tol-sdk 1.8.4__tar.gz → 1.8.5__tar.gz

{tol_sdk-1.8.4/src/tol_sdk.egg-info → tol_sdk-1.8.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.4
+Version: 1.8.5
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.4 → tol_sdk-1.8.5}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tol-sdk"
-version = "1.8.4"
+version = "1.8.5"
 description = "SDK for interaction with ToL, Sanger and external services"
 readme = "README.md"
 authors = [

{tol_sdk-1.8.4 → tol_sdk-1.8.5}/src/tol/api_client/view.py

@@ -197,7 +197,7 @@ class DefaultView(View):
             sub_tree = tree.get_sub_tree(rel)
             if sub_tree and rel in data_object._to_many_objects:
                 many_obj = data_object._to_many_objects.get(rel)
-                to_many[rel] = [self.__dump_stub(x, rel) for x in many_obj]
+                to_many[rel] = {'data': [self.__dump_stub(x, rel) for x in many_obj]}
                 for obj in many_obj:
                     included.add_dump(self.__dump_object(obj, included, sub_tree))
             elif quoted_id:

tol_sdk-1.8.5/src/tol/flows/converters/time_string_to_time.py

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

{tol_sdk-1.8.4 → tol_sdk-1.8.5}/src/tol/validators/ena_checklist.py

@@ -12,6 +12,11 @@ from tol.sources.ena import ena
 
 
 class EnaChecklistValidator(Validator):
+    ENA_TO_INTERNAL_FIELD_MAP = {
+        'geographic location (longitude)': 'DECIMAL_LONGITUDE',
+        'geographic location (latitude)': 'DECIMAL_LATITUDE',
+    }
+
     """
     validates the ENA_CHECKLIST for each samples
     """
@@ -37,16 +42,18 @@ class EnaChecklistValidator(Validator):
             field_name = key
             if 'field' in validation:
                 field_name = validation['field']
+            internal_field = self.ENA_TO_INTERNAL_FIELD_MAP.get(field_name, field_name)
+
             if 'mandatory' in validation and key not in obj.attributes:
-                self.add_error(object_id=obj.id, detail='Must be given', field=[field_name])
+                self.add_error(object_id=obj.id, detail='Must be given', field=[internal_field])
                 continue
             if 'mandatory' in validation and obj.attributes[key] is None:
-                self.add_error(object_id=obj.id, detail='Must be given', field=[field_name])
+                self.add_error(object_id=obj.id, detail='Must be given', field=[internal_field])
                 continue
             if 'mandatory' in validation and obj.attributes.get(key) == '':
                 self.add_error(
                     object_id=obj.id,
-                    detail='Must not be empty', field=[field_name]
+                    detail='Must not be empty', field=[internal_field]
                 )
 
             if 'restricted text' in validation and key in obj.attributes:
@@ -55,12 +62,25 @@ class EnaChecklistValidator(Validator):
                         regex = condition
                 compiled_re = re.compile(regex)
                 if not compiled_re.search(obj.attributes.get(key)):
-                    self.add_error(
-                        object_id=obj.id,
-                        detail='Must match specific pattern', field=[field_name]
-                    )
+                    if internal_field in ('DECIMAL_LONGITUDE', 'DECIMAL_LATITUDE'):
+                        self.add_error(
+                            object_id=obj.id,
+                            detail=(
+                                f'Value for {internal_field} must be a valid decimal in the'
+                                f' format required by ENA (e.g. 12.3456). '
+                                f'See ENA checklist for accepted format.',
+                            ),
+                            field=[internal_field]
+                        )
+                    else:
+                        self.add_error(
+                            object_id=obj.id,
+                            detail=(
+                                f'Value for {internal_field} must match the required pattern.'
+                            ),
+                            field=[internal_field]
+                        )
 
-            # Check against allowed values
             if 'text choice' in validation and key in obj.attributes:
                 for condition in validation:
                     if isinstance(condition, list):
@@ -69,5 +89,5 @@ class EnaChecklistValidator(Validator):
                         [x.lower() for x in allowed_values]:
                     self.add_error(
                         object_id=obj.id,
-                        detail='Must be in allowed values', field=[field_name]
+                        detail='Must be in allowed values', field=[internal_field]
                     )

{tol_sdk-1.8.4 → tol_sdk-1.8.5}/src/tol/validators/specimens_have_same_taxon.py

@@ -53,7 +53,7 @@ class SpecimensHaveSameTaxonValidator(Validator):
             if specimen_id in self.__seen and taxon_id != self.__seen[specimen_id]:
                 self.add_error(
                     object_id=obj.id,
-                    detail='A non-symbiont must have a matching Specimen ID and Taxon ID',
+                    detail='All samples from the same specimen_ID must have the same TAXON_ID.',
                     field=self.__config.specimen_id_field,
                 )
             if specimen_id not in self.__seen:

{tol_sdk-1.8.4 → tol_sdk-1.8.5}/src/tol/validators/types.py

@@ -55,12 +55,19 @@ class TypesValidator(Validator):
                     continue
                 type_class = type_map.get(expected_type)
                 if type_class and not isinstance(actual_value, type_class):
-                    self.__add_result(
-                        obj,
-                        key,
-                        detail=f'Field {key} value "{actual_value}" is not of type '
-                               f'"{expected_type}"',
-                    )
+                    if expected_type == 'time':
+                        self.__add_result(
+                            obj,
+                            key,
+                            detail='Only HH:MM format is accepted.',
+                        )
+                    else:
+                        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
                     if expected_type == 'int' and isinstance(actual_value, bool):

{tol_sdk-1.8.4 → tol_sdk-1.8.5}/src/tol/validators/value_check.py

@@ -26,11 +26,12 @@ class ValueCheckValidator(Validator):
         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:
+        if obj.attributes.get(self.__config.field) != self.__config.value:
             self.add_error(
                 object_id=obj.id,
-                detail=f'{self.__config.value} is detected',
+                detail=(
+                    f"Expected '{self.__config.value}' for field "
+                    f"'{self.__config.field}', but got '{obj.attributes.get(self.__config.field)}'"
+                ),
                 field=self.__config.field,
             )

{tol_sdk-1.8.4 → tol_sdk-1.8.5/src/tol_sdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.8.4
+Version: 1.8.5
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.8.4 → tol_sdk-1.8.5}/src/tol_sdk.egg-info/SOURCES.txt

@@ -203,6 +203,7 @@ src/tol/flows/converters/sts_sample_project_to_elastic_sample_converter.py
 src/tol/flows/converters/sts_sample_to_casm_benchling_converter.py
 src/tol/flows/converters/sts_sampleset_to_elastic_sampleset_converter.py
 src/tol/flows/converters/sts_species_to_elastic_species_converter.py
+src/tol/flows/converters/time_string_to_time.py
 src/tol/flows/converters/tolid_specimen_to_elastic_tolid_converter.py
 src/tol/flows/converters/tolqc_data_to_elastic_run_data_converter.py
 src/tol/flows/converters/tolqc_sample_to_elastic_sequencing_request_converter.py