liminal-orm 2.0.3a1__py3-none-any.whl → 3.0.0__py3-none-any.whl

liminal/base/base_operation.py

@@ -13,13 +13,13 @@ Order of operations based on order class var:
     6. ArchiveDropdownOption
     7. ReorderDropdownOptions
     8. CreateSchema
-    9. UpdateSchema
-    10. UnarchiveSchema
-    11. CreateField
-    12. UnarchiveField
-    13. UpdateField
-    14. ArchiveField
-    15. UpdateEntitySchemaNameTemplate
+    9. UnarchiveSchema
+    10. CreateField
+    11. UpdateEntitySchemaNameTemplate
+    12. UpdateSchema
+    13. UnarchiveField
+    14. UpdateField
+    15. ArchiveField
     16. ReorderFields
     17. ArchiveSchema
     18. ArchiveDropdown

liminal/base/properties/base_field_properties.py

@@ -49,6 +49,8 @@ class BaseFieldProperties(BaseModel):
     dropdown_link: str | None = None
     entity_link: str | None = None
     tooltip: str | None = None
+    decimal_places: int | None = None
+    unit_name: str | None = None
     _archived: bool | None = PrivateAttr(default=None)
 
     model_config = ConfigDict(arbitrary_types_allowed=True)
@@ -122,4 +124,4 @@ class BaseFieldProperties(BaseModel):
 
     def __repr__(self) -> str:
         """Generates a string representation of the class so that it can be executed."""
-        return f"{self.__class__.__name__}({', '.join([f'{k}={v.__repr__()}' for k, v in self.model_dump(exclude_unset=True, exclude_defaults=True).items()])})"
+        return f"{self.__class__.__name__}({', '.join([f'{k}={v.__repr__()}' for k, v in self.model_dump(exclude_unset=True).items()])})"

liminal/base/properties/base_schema_properties.py

@@ -66,8 +66,13 @@ class BaseSchemaProperties(BaseModel):
     include_registry_id_in_chips : bool | None = None
         Flag for configuring the chip label for entities. Determines if the chip will include the Registry ID in the chip label.
     constraint_fields : set[str] | None
-        Set of constraints for field values for the schema. Must be a set of column names that specify that their values must be a unique combination within an entity.
-        If the entity type is a Sequence, "bases" can be a constraint field.
+        Set of constraints for field values for the schema. Must be a set of warehouse column names. This specifies that their entity field values must be a unique combination within an entity.
+        The following sequence constraints are also supported:
+        - bases: only supported for nucleotide sequence entity types. hasUniqueResidues=True
+        - amino_acids_ignore_case: only supported for amino acid sequence entity types. hasUniqueResidues=True
+        - amino_acids_exact_match: only supported for amino acid sequence entity types. hasUniqueResidues=True, areUniqueResiduesCaseSensitive=True
+    show_bases_in_expanded_view : bool | None
+        Whether the bases should be shown in the expanded view of the entity.
     _archived : bool | None
         Whether the schema is archived in Benchling.
     """
@@ -81,6 +86,7 @@ class BaseSchemaProperties(BaseModel):
     use_registry_id_as_label: bool | None = None
     include_registry_id_in_chips: bool | None = None
     constraint_fields: set[str] | None = None
+    show_bases_in_expanded_view: bool | None = None
     _archived: bool | None = None
 
     def __init__(self, **data: Any):

liminal/entity_schemas/compare.py

@@ -18,6 +18,7 @@ from liminal.entity_schemas.operations import (
     UpdateEntitySchemaNameTemplate,
 )
 from liminal.entity_schemas.utils import get_converted_tag_schemas
+from liminal.enums.benchling_naming_strategy import BenchlingNamingStrategy
 from liminal.orm.base_model import BaseModel
 from liminal.orm.column import Column
 from liminal.utils import to_snake_case
@@ -275,6 +276,16 @@ def compare_entity_schemas(
                 col.properties.set_warehouse_name(wh_name)
                 for wh_name, col in model_columns.items()
             ]
+            template_based_naming_strategies = {
+                s
+                for s in model.__schema_properties__.naming_strategies
+                if BenchlingNamingStrategy.is_template_based(s)
+            }
+            model.__schema_properties__.naming_strategies = {
+                s
+                for s in model.__schema_properties__.naming_strategies
+                if not BenchlingNamingStrategy.is_template_based(s)
+            }
             ops.append(
                 CompareOperation(
                     op=CreateEntitySchema(
@@ -288,28 +299,10 @@ def compare_entity_schemas(
                     ),
                 )
             )
-            benchling_given_wh_name = to_snake_case(model.__schema_properties__.name)
-            if model.__schema_properties__.warehouse_name != benchling_given_wh_name:
-                ops.append(
-                    CompareOperation(
-                        op=UpdateEntitySchema(
-                            benchling_given_wh_name,
-                            BaseSchemaProperties(
-                                warehouse_name=model.__schema_properties__.warehouse_name
-                            ),
-                        ),
-                        reverse_op=UpdateEntitySchema(
-                            model.__schema_properties__.warehouse_name,
-                            BaseSchemaProperties(
-                                warehouse_name=benchling_given_wh_name
-                            ),
-                        ),
-                    )
-                )
             benchling_given_name_template = BaseNameTemplate(
                 parts=[], order_name_parts_by_sequence=False
             )
-            if benchling_name_template != model.__name_template__:
+            if benchling_given_name_template != model.__name_template__:
                 ops.append(
                     CompareOperation(
                         op=UpdateEntitySchemaNameTemplate(
@@ -323,13 +316,39 @@ def compare_entity_schemas(
                         reverse_op=UpdateEntitySchemaNameTemplate(
                             model.__schema_properties__.warehouse_name,
                             BaseNameTemplate(
-                                **benchling_given_name_template.merge(
-                                    model.__name_template__
+                                **model.__name_template__.merge(
+                                    benchling_given_name_template
                                 )
                             ),
                         ),
                     )
                 )
+            benchling_given_wh_name = to_snake_case(model.__schema_properties__.name)
+            new_schema_props = BaseSchemaProperties()
+            rollback_schema_props = BaseSchemaProperties()
+            if model.__schema_properties__.warehouse_name != benchling_given_wh_name:
+                new_schema_props.warehouse_name = (
+                    model.__schema_properties__.warehouse_name
+                )
+                rollback_schema_props.warehouse_name = benchling_given_wh_name
+            if template_based_naming_strategies:
+                new_schema_props.naming_strategies = template_based_naming_strategies
+                rollback_schema_props.naming_strategies = (
+                    model.__schema_properties__.naming_strategies
+                )
+            if new_schema_props.model_dump(exclude_unset=True) != {}:
+                ops.append(
+                    CompareOperation(
+                        op=UpdateEntitySchema(
+                            benchling_given_wh_name,
+                            new_schema_props,
+                        ),
+                        reverse_op=UpdateEntitySchema(
+                            model.__schema_properties__.warehouse_name,
+                            rollback_schema_props,
+                        ),
+                    )
+                )
 
         model_operations[model.__schema_properties__.warehouse_name] = ops
         running_benchling_schema_names = [

liminal/entity_schemas/entity_schema_models.py

@@ -9,8 +9,10 @@ from liminal.connection import BenchlingService
 from liminal.dropdowns.utils import get_benchling_dropdown_summary_by_name
 from liminal.entity_schemas.tag_schema_models import TagSchemaModel
 from liminal.enums import BenchlingEntityType
+from liminal.enums.sequence_constraint import SequenceConstraint
 from liminal.mappers import convert_field_type_to_api_field_type
 from liminal.orm.schema_properties import MixtureSchemaConfig, SchemaProperties
+from liminal.unit_dictionary.utils import get_unit_id_from_name
 
 
 class FieldLinkShortModel(BaseModel):
@@ -26,28 +28,44 @@ class EntitySchemaConstraint(BaseModel):
     """
 
     areUniqueResiduesCaseSensitive: bool | None = None
-    fields: dict[str, Any] | None = None
-    hasUniqueCanonicalSmilers: bool | None = None
+    fields: list[dict[str, Any]] | None = None
+    hasUniqueCanonicalSmiles: bool | None = None
     hasUniqueResidues: bool | None = None
 
     @classmethod
     def from_constraint_fields(
-        cls, constraint_fields: set[str]
+        cls,
+        constraint_fields: set[str],
+        benchling_service: BenchlingService | None = None,
     ) -> EntitySchemaConstraint:
         """
         Generates a Constraint object from a set of constraint fields to create a constraint on a schema.
         """
-        if constraint_fields is None:
-            return None
         hasUniqueResidues = False
-        if "bases" in constraint_fields:
-            constraint_fields.discard("bases")
+        areUniqueResiduesCaseSensitive = False
+        if SequenceConstraint.BASES in constraint_fields:
+            constraint_fields.discard(SequenceConstraint.BASES)
+            hasUniqueResidues = True
+        elif SequenceConstraint.AMINO_ACIDS_IGNORE_CASE in constraint_fields:
+            constraint_fields.discard(SequenceConstraint.AMINO_ACIDS_IGNORE_CASE)
             hasUniqueResidues = True
+        elif SequenceConstraint.AMINO_ACIDS_EXACT_MATCH in constraint_fields:
+            constraint_fields.discard(SequenceConstraint.AMINO_ACIDS_EXACT_MATCH)
+            hasUniqueResidues = True
+            areUniqueResiduesCaseSensitive = True
+        fields = []
+        for field_name in constraint_fields:
+            if benchling_service is None:
+                raise ValueError(
+                    "Benchling SDK must be provided to update constraint fields."
+                )
+            field = TagSchemaModel.get_one(benchling_service, field_name)
+            fields.append({"name": field.name, "id": field.id})
         return cls(
-            fields=[{"name": f} for f in constraint_fields],
+            fields=fields,
             hasUniqueResidues=hasUniqueResidues,
-            hasUniqueCanonicalSmilers=False,
-            areUniqueResiduesCaseSensitive=False,
+            hasUniqueCanonicalSmiles=False,
+            areUniqueResiduesCaseSensitive=areUniqueResiduesCaseSensitive,
         )
 
 
@@ -63,6 +81,8 @@ class CreateEntitySchemaFieldModel(BaseModel):
     isParentLink: bool = False
     dropdownId: str | None = None
     link: FieldLinkShortModel | None = None
+    unitId: str | None = None
+    decimalPrecision: int | None = None
 
     @classmethod
     def from_benchling_props(
@@ -107,6 +127,11 @@ class CreateEntitySchemaFieldModel(BaseModel):
             dropdown_summary_id = get_benchling_dropdown_summary_by_name(
                 benchling_service, field_props.dropdown_link
             ).id
+        unit_id = None
+        if field_props.unit_name is not None:
+            if benchling_service is None:
+                raise ValueError("Benchling SDK must be provided to update unit field.")
+            unit_id = get_unit_id_from_name(benchling_service, field_props.unit_name)
         return CreateEntitySchemaFieldModel(
             name=field_props.name,
             systemName=field_props.warehouse_name,
@@ -118,6 +143,8 @@ class CreateEntitySchemaFieldModel(BaseModel):
             link=FieldLinkShortModel(
                 tagSchema=tag_schema, folderItemType=folder_item_type
             ),
+            unitId=unit_id,
+            decimalPrecision=field_props.decimal_places,
         )
 
 
@@ -135,6 +162,7 @@ class CreateEntitySchemaModel(BaseModel):
     useOrganizationCollectionAliasForDisplayLabel: bool | None = None
     labelingStrategies: list[str] | None = None
     constraint: EntitySchemaConstraint | None = None
+    showResidues: bool | None = None
 
     @classmethod
     def from_benchling_props(
@@ -168,11 +196,10 @@ class CreateEntitySchemaModel(BaseModel):
             includeRegistryIdInChips=benchling_props.include_registry_id_in_chips,
             useOrganizationCollectionAliasForDisplayLabel=benchling_props.use_registry_id_as_label,
             labelingStrategies=[s.value for s in benchling_props.naming_strategies],
+            showResidues=benchling_props.show_bases_in_expanded_view,
             constraint=EntitySchemaConstraint.from_constraint_fields(
                 benchling_props.constraint_fields
-            )
-            if benchling_props.constraint_fields
-            else None,
+            ),
             fields=[
                 CreateEntitySchemaFieldModel.from_benchling_props(
                     field_props, benchling_service

liminal/entity_schemas/generate_files.py

@@ -91,7 +91,7 @@ def generate_all_entity_schema_files(
                 dropdown_classname = dropdown_name_to_classname_map[col.dropdown_link]
                 dropdowns.append(dropdown_classname)
             column_strings.append(
-                f"""{tab}{col_name}: SqlColumn = Column(name="{col.name}", type={str(col.type)}, required={col.required}{', is_multi=True' if col.is_multi else ''}{', parent_link=True' if col.parent_link else ''}{f', entity_link="{col.entity_link}"' if col.entity_link else ''}{f', dropdown={dropdown_classname}' if dropdown_classname else ''}{f', tooltip="{col.tooltip}"' if col.tooltip else ''})"""
+                f"""{tab}{col_name}: SqlColumn = Column(name="{col.name}", type={str(col.type)}, required={col.required}{', is_multi=True' if col.is_multi else ''}{', parent_link=True' if col.parent_link else ''}{f', entity_link="{col.entity_link}"' if col.entity_link else ''}{f', dropdown={dropdown_classname}' if dropdown_classname else ''}{f', tooltip="{col.tooltip}"' if col.tooltip else ''}{f', unit_name="{col.unit_name}"' if col.unit_name else ''}{f', decimal_places={col.decimal_places}' if col.decimal_places is not None else ''})"""
             )
             if col.required and col.type:
                 init_strings.append(
@@ -105,7 +105,7 @@ def generate_all_entity_schema_files(
                 if not has_date:
                     import_strings.append("from datetime import datetime")
             if (
-                col.type == BenchlingFieldType.ENTITY_LINK
+                col.type in BenchlingFieldType.get_entity_link_types()
                 and col.entity_link is not None
             ):
                 if not col.is_multi:

liminal/entity_schemas/operations.py

@@ -1,3 +1,4 @@
+import logging
 from typing import Any, ClassVar
 
 from liminal.base.base_operation import BaseOperation
@@ -25,8 +26,14 @@ from liminal.entity_schemas.utils import (
 )
 from liminal.enums import BenchlingNamingStrategy
 from liminal.orm.schema_properties import SchemaProperties
+from liminal.unit_dictionary.utils import (
+    get_unit_id_to_name_map,
+    get_unit_name_to_id_map,
+)
 from liminal.utils import to_snake_case
 
+LOGGER = logging.getLogger(__name__)
+
 
 class CreateEntitySchema(BaseOperation):
     order: ClassVar[int] = 80
@@ -39,7 +46,7 @@ class CreateEntitySchema(BaseOperation):
         self.schema_properties = schema_properties
         self.fields = fields
         self._validated_schema_properties = SchemaProperties(
-            **schema_properties.model_dump()
+            **schema_properties.model_dump(exclude_unset=True)
         )
 
     def execute(self, benchling_service: BenchlingService) -> dict[str, Any]:
@@ -83,6 +90,15 @@ class CreateEntitySchema(BaseOperation):
                 Either set warehouse_access to True in BenchlingConnection or set the schema warehouse_name to the given Benchling warehouse name: {to_snake_case(self._validated_schema_properties.name)}. \
                 Reach out to Benchling support if you need help setting up warehouse access."
             )
+        for field in self.fields:
+            if (
+                field.unit_name
+                and field.unit_name
+                not in get_unit_name_to_id_map(benchling_service).keys()
+            ):
+                raise ValueError(
+                    f"{self._validated_schema_properties.warehouse_name}: On field {field.warehouse_name}, unit {field.unit_name} not found in Benchling Unit Dictionary as a valid unit. Please check the field definition or your Unit Dictionary."
+                )
 
     def _validate_create(self, benchling_service: BenchlingService) -> None:
         all_schemas = TagSchemaModel.get_all_json(benchling_service)
@@ -123,8 +139,11 @@ class CreateEntitySchema(BaseOperation):
                 f"Entity schema {self._validated_schema_properties.warehouse_name} is already active in Benchling."
             )
         dropdowns_map = get_benchling_dropdown_id_name_map(benchling_service)
+        unit_id_to_name_map = get_unit_id_to_name_map(benchling_service)
         benchling_schema_props, _, benchling_fields_props = (
-            convert_tag_schema_to_internal_schema(schema, dropdowns_map)
+            convert_tag_schema_to_internal_schema(
+                schema, dropdowns_map, unit_id_to_name_map
+            )
         )
         if (
             self._validated_schema_properties != benchling_schema_props
@@ -162,7 +181,7 @@ class ArchiveEntitySchema(BaseOperation):
 
 
 class UnarchiveEntitySchema(BaseOperation):
-    order: ClassVar[int] = 100
+    order: ClassVar[int] = 90
 
     def __init__(self, wh_schema_name: str) -> None:
         self.wh_schema_name = wh_schema_name
@@ -187,7 +206,7 @@ class UnarchiveEntitySchema(BaseOperation):
 
 
 class UpdateEntitySchema(BaseOperation):
-    order: ClassVar[int] = 90
+    order: ClassVar[int] = 120
 
     def __init__(
         self,
@@ -251,7 +270,7 @@ class UpdateEntitySchema(BaseOperation):
 
 
 class UpdateEntitySchemaNameTemplate(BaseOperation):
-    order: ClassVar[int] = 150
+    order: ClassVar[int] = 110
 
     def __init__(
         self,
@@ -283,7 +302,7 @@ class UpdateEntitySchemaNameTemplate(BaseOperation):
 
 
 class CreateEntitySchemaField(BaseOperation):
-    order: ClassVar[int] = 110
+    order: ClassVar[int] = 100
 
     def __init__(
         self,
@@ -316,13 +335,20 @@ class CreateEntitySchemaField(BaseOperation):
                     f"Field {self._wh_field_name} is already active on entity schema {self.wh_schema_name}."
                 )
             dropdowns_map = get_benchling_dropdown_id_name_map(benchling_service)
+            unit_id_to_name_map = get_unit_id_to_name_map(benchling_service)
             if self.field_props == convert_tag_schema_field_to_field_properties(
-                field, dropdowns_map
-            ):
+                field, dropdowns_map, unit_id_to_name_map
+            ).set_warehouse_name(self._wh_field_name):
                 return UnarchiveEntitySchemaField(
                     self.wh_schema_name, self._wh_field_name, self.index
                 ).execute(benchling_service)
             else:
+                print(self.field_props)
+                print(
+                    convert_tag_schema_field_to_field_properties(
+                        field, dropdowns_map, unit_id_to_name_map
+                    )
+                )
                 raise ValueError(
                     f"Field {self._wh_field_name} on entity schema {self.wh_schema_name} is different in code versus Benchling."
                 )
@@ -367,10 +393,18 @@ class CreateEntitySchemaField(BaseOperation):
                 Either set warehouse_access to True in BenchlingConnection or set the column variable name to the given Benchling field warehouse name: {to_snake_case(self.field_props.name)}. \
                 Reach out to Benchling support if you need help setting up warehouse access."
             )
+        if (
+            self.field_props.unit_name
+            and self.field_props.unit_name
+            not in get_unit_name_to_id_map(benchling_service).keys()
+        ):
+            raise ValueError(
+                f"{self.wh_schema_name}: On field {self._wh_field_name}, unit {self.field_props.unit_name} not found in Benchling Unit Dictionary as a valid unit. Please check the field definition or your Unit Dictionary."
+            )
 
 
 class ArchiveEntitySchemaField(BaseOperation):
-    order: ClassVar[int] = 140
+    order: ClassVar[int] = 150
 
     def __init__(
         self, wh_schema_name: str, wh_field_name: str, index: int | None = None
@@ -421,7 +455,7 @@ class ArchiveEntitySchemaField(BaseOperation):
 
 
 class UnarchiveEntitySchemaField(BaseOperation):
-    order: ClassVar[int] = 120
+    order: ClassVar[int] = 130
 
     def __init__(
         self, wh_schema_name: str, wh_field_name: str, index: int | None = None
@@ -468,7 +502,7 @@ class UnarchiveEntitySchemaField(BaseOperation):
 
 
 class UpdateEntitySchemaField(BaseOperation):
-    order: ClassVar[int] = 130
+    order: ClassVar[int] = 140
 
     def __init__(
         self,
@@ -500,6 +534,9 @@ class UpdateEntitySchemaField(BaseOperation):
         return f"{self.wh_schema_name}: Entity schema field '{self.wh_field_name}' in Benchling is different than in code: {str(self.update_props)}."
 
     def validate(self, benchling_service: BenchlingService) -> None:
+        tag_schema = TagSchemaModel.get_one_cached(
+            benchling_service, self.wh_schema_name
+        )
         if (
             not benchling_service.connection.warehouse_access
             and self.update_props.warehouse_name is not None
@@ -509,6 +546,19 @@ class UpdateEntitySchemaField(BaseOperation):
                 Either set warehouse_access to True in BenchlingConnection or do not change the warehouse name. \
                 Reach out to Benchling support if you need help setting up warehouse access."
             )
+        if "unit_name" in self.update_props.model_dump(exclude_unset=True):
+            no_change_message = f"{self.wh_schema_name}: On field {self.wh_field_name}, updating unit name to {self.update_props.unit_name}. The unit of this field CANNOT be changed once it's been set."
+            if tag_schema.get_field(self.wh_field_name).unitApiIdentifier:
+                raise ValueError(no_change_message)
+            else:
+                LOGGER.warning(no_change_message)
+            if (
+                self.update_props.unit_name
+                not in get_unit_name_to_id_map(benchling_service).keys()
+            ):
+                raise ValueError(
+                    f"{self.wh_schema_name}: On field {self.wh_field_name}, unit {self.update_props.unit_name} not found in Benchling Unit Dictionary as a valid unit. Please check the field definition or your Unit Dictionary."
+                )
 
     def _validate(self, benchling_service: BenchlingService) -> TagSchemaModel:
         tag_schema = TagSchemaModel.get_one(benchling_service, self.wh_schema_name)

liminal/entity_schemas/tag_schema_models.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from functools import lru_cache
 from typing import Any
 
 import requests
@@ -17,6 +18,7 @@ from liminal.enums import (
     BenchlingSequenceType,
 )
 from liminal.enums.name_template_part_type import NameTemplatePartType
+from liminal.enums.sequence_constraint import SequenceConstraint
 from liminal.mappers import (
     convert_entity_type_to_api_entity_type,
     convert_field_type_to_api_field_type,
@@ -25,6 +27,7 @@ from liminal.orm.name_template_parts import (
     NameTemplatePart,
 )
 from liminal.orm.schema_properties import MixtureSchemaConfig
+from liminal.unit_dictionary.utils import get_unit_id_from_name
 
 
 class FieldRequiredLinkShortModel(BaseModel):
@@ -91,16 +94,28 @@ class TagSchemaConstraint(BaseModel):
 
     @classmethod
     def from_constraint_fields(
-        cls, constraint_fields: list[TagSchemaFieldModel], bases: bool
+        cls,
+        constraint_fields: list[TagSchemaFieldModel],
+        sequence_constraint: SequenceConstraint | None = None,
     ) -> TagSchemaConstraint:
         """
         Generates a Constraint object from a set of constraint fields to create a constraint on a schema.
         """
+        uniqueResidues = False
+        areUniqueResiduesCaseSensitive = False
+        match sequence_constraint:
+            case SequenceConstraint.BASES:
+                uniqueResidues = True
+            case SequenceConstraint.AMINO_ACIDS_IGNORE_CASE:
+                uniqueResidues = True
+            case SequenceConstraint.AMINO_ACIDS_EXACT_MATCH:
+                uniqueResidues = True
+                areUniqueResiduesCaseSensitive = True
         return cls(
             fields=constraint_fields,
-            uniqueResidues=bases,
+            uniqueResidues=uniqueResidues,
             uniqueCanonicalSmilers=False,
-            areUniqueResiduesCaseSensitive=False,
+            areUniqueResiduesCaseSensitive=areUniqueResiduesCaseSensitive,
         )
 
 
@@ -135,6 +150,8 @@ class CreateTagSchemaFieldModel(BaseModel):
     name: str
     requiredLink: FieldRequiredLinkShortModel | None = None
     tooltipText: str | None = None
+    decimalPrecision: int | None = None
+    unitApiIdentifier: str | None = None
 
     @classmethod
     def from_props(
@@ -164,7 +181,7 @@ class CreateTagSchemaFieldModel(BaseModel):
         )
 
         tagSchema = None
-        if new_props.type == BenchlingFieldType.ENTITY_LINK:
+        if new_props.type in BenchlingFieldType.get_entity_link_types():
             if new_props.entity_link is not None:
                 if benchling_service is None:
                     raise ValueError(
@@ -184,6 +201,13 @@ class CreateTagSchemaFieldModel(BaseModel):
             dropdown_summary_id = get_benchling_dropdown_summary_by_name(
                 benchling_service, new_props.dropdown_link
             ).id
+        unit_api_identifier = None
+        if new_props.unit_name:
+            if benchling_service is None:
+                raise ValueError("Benchling SDK must be provided to update unit field.")
+            unit_api_identifier = get_unit_id_from_name(
+                benchling_service, new_props.unit_name
+            )
         return cls(
             name=new_props.name,
             systemName=new_props.warehouse_name,
@@ -197,6 +221,8 @@ class CreateTagSchemaFieldModel(BaseModel):
                 tagSchema=tagSchema,
             ),
             tooltipText=new_props.tooltip,
+            unitApiIdentifier=unit_api_identifier,
+            decimalPrecision=new_props.decimal_places,
         )
 
 
@@ -230,6 +256,8 @@ class TagSchemaFieldModel(BaseModel):
     strictSelector: bool | None
     systemName: str
     tooltipText: str | None
+    unitApiIdentifier: str | None
+    unitSymbol: str | None = None
 
     def update_from_props(
         self,
@@ -307,6 +335,22 @@ class TagSchemaFieldModel(BaseModel):
                 benchling_service, update_props.dropdown_link
             ).id
             self.schemaFieldSelectorId = dropdown_summary_id
+        self.decimalPrecision = (
+            update_props.decimal_places
+            if "decimal_places" in update_diff_names
+            else self.decimalPrecision
+        )
+        if "unit_name" in update_diff_names:
+            if update_props.unit_name is None:
+                self.unitApiIdentifier = None
+            else:
+                if benchling_service is None:
+                    raise ValueError(
+                        "Benchling SDK must be provided to update unit field."
+                    )
+                self.unitApiIdentifier = get_unit_id_from_name(
+                    benchling_service, update_props.unit_name
+                )
         return self
 
 
@@ -405,6 +449,15 @@ class TagSchemaModel(BaseModel):
             )
         return cls.model_validate(schema)
 
+    @classmethod
+    @lru_cache(maxsize=100)
+    def get_one_cached(
+        cls,
+        benchling_service: BenchlingService,
+        wh_schema_name: str,
+    ) -> TagSchemaModel:
+        return cls.get_one(benchling_service, wh_schema_name)
+
     def get_field(self, wh_field_name: str) -> TagSchemaFieldModel:
         """Returns a field from the tag schema by its warehouse field name."""
         for field in self.allFields:
@@ -437,37 +490,31 @@ class TagSchemaModel(BaseModel):
             )
         if "include_registry_id_in_chips" in update_diff_names:
             self.includeRegistryIdInChips = update_props.include_registry_id_in_chips
+        if "show_bases_in_expanded_view" in update_diff_names:
+            self.showResidues = update_props.show_bases_in_expanded_view
 
         if "constraint_fields" in update_diff_names:
             if update_props.constraint_fields:
-                has_bases = False
-                if "bases" in update_props.constraint_fields:
-                    has_bases = True
-                    update_props.constraint_fields.discard("bases")
-                constraint_fields = [
-                    f
-                    for f in self.fields
-                    if f.systemName in update_props.constraint_fields
-                ]
-                self.constraint = TagSchemaConstraint.from_constraint_fields(
-                    constraint_fields, has_bases
+                sequence_constraint = next(
+                    (
+                        SequenceConstraint(c)
+                        for c in update_props.constraint_fields
+                        if SequenceConstraint.is_sequence_constraint(c)
+                    ),
+                    None,
                 )
-            else:
-                self.constraint = None
-
-        if "constraint_fields" in update_diff_names:
-            if update_props.constraint_fields:
-                has_bases = False
-                if "bases" in update_props.constraint_fields:
-                    has_bases = True
-                    update_props.constraint_fields.discard("bases")
+                update_props.constraint_fields = {
+                    c
+                    for c in update_props.constraint_fields
+                    if not SequenceConstraint.is_sequence_constraint(c)
+                }
                 constraint_fields = [
                     f
                     for f in self.fields
                     if f.systemName in update_props.constraint_fields
                 ]
                 self.constraint = TagSchemaConstraint.from_constraint_fields(
-                    constraint_fields, has_bases
+                    constraint_fields, sequence_constraint
                 )
             else:
                 self.constraint = None

liminal/entity_schemas/utils.py

@@ -5,12 +5,15 @@ from liminal.connection import BenchlingService
 from liminal.dropdowns.utils import get_benchling_dropdown_id_name_map
 from liminal.entity_schemas.tag_schema_models import TagSchemaFieldModel, TagSchemaModel
 from liminal.enums import BenchlingAPIFieldType, BenchlingNamingStrategy
+from liminal.enums.benchling_entity_type import BenchlingEntityType
+from liminal.enums.sequence_constraint import SequenceConstraint
 from liminal.mappers import (
     convert_api_entity_type_to_entity_type,
     convert_api_field_type_to_field_type,
 )
 from liminal.orm.name_template import NameTemplate
 from liminal.orm.schema_properties import MixtureSchemaConfig, SchemaProperties
+from liminal.unit_dictionary.utils import get_unit_id_to_name_map
 
 
 def get_converted_tag_schemas(
@@ -24,6 +27,7 @@ def get_converted_tag_schemas(
     """
     all_schemas = TagSchemaModel.get_all(benchling_service, wh_schema_names)
     dropdowns_map = get_benchling_dropdown_id_name_map(benchling_service)
+    unit_id_to_name_map = get_unit_id_to_name_map(benchling_service)
     all_schemas = (
         all_schemas
         if include_archived
@@ -31,7 +35,7 @@ def get_converted_tag_schemas(
     )
     return [
         convert_tag_schema_to_internal_schema(
-            tag_schema, dropdowns_map, include_archived
+            tag_schema, dropdowns_map, unit_id_to_name_map, include_archived
         )
         for tag_schema in all_schemas
     ]
@@ -40,24 +44,38 @@ def get_converted_tag_schemas(
 def convert_tag_schema_to_internal_schema(
     tag_schema: TagSchemaModel,
     dropdowns_map: dict[str, str],
+    unit_id_to_name_map: dict[str, str],
     include_archived_fields: bool = False,
 ) -> tuple[SchemaProperties, NameTemplate, dict[str, BaseFieldProperties]]:
     all_fields = tag_schema.allFields
     if not include_archived_fields:
         all_fields = [f for f in all_fields if not f.archiveRecord]
-    constraint_fields: set[str] | None = None
+    constraint_fields: set[str] = set()
+    entity_type = convert_api_entity_type_to_entity_type(
+        tag_schema.folderItemType, tag_schema.sequenceType
+    )
     if tag_schema.constraint:
-        constraint_fields = set([f.systemName for f in tag_schema.constraint.fields])
+        constraint_fields = constraint_fields.union(
+            [f.systemName for f in tag_schema.constraint.fields]
+        )
         if tag_schema.constraint.uniqueResidues:
-            constraint_fields.add("bases")
+            if entity_type.is_nt_sequence():
+                constraint_fields.add(SequenceConstraint.BASES.value)
+            elif entity_type == BenchlingEntityType.AA_SEQUENCE:
+                if tag_schema.constraint.areUniqueResiduesCaseSensitive:
+                    constraint_fields.add(
+                        SequenceConstraint.AMINO_ACIDS_EXACT_MATCH.value
+                    )
+                else:
+                    constraint_fields.add(
+                        SequenceConstraint.AMINO_ACIDS_IGNORE_CASE.value
+                    )
     return (
         SchemaProperties(
             name=tag_schema.name,
             prefix=tag_schema.prefix,
             warehouse_name=tag_schema.sqlIdentifier,
-            entity_type=convert_api_entity_type_to_entity_type(
-                tag_schema.folderItemType, tag_schema.sequenceType
-            ),
+            entity_type=entity_type,
             mixture_schema_config=MixtureSchemaConfig(
                 allowMeasuredIngredients=tag_schema.mixtureSchemaConfig.allowMeasuredIngredients,
                 componentLotStorageEnabled=tag_schema.mixtureSchemaConfig.componentLotStorageEnabled,
@@ -73,20 +91,25 @@ def convert_tag_schema_to_internal_schema(
             _archived=tag_schema.archiveRecord is not None,
             use_registry_id_as_label=tag_schema.useOrganizationCollectionAliasForDisplayLabel,
             include_registry_id_in_chips=tag_schema.includeRegistryIdInChips,
+            show_bases_in_expanded_view=tag_schema.showResidues,
         ),
         NameTemplate(
             parts=tag_schema.get_internal_name_template_parts(),
             order_name_parts_by_sequence=tag_schema.shouldOrderNamePartsBySequence,
         ),
         {
-            f.systemName: convert_tag_schema_field_to_field_properties(f, dropdowns_map)
+            f.systemName: convert_tag_schema_field_to_field_properties(
+                f, dropdowns_map, unit_id_to_name_map
+            )
             for f in all_fields
         },
     )
 
 
 def convert_tag_schema_field_to_field_properties(
-    field: TagSchemaFieldModel, dropdowns_map: dict[str, str]
+    field: TagSchemaFieldModel,
+    dropdowns_map: dict[str, str],
+    unit_id_to_name_map: dict[str, str],
 ) -> BaseFieldProperties:
     return BaseFieldProperties(
         name=field.name,
@@ -105,6 +128,10 @@ def convert_tag_schema_field_to_field_properties(
         else None,
         tooltip=field.tooltipText,
         _archived=field.archiveRecord is not None,
+        unit_name=unit_id_to_name_map.get(field.unitApiIdentifier)
+        if field.unitApiIdentifier
+        else None,
+        decimal_places=field.decimalPrecision,
     )
 
 

liminal/enums/__init__.py

@@ -5,3 +5,4 @@ from liminal.enums.benchling_field_type import BenchlingFieldType
 from liminal.enums.benchling_folder_item_type import BenchlingFolderItemType
 from liminal.enums.benchling_naming_strategy import BenchlingNamingStrategy
 from liminal.enums.benchling_sequence_type import BenchlingSequenceType
+from liminal.enums.sequence_constraint import SequenceConstraint

liminal/enums/benchling_entity_type.py

@@ -14,10 +14,19 @@ class BenchlingEntityType(StrEnum):
     MIXTURE = "mixture"
     MOLECULE = "molecule"
 
+    def is_nt_sequence(self) -> bool:
+        return self in [
+            self.DNA_SEQUENCE,
+            self.RNA_SEQUENCE,
+            self.DNA_OLIGO,
+            self.RNA_OLIGO,
+        ]
+
     def is_sequence(self) -> bool:
         return self in [
             self.DNA_SEQUENCE,
             self.RNA_SEQUENCE,
             self.DNA_OLIGO,
             self.RNA_OLIGO,
+            self.AA_SEQUENCE,
         ]

liminal/enums/benchling_field_type.py

@@ -32,3 +32,11 @@ class BenchlingFieldType(StrEnum):
             cls.DATE,
             cls.DATETIME,
         ]
+
+    @classmethod
+    def get_entity_link_types(cls) -> list[str]:
+        return [cls.ENTITY_LINK, cls.TRANSLATION_LINK, cls.PART_LINK]
+
+    @classmethod
+    def get_number_field_types(cls) -> list[str]:
+        return [cls.INTEGER, cls.DECIMAL]

liminal/enums/benchling_naming_strategy.py

@@ -11,6 +11,7 @@ class BenchlingNamingStrategy(StrEnum):
     )
     RENAME_WITH_TEMPLATE_WITH_ALIAS = "SET_FROM_NAME_PARTS"  # Generate new registry IDs, rename according to name template, and keep old name as alias
     REPLACE_NAMES_WITH_TEMPLATE = "REPLACE_NAMES_FROM_PARTS"  # Generate new registry IDs, and replace name according to name template
+    KEEP_NAMES = "KEEP_NAMES"  # Keeps the original name
 
     @classmethod
     def is_template_based(cls, strategy: BenchlingNamingStrategy) -> bool:

liminal/enums/sequence_constraint.py

@@ -0,0 +1,13 @@
+from liminal.base.str_enum import StrEnum
+
+
+class SequenceConstraint(StrEnum):
+    """This enum represents hardcoded sequence constraints."""
+
+    BASES = "bases"
+    AMINO_ACIDS_IGNORE_CASE = "amino_acids_ignore_case"
+    AMINO_ACIDS_EXACT_MATCH = "amino_acids_exact_match"
+
+    @classmethod
+    def is_sequence_constraint(cls, constraint: str) -> bool:
+        return constraint in cls._value2member_map_

liminal/mappers.py

@@ -22,6 +22,8 @@ def convert_benchling_type_to_python_type(benchling_type: BenchlingFieldType) ->
         BenchlingFieldType.BLOB_LINK: dict[str, Any],
         BenchlingFieldType.CUSTOM_ENTITY_LINK: str,
         BenchlingFieldType.DNA_SEQUENCE_LINK: str,
+        BenchlingFieldType.AA_SEQUENCE_LINK: str,
+        BenchlingFieldType.TRANSLATION_LINK: str,
         BenchlingFieldType.DROPDOWN: str,
         BenchlingFieldType.ENTITY_LINK: str,
         BenchlingFieldType.ENTRY_LINK: str,
@@ -48,6 +50,8 @@ def convert_benchling_type_to_sql_alchemy_type(
         BenchlingFieldType.BLOB_LINK: JSON,
         BenchlingFieldType.CUSTOM_ENTITY_LINK: String,
         BenchlingFieldType.DNA_SEQUENCE_LINK: String,
+        BenchlingFieldType.AA_SEQUENCE_LINK: String,
+        BenchlingFieldType.TRANSLATION_LINK: String,
         BenchlingFieldType.DROPDOWN: String,
         BenchlingFieldType.ENTITY_LINK: String,
         BenchlingFieldType.ENTRY_LINK: String,
@@ -55,7 +59,6 @@ def convert_benchling_type_to_sql_alchemy_type(
         BenchlingFieldType.STORAGE_LINK: String,
         BenchlingFieldType.PART_LINK: String,
         BenchlingFieldType.MIXTURE_LINK: String,
-        BenchlingFieldType.AA_SEQUENCE_LINK: String,
         BenchlingFieldType.TEXT: String,
     }
     if benchling_type in benchling_to_sql_alchemy_type_map:
@@ -88,13 +91,10 @@ def convert_field_type_to_api_field_type(
             BenchlingAPIFieldType.FILE_LINK,
             BenchlingFolderItemType.SEQUENCE,
         ),
-        BenchlingFieldType.PART_LINK: (
-            BenchlingAPIFieldType.PART_LINK,
-            BenchlingFolderItemType.SEQUENCE,
-        ),
+        BenchlingFieldType.PART_LINK: (BenchlingAPIFieldType.PART_LINK, None),
         BenchlingFieldType.TRANSLATION_LINK: (
             BenchlingAPIFieldType.TRANSLATION_LINK,
-            BenchlingFolderItemType.SEQUENCE,
+            None,
         ),
         BenchlingFieldType.ENTITY_LINK: (BenchlingAPIFieldType.FILE_LINK, None),
         BenchlingFieldType.DECIMAL: (BenchlingAPIFieldType.FLOAT, None),
@@ -135,13 +135,10 @@ def convert_api_field_type_to_field_type(
             BenchlingAPIFieldType.FILE_LINK,
             BenchlingFolderItemType.PROTEIN,
         ): BenchlingFieldType.AA_SEQUENCE_LINK,
-        (
-            BenchlingAPIFieldType.PART_LINK,
-            BenchlingFolderItemType.SEQUENCE,
-        ): BenchlingFieldType.PART_LINK,
+        (BenchlingAPIFieldType.PART_LINK, None): BenchlingFieldType.PART_LINK,
         (
             BenchlingAPIFieldType.TRANSLATION_LINK,
-            BenchlingFolderItemType.SEQUENCE,
+            None,
         ): BenchlingFieldType.TRANSLATION_LINK,
         (BenchlingAPIFieldType.FILE_LINK, None): BenchlingFieldType.ENTITY_LINK,
         (BenchlingAPIFieldType.FLOAT, None): BenchlingFieldType.DECIMAL,

liminal/orm/base_model.py

@@ -13,6 +13,8 @@ from sqlalchemy.orm.decl_api import declared_attr
 
 from liminal.base.base_validation_filters import BaseValidatorFilters
 from liminal.enums import BenchlingNamingStrategy
+from liminal.enums.benchling_entity_type import BenchlingEntityType
+from liminal.enums.sequence_constraint import SequenceConstraint
 from liminal.orm.base import Base
 from liminal.orm.base_tables.user import User
 from liminal.orm.name_template import NameTemplate
@@ -63,16 +65,49 @@ class BaseModel(Generic[T], Base):
             c[0] for c in cls.__dict__.items() if isinstance(c[1], SqlColumn)
         ]
         # Validate constraints
-        if cls.__schema_properties__.constraint_fields:
-            invalid_constraints = [
-                c
-                for c in cls.__schema_properties__.constraint_fields
-                if c not in (set(column_wh_names) | {"bases"})
-            ]
-            if invalid_constraints:
-                raise ValueError(
-                    f"Constraints {', '.join(invalid_constraints)} are not fields on schema {cls.__schema_properties__.name}."
-                )
+        invalid_constraints = [
+            c
+            for c in cls.__schema_properties__.constraint_fields
+            if c
+            not in set(column_wh_names)
+            | set(SequenceConstraint._value2member_map_.keys())
+        ]
+        if invalid_constraints:
+            raise ValueError(
+                f"Constraints {', '.join(invalid_constraints)} are not fields on schema {cls.__schema_properties__.name}."
+            )
+        sequence_constraints = [
+            SequenceConstraint(c)
+            for c in cls.__schema_properties__.constraint_fields
+            if SequenceConstraint.is_sequence_constraint(c)
+        ]
+        if len(sequence_constraints) > 1:
+            raise ValueError(
+                "Only one sequence constraint field can be set for a schema."
+            )
+        sequence_constraint = sequence_constraints[0] if sequence_constraints else None
+        match sequence_constraint:
+            case SequenceConstraint.BASES:
+                if not cls.__schema_properties__.entity_type.is_nt_sequence():
+                    raise ValueError(
+                        "`bases` constraint is only supported for nucleotide sequence entities."
+                    )
+            case SequenceConstraint.AMINO_ACIDS_IGNORE_CASE:
+                if (
+                    cls.__schema_properties__.entity_type
+                    != BenchlingEntityType.AA_SEQUENCE
+                ):
+                    raise ValueError(
+                        "`amino_acids_ignore_case` constraint is only supported for aa_sequence entities."
+                    )
+            case SequenceConstraint.AMINO_ACIDS_EXACT_MATCH:
+                if (
+                    cls.__schema_properties__.entity_type
+                    != BenchlingEntityType.AA_SEQUENCE
+                ):
+                    raise ValueError(
+                        "`amino_acids_exact_match` constraint is only supported for aa_sequence entities."
+                    )
         # Validate naming strategies
         if any(
             BenchlingNamingStrategy.is_template_based(strategy)
@@ -84,7 +119,7 @@ class BaseModel(Generic[T], Base):
                 )
         # Validate name template
         if cls.__name_template__:
-            if not cls.__schema_properties__.entity_type.is_sequence():
+            if not cls.__schema_properties__.entity_type.is_nt_sequence():
                 if cls.__name_template__.order_name_parts_by_sequence is True:
                     raise ValueError(
                         "order_name_parts_by_sequence is only supported for sequence entities. Must be set to False if entity type is not a sequence."

liminal/orm/column.py

@@ -32,6 +32,10 @@ class Column(SqlColumn):
         The dropdown for the field.
     entity_link : str | None = None
         The warehouse name of the entity the field links to.
+    unit : str | None = None
+        The unit of the field. Searches for the unit warehouse name in the Unit Dictionary.
+    decimal_places : int | None = None
+        The number of decimal places for the field. Must be (0-15).
     _warehouse_name : str | None = None
         The warehouse name of the column. Necessary when the variable name is not the same as the warehouse name.
     _archived : bool = False
@@ -48,6 +52,8 @@ class Column(SqlColumn):
         tooltip: str | None = None,
         dropdown: Type[BaseDropdown] | None = None,  # noqa: UP006
         entity_link: str | None = None,
+        unit_name: str | None = None,
+        decimal_places: int | None = None,
         _warehouse_name: str | None = None,
         _archived: bool = False,
         **kwargs: Any,
@@ -64,6 +70,8 @@ class Column(SqlColumn):
             entity_link=entity_link,
             tooltip=tooltip,
             _archived=_archived,
+            unit_name=unit_name,
+            decimal_places=decimal_places,
         )
         self.properties = properties
 
@@ -73,19 +81,29 @@ class Column(SqlColumn):
             raise ValueError("Dropdown can only be set if the field type is DROPDOWN.")
         if dropdown is None and type == BenchlingFieldType.DROPDOWN:
             raise ValueError("Dropdown must be set if the field type is DROPDOWN.")
-        if entity_link and type != BenchlingFieldType.ENTITY_LINK:
+        if unit_name and type not in BenchlingFieldType.get_number_field_types():
             raise ValueError(
-                "Entity link can only be set if the field type is ENTITY_LINK."
+                f"Unit can only be set if the field type is one of {BenchlingFieldType.get_number_field_types()}."
             )
-        if parent_link and type != BenchlingFieldType.ENTITY_LINK:
+        if decimal_places and type not in BenchlingFieldType.DECIMAL:
             raise ValueError(
-                "Parent link can only be set if the field type is ENTITY_LINK."
+                "Decimal places can only be set if the field type is DECIMAL."
+            )
+        if decimal_places and (decimal_places < 0 or decimal_places > 15):
+            raise ValueError("Decimal places must be between 0 and 15.")
+        if entity_link and type not in BenchlingFieldType.get_entity_link_types():
+            raise ValueError(
+                f"Entity link can only be set if the field type is one of {BenchlingFieldType.get_entity_link_types()}."
+            )
+        if parent_link and type not in BenchlingFieldType.get_entity_link_types():
+            raise ValueError(
+                f"Parent link can only be set if the field type is one of {BenchlingFieldType.get_entity_link_types()}."
             )
         if type in BenchlingFieldType.get_non_multi_select_types() and is_multi is True:
             raise ValueError(f"Field type {type} cannot have multi-value set as True.")
         self.sqlalchemy_type = sqlalchemy_type
         foreign_key = None
-        if type == BenchlingFieldType.ENTITY_LINK and entity_link:
+        if type in BenchlingFieldType.get_entity_link_types() and entity_link:
             foreign_key = ForeignKey(f"{entity_link}$raw.id")
         if _warehouse_name:
             kwargs["name"] = _warehouse_name

liminal/orm/schema_properties.py

@@ -35,9 +35,14 @@ class SchemaProperties(BaseSchemaProperties):
         Flag for configuring the chip label for entities. Determines if the chip will use the Registry ID as the main label for items.
     include_registry_id_in_chips : bool | None = None
         Flag for configuring the chip label for entities. Determines if the chip will include the Registry ID in the chip label.
-    constraint_fields : set[str] | None
-        Set of constraints for field values for the schema. Must be a set of column names that specify that their values must be a unique combination within an entity.
-        If the entity type is a Sequence, "bases" can be a constraint field.
+    constraint_fields : set[str]
+        Set of constraints for field values for the schema. Must be a set of warehouse column names. This specifies that their entity field values must be a unique combination within an entity.
+        The following sequence constraints are also supported:
+        - bases: only supported for nucleotide sequence entity types. hasUniqueResidues=True
+        - amino_acids_ignore_case: only supported for amino acid sequence entity types. hasUniqueResidues=True
+        - amino_acids_exact_match: only supported for amino acid sequence entity types. hasUniqueResidues=True, areUniqueResiduesCaseSensitive=True
+    show_bases_in_expanded_view : bool | None = None
+        Whether the bases should be shown in the expanded view of the entity.
     _archived : bool | None
         Whether the schema is archived in Benchling.
     """
@@ -50,7 +55,8 @@ class SchemaProperties(BaseSchemaProperties):
     use_registry_id_as_label: bool | None = False
     include_registry_id_in_chips: bool | None = False
     mixture_schema_config: MixtureSchemaConfig | None = None
-    constraint_fields: set[str] | None = None
+    constraint_fields: set[str] = set()
+    show_bases_in_expanded_view: bool | None = False
     _archived: bool = False
 
     def __init__(self, **data: Any):
@@ -73,7 +79,10 @@ class SchemaProperties(BaseSchemaProperties):
             raise ValueError(
                 "The entity type is not a Mixture. Remove the mixture schema config."
             )
-
+        if not self.entity_type.is_sequence() and self.show_bases_in_expanded_view:
+            raise ValueError(
+                "show_bases_in_expanded_view can only be set for sequence entities."
+            )
         if self.naming_strategies and len(self.naming_strategies) == 0:
             raise ValueError(
                 "Schema must have at least 1 registry naming option enabled"

liminal/unit_dictionary/utils.py

@@ -0,0 +1,48 @@
+import json
+from functools import lru_cache
+
+from liminal.connection.benchling_service import BenchlingService
+
+
+@lru_cache(maxsize=1)
+def get_unit_name_to_id_map(benchling_service: BenchlingService) -> dict[str, str]:
+    response = benchling_service.api.get_response(
+        url="/api/v2-alpha/unit-types?pageSize=50"
+    )
+    unit_types = json.loads(response.content)["unitTypes"]
+    all_unit_types_flattened = {}
+    for unit_type in unit_types:
+        for unit in unit_type["units"]:
+            all_unit_types_flattened[unit["name"]] = unit["id"]
+    return all_unit_types_flattened
+
+
+def get_unit_id_from_name(benchling_service: BenchlingService, unit_name: str) -> str:
+    unit_id = get_unit_name_to_id_map(benchling_service).get(unit_name)
+    if unit_id is None:
+        raise ValueError(
+            f"Unit {unit_name} not found in Benchling Unit Dictionary. Please check the field definition or your Unit Dictionary."
+        )
+    return unit_id
+
+
+@lru_cache(maxsize=1)
+def get_unit_id_to_name_map(benchling_service: BenchlingService) -> dict[str, str]:
+    response = benchling_service.api.get_response(
+        url="/api/v2-alpha/unit-types?pageSize=50"
+    )
+    unit_types = json.loads(response.content)["unitTypes"]
+    all_unit_types_flattened = {}
+    for unit_type in unit_types:
+        for unit in unit_type["units"]:
+            all_unit_types_flattened[unit["id"]] = unit["name"]
+    return all_unit_types_flattened
+
+
+def get_unit_name_from_id(benchling_service: BenchlingService, unit_id: str) -> str:
+    unit_name = get_unit_id_to_name_map(benchling_service).get(unit_id)
+    if unit_name is None:
+        raise ValueError(
+            f"Unit {unit_id} not found in Benchling Unit Dictionary. Please check the field definition or your Unit Dictionary."
+        )
+    return unit_name

liminal/validation/__init__.py

@@ -1,4 +1,3 @@
-import inspect
 from datetime import datetime
 from functools import partial, wraps
 from typing import TYPE_CHECKING, Any, Callable
@@ -102,7 +101,7 @@ class BenchlingValidatorReport(BaseModel):
 
 
 def liminal_validator(
-    func: Callable[[type["BenchlingBaseModel"]], BenchlingValidatorReport | None]
+    func: Callable[["BenchlingBaseModel"], BenchlingValidatorReport | None]
     | None = None,
     *,
     validator_level: ValidationSeverity = ValidationSeverity.LOW,
@@ -125,15 +124,9 @@ def liminal_validator(
             validator_level=validator_level,
             validator_name=validator_name,
         )
-    elif not isinstance(
-        func, Callable[[["BenchlingBaseModel"]], BenchlingValidatorReport | None]
-    ):
-        raise ValueError(
-            "Parameters passed to liminal_validator must be keyword arguments, not positional arguments."
-        )
 
     @wraps(func)
-    def wrapper(self: type["BenchlingBaseModel"]) -> BenchlingValidatorReport:
+    def wrapper(self: "BenchlingBaseModel") -> BenchlingValidatorReport:
         """Wrapper that runs the validator function and returns a BenchlingValidatorReport."""
         try:
             ret_val = func(self)

{liminal_orm-2.0.3a1.dist-info → liminal_orm-3.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 2.0.3a1
+Version: 3.0.0
 Summary: An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync.
 Home-page: https://github.com/dynotx/liminal-orm
 Author: DynoTx Open Source

{liminal_orm-2.0.3a1.dist-info → liminal_orm-3.0.0.dist-info}/RECORD

@@ -1,12 +1,13 @@
+liminal/.DS_Store,sha256=s_ehSI1aIzOjVRnFlcSzhtWS3irmEDSGHyS6l0QRcus,8196
 liminal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 liminal/base/base_dropdown.py,sha256=Unk4l_5Y8rj_eSWYqzFi2BAFSQToQDWW2qdXwiCHTg8,2523
-liminal/base/base_operation.py,sha256=RjGRaCTNQ5oVI4PAQ5D3svymw_HAcGvzBXWWrMRo29k,3128
+liminal/base/base_operation.py,sha256=opQfFZeC49YAFkg5ahE6CFpeSUNPh1ootWZxXyEXfFI,3128
 liminal/base/base_validation_filters.py,sha256=kHG3G5gXkuNHQosMTrxRc57OTmczcaoSx0DmkrScIr4,1043
 liminal/base/compare_operation.py,sha256=hkpv4ewHhxy4dlTPKgJuzBjsAqO6Km7OrrKB44pRA_o,352
 liminal/base/name_template_parts.py,sha256=dJeyrhhhZHDwKXe_p7AtgDlbZlzsnYQ8FoM8FXVF7q0,271
-liminal/base/properties/base_field_properties.py,sha256=NvuQjYZ5U_2363P2c8FXmmLfOtdzUqTuZTjDDfXnO-E,4922
+liminal/base/properties/base_field_properties.py,sha256=ze8CLf0jPPYwklFYVKXkRvXiBBA9ilG5nK1_oP0rS04,4970
 liminal/base/properties/base_name_template.py,sha256=AOtaW4QEDRC-mjZOZk6jgc_mopUMsHS2Fj6VVsO07WY,3150
-liminal/base/properties/base_schema_properties.py,sha256=pVeIVHea-3Wt0fde9CsOvluwVmYMbsMhGeSncRL2Ats,5351
+liminal/base/properties/base_schema_properties.py,sha256=11QaxtUoHZx25QFv7HP8gQBpknrFthVeyWuMnI_lV5g,5891
 liminal/base/str_enum.py,sha256=jF3d-Lo8zsHUe6GsctX2L-TSj92Y3qCYDrTD-saeJoc,210
 liminal/cli/cli.py,sha256=JxWHLO9KMeMaOnOYwzdH0w71l0477ScFOkWNtTlc97Y,9045
 liminal/cli/controller.py,sha256=QNj3QO9TMb9hfc6U-VhLuFa0_aohOHZUmvY4XkATPhw,10118
@@ -21,48 +22,51 @@ liminal/dropdowns/generate_files.py,sha256=IqnBs-IyLsIZE0NUkdB99zd5EAF-1f9CPBebl
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 liminal/dropdowns/utils.py,sha256=1-H7bTszCUeqeRBpiYXjRjreDzhn1Fd1MFwIsrEI-o4,4109
 liminal/entity_schemas/api.py,sha256=Emn_Y95cAG9Wis6tpchw6QBVKQh4If86LOdgKk0Ndjw,3575
-liminal/entity_schemas/compare.py,sha256=CIYglq1F-g9jGc1eRRD4LnNErrH2n__pPIJc4EB1hkM,16570
-liminal/entity_schemas/entity_schema_models.py,sha256=YDpz1XkNc9e51zah8Z6qCk30gAuXP6xLEYv1Lb3ECpA,6838
-liminal/entity_schemas/generate_files.py,sha256=oYx0t76oRa36gWwVl1W5jHryh-POIyZPDMbGNjT5bfY,8877
-liminal/entity_schemas/operations.py,sha256=rs9EXmHDgnUad2SSfZ3tnDPFA6L-2wvllAGqBwBurMs,24020
-liminal/entity_schemas/tag_schema_models.py,sha256=h6Zf_zXYG_gTh2eQh_lEGZKUAmvzdnnArlmAhIeX1bM,22016
-liminal/entity_schemas/utils.py,sha256=iZ1_M2r8zKOCFj9QSMdrv-_4XznDn_znAOfoP4Mh1jA,4943
-liminal/enums/__init__.py,sha256=Ue_3QtElW-JMSWtu4vGsAOFQbYnzHHZUdkWpdkzkKA4,453
+liminal/entity_schemas/compare.py,sha256=t6tl67GWaMoNNcPxyLpCuNAlN3OWNqURTo3EUEMtETE,17549
+liminal/entity_schemas/entity_schema_models.py,sha256=v5A1ELaiuBnUSl1HkUNAeMuIRQeQnIKzfpFxmsiKWh0,8349
+liminal/entity_schemas/generate_files.py,sha256=u9SoDO9f4qL2nZaddln__2J0zJ3QMFBQhiUabn22aUY,9032
+liminal/entity_schemas/operations.py,sha256=jd6Wiq_rW0UIjiVqUACio_Lwbv3fGrtoyQRGBHtXJHo,26654
+liminal/entity_schemas/tag_schema_models.py,sha256=FlpoDWh083nA8iT7Pl84HVXKb7StIApV1ExvwHKiAfc,24002
+liminal/entity_schemas/utils.py,sha256=2ZHyLxnYITVEuyAWxNdsq5hcNSgvN7pN3-uUzyocYSk,6161
+liminal/enums/__init__.py,sha256=-szuqAwMED4ai0NaPVUfgihQJAJ27wPu_nDnj4cEgTk,518
 liminal/enums/benchling_api_field_type.py,sha256=0QamSWEMnxZtedZXlh6zNhSRogS9ZqvWskdHHN19xJo,633
-liminal/enums/benchling_entity_type.py,sha256=BS6U8qnRM3I3xTTqp9BbInV7yjPh9gC3ULvN6-zLaCM,624
-liminal/enums/benchling_field_type.py,sha256=uinDm5Mn_yGK1jlmlRH3NlAlXUzA1guNk8wF6lbUKD4,947
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 liminal/enums/benchling_folder_item_type.py,sha256=Jb-YxCvB8O86_qTsfwtLQOkKGjTWGKHFwIKf24eemYk,248
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 liminal/external/__init__.py,sha256=nMpyzpBXpYhTvN3R3HQEiYb24_U2AYjz_20seAUUK9s,1264
-liminal/mappers.py,sha256=O9gc95b7JvfaR8xVrn0X1d0Tcs6Iwh-yhBHXhWSX8i0,9616
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 liminal/migrate/components.py,sha256=2HuFp5KDNhofROMRI-BioUoA4CCjhQ_v_F0QmGJzUBU,3480
 liminal/migrate/revision.py,sha256=KppU0u-d0JsfPsXsmncxy9Q_XBJyf-o4e16wNZAJODM,7774
 liminal/migrate/revisions_timeline.py,sha256=G9VwxPrLhLqKOrIXyxrXyHpujc-72m7omsZjI5-0D0M,14520
 liminal/migrate/utils.py,sha256=HdSr3N2WN_1S-PLRGVWSMYl-4gIcP-Ph2wPycGi2cGg,3404
 liminal/orm/base.py,sha256=fFSpiNRYgK5UG7lbXdQGV8KgO8pwjMqt0pycM3rWJ2o,615
-liminal/orm/base_model.py,sha256=Nf4gSEwvORRdnY5ODW79ddJWxnshLLvrPo8xcimHH6c,13891
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 liminal/orm/base_tables/registry_entity.py,sha256=4ET1cepTGjZ3AMFI5q-iMYxMObzXwuUDBD0jNNqCipE,2126
 liminal/orm/base_tables/schema.py,sha256=7_btCVSUJxjVdGcKVRKL8sKcNw7-_gazTpfEh1jru3o,921
 liminal/orm/base_tables/user.py,sha256=elRAHj7HgO3iVLK_pNCIwf_9Rl_9k6vkBgaYazoJSQc,818
-liminal/orm/column.py,sha256=e4JWn97s_4EVJ1LOO5l6iucHQUd39Vl0stqMEj0uet8,5114
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 liminal/orm/mixins.py,sha256=yEeUDF1qEBLP523q8bZra4KtNVK0gwZN9mXJSNe3GEE,4802
 liminal/orm/name_template.py,sha256=ftXZOiRR6gGGvGaZkFVDXKOboIHFWauhQENRguBGWMI,1739
 liminal/orm/name_template_parts.py,sha256=KCGXAcCuOqCjlgYn-mw1K7fwDI92D20l-FnlpEVrbM8,2771
 liminal/orm/relationship.py,sha256=Zl4bMHbtDSPx1psGHYnojGGJpA8B8hwcPJdgjB1lmW0,2490
-liminal/orm/schema_properties.py,sha256=yv6MOsE_16OWJnGDh2K8wI_054PJwafYmHgY_Awr3XA,3420
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 liminal/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 liminal/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 liminal/tests/conftest.py,sha256=B463eOfe1uCHDJsUNvG-6tY8Qx8FJMByGDOtuyM87lA,17669
 liminal/tests/from benchling_sdk.py,sha256=CjRUHFB3iaa4rUPLGOqDiBq5EPKldm-Fd8aQQr92zF4,147
 liminal/tests/test_dropdown_compare.py,sha256=yHB0ovQlBLRu8-qYkqIPd8VtYEOmOft_93FQM86g_z8,8198
 liminal/tests/test_entity_schema_compare.py,sha256=-26Bu5eYIuHRswB5kYjGDo5Wed5LUWjm1e6IRI1Q-lE,18952
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 liminal/utils.py,sha256=radRtRsZmCiNblMvxOX1DH0rcO5TR09kFlp6OONIPBU,2951
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 liminal/validation/validation_severity.py,sha256=ib03PTZCQHcbBDc01v4gJF53YtA-ANY6QSFnhTV-FbU,259
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