liminal-orm 2.0.3a0__tar.gz → 2.0.4__tar.gz

{liminal_orm-2.0.3a0 → liminal_orm-2.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 2.0.3a0
+Version: 2.0.4
 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-2.0.3a0 → liminal_orm-2.0.4}/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. UpdateEntitySchemaNameTemplate
+    10. UpdateSchema
+    11. UnarchiveSchema
+    12. CreateField
+    13. UnarchiveField
+    14. UpdateField
+    15. ArchiveField
     16. ReorderFields
     17. ArchiveSchema
     18. ArchiveDropdown

{liminal_orm-2.0.3a0 → liminal_orm-2.0.4}/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_orm-2.0.3a0 → liminal_orm-2.0.4}/liminal/entity_schemas/generate_files.py

@@ -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_orm-2.0.3a0 → liminal_orm-2.0.4}/liminal/entity_schemas/tag_schema_models.py

@@ -164,7 +164,7 @@ 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(

{liminal_orm-2.0.3a0 → liminal_orm-2.0.4}/liminal/enums/benchling_field_type.py

@@ -32,3 +32,7 @@ class BenchlingFieldType(StrEnum):
             cls.DATE,
             cls.DATETIME,
         ]
+
+    @classmethod
+    def get_entity_link_types(cls) -> list[str]:
+        return [cls.ENTITY_LINK, cls.TRANSLATION_LINK]

{liminal_orm-2.0.3a0 → liminal_orm-2.0.4}/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_orm-2.0.3a0 → liminal_orm-2.0.4}/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:
@@ -141,7 +144,7 @@ def convert_api_field_type_to_field_type(
         ): 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-2.0.3a0 → liminal_orm-2.0.4}/liminal/orm/column.py

@@ -73,19 +73,19 @@ 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 entity_link and type not in BenchlingFieldType.get_entity_link_types():
             raise ValueError(
-                "Entity link can only be set if the field type is ENTITY_LINK."
+                "Entity link can only be set if the field type is ENTITY_LINK or TRANSLATION_LINK."
             )
-        if parent_link and type != BenchlingFieldType.ENTITY_LINK:
+        if parent_link and type not in BenchlingFieldType.get_entity_link_types():
             raise ValueError(
-                "Parent link can only be set if the field type is ENTITY_LINK."
+                "Parent link can only be set if the field type is ENTITY_LINK or TRANSLATION_LINK."
             )
         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-2.0.3a0 → liminal_orm-2.0.4}/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[[type["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-2.0.3a0 → liminal_orm-2.0.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "liminal-orm"
-version = "2.0.3a0"
+version = "2.0.4"
 description = "An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync."
 authors = ["DynoTx Open Source <opensource@dynotx.com>"]
 readme = "README.md"

{liminal_orm-2.0.3a0 → liminal_orm-2.0.4}/liminal/entity_schemas/operations.py

@@ -162,7 +162,7 @@ class ArchiveEntitySchema(BaseOperation):
 
 
 class UnarchiveEntitySchema(BaseOperation):
-    order: ClassVar[int] = 100
+    order: ClassVar[int] = 110
 
     def __init__(self, wh_schema_name: str) -> None:
         self.wh_schema_name = wh_schema_name
@@ -187,7 +187,7 @@ class UnarchiveEntitySchema(BaseOperation):
 
 
 class UpdateEntitySchema(BaseOperation):
-    order: ClassVar[int] = 90
+    order: ClassVar[int] = 100
 
     def __init__(
         self,
@@ -251,7 +251,7 @@ class UpdateEntitySchema(BaseOperation):
 
 
 class UpdateEntitySchemaNameTemplate(BaseOperation):
-    order: ClassVar[int] = 150
+    order: ClassVar[int] = 90
 
     def __init__(
         self,
@@ -283,7 +283,7 @@ class UpdateEntitySchemaNameTemplate(BaseOperation):
 
 
 class CreateEntitySchemaField(BaseOperation):
-    order: ClassVar[int] = 110
+    order: ClassVar[int] = 120
 
     def __init__(
         self,
@@ -370,7 +370,7 @@ class CreateEntitySchemaField(BaseOperation):
 
 
 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 +421,7 @@ 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 +468,7 @@ class UnarchiveEntitySchemaField(BaseOperation):
 
 
 class UpdateEntitySchemaField(BaseOperation):
-    order: ClassVar[int] = 130
+    order: ClassVar[int] = 140
 
     def __init__(
         self,