       f'"{field_value}" is longer than maximum length '
+                       f'"{field.get("max")}" for project '
+                       f'{self.__config.project_code}',
+                field=field.get('data_input_key'),
+            )
+
+    def __validate_number(
+        self,
+        obj: DataObject,
+        field: dict,
+        field_value: str | int | float | None
+    ) -> None:
+        # Check type is a number
+        if not isinstance(field_value, (int, float)):
+            self.add_error(
+                object_id=obj.id,
+                detail=f'Field {field.get("data_input_key")} value '
+                       f'"{field_value}" is not a number for project '
+                       f'{self.__config.project_code}',
+                field=field.get('data_input_key'),
+            )
+            return
+
+        # Min/Max validations for number
+        if field.get('min') is not None and field_value < field.get('min'):
+            self.add_error(
+                object_id=obj.id,
+                detail=f'Field {field.get("data_input_key")} value '
+                       f'"{field_value}" is less than minimum value '
+                       f'"{field.get("min")}" for project '
+                       f'{self.__config.project_code}',
+                field=field.get('data_input_key'),
+            )
+        if field.get('max') is not None and field_value > field.get('max'):
+            self.add_error(
+                object_id=obj.id,
+                detail=f'Field {field.get("data_input_key")} value '
+                       f'"{field_value}" is greater than maximum value '
+                       f'"{field.get("max")}" for project '
+                       f'{self.__config.project_code}',
+                field=field.get('data_input_key'),
+            )
+
+    def __validate_boolean(
+        self,
+        obj: DataObject,
+        field: dict,
+        field_value: str | int | float | None
+    ) -> None:
+        # Check type is a boolean
+        if field_value not in ['Y', 'N']:
+            self.add_error(
+                object_id=obj.id,
+                detail=f'Field {field.get("data_input_key")} value '
+                       f'"{field_value}" is not a boolean (Y/N) for project '
+                       f'{self.__config.project_code}',
+                field=field.get('data_input_key'),
+            )
+
+    def __validate_date(
+        self,
+        obj: DataObject,
+        field: dict,
+        field_value: str | int | float | None
+    ) -> None:
+        if not isinstance(field_value, datetime):
+            self.add_error(
+                object_id=obj.id,
+                detail=f'Field {field.get("data_input_key")} value '
+                       f'"{field_value}" is not a date string for project '
+                       f'{self.__config.project_code}',
+                field=field.get('data_input_key'),
+            )
+            return
+        if field.get('range_limit'):
+            earliest_date = datetime.now() - timedelta(days=field.get('min'))
+            latest_date = datetime.now() + timedelta(days=field.get('max'))
+            if field_value < earliest_date or field_value > latest_date:
+                self.add_error(
+                    object_id=obj.id,
+                    detail=f'Field {field.get("data_input_key")} value '
+                           f'"{field_value}" is not within the allowed date '
+                           f'range for project {self.__config.project_code}',
+                    field=field.get('data_input_key'),
+                )

{tol_sdk-1.8.0 → tol_sdk-1.8.2}/src/tol/validators/types.py

@@ -58,6 +58,8 @@ class TypesValidator(Validator):
                     self.__add_result(
                         obj,
                         key,
+                        detail=f'Field {key} value "{actual_value}" is not of type '
+                               f'"{expected_type}"',
                     )
                 if type_class and isinstance(actual_value, type_class):
                     # Special case for bool since isinstance(True, int) is True
@@ -71,12 +73,13 @@ class TypesValidator(Validator):
         self,
         obj: DataObject,
         key: str,
+        detail: str = None,
     ) -> None:
 
         if self.__config.is_error:
             self.add_error(
                 object_id=obj.id,
-                detail=self.__config.detail,
+                detail=detail or self.__config.detail,
                 field=key,
             )
         else:

{tol_sdk-1.8.0 → tol_sdk-1.8.2/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.0
+Version: 1.8.2
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.0 → tol_sdk-1.8.2}/src/tol_sdk.egg-info/SOURCES.txt

@@ -52,6 +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_extraction_type_dna.sql
 src/tol/benchling/sql/extraction_extraction_type_lres.sql
 src/tol/benchling/sql/extraction_extraction_type_pooled_dna.sql