liminal-orm 1.0.6__py3-none-any.whl → 1.1.1__py3-none-any.whl

liminal/orm/schema_properties.py

@@ -1,6 +1,8 @@
 from __future__ import annotations
 
-from pydantic import PrivateAttr, model_validator
+from typing import Any
+
+from pydantic import model_validator
 
 from liminal.base.properties.base_schema_properties import (
     BaseSchemaProperties,
@@ -22,7 +24,11 @@ class SchemaProperties(BaseSchemaProperties):
     entity_type: BenchlingEntityType
     naming_strategies: set[BenchlingNamingStrategy]
     mixture_schema_config: MixtureSchemaConfig | None = None
-    _archived: bool | None = PrivateAttr(default=None)
+    _archived: bool = False
+
+    def __init__(self, **data: Any):
+        super().__init__(**data)
+        self._archived = data.get("_archived", False)
 
     @model_validator(mode="after")
     def validate_mixture_schema_config(self) -> SchemaProperties:

liminal/tests/conftest.py

@@ -136,7 +136,8 @@ def mock_benchling_schema(
             parent_link=False,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "string_field_req": Props(
             name="String Field Required",
             type=Type.TEXT,
@@ -146,7 +147,8 @@ def mock_benchling_schema(
             dropdown_link=None,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "string_field_not_req": Props(
             name="String Field Not Required",
             type=Type.TEXT,
@@ -156,7 +158,8 @@ def mock_benchling_schema(
             dropdown_link=None,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "string_field_tooltip": Props(
             name="String Field Not Required",
             type=Type.TEXT,
@@ -166,7 +169,8 @@ def mock_benchling_schema(
             dropdown_link=None,
             entity_link=None,
             tooltip="test tooltip",
-        ).set_archived(False),
+            _archived=False,
+        ),
         "float_field": Props(
             name="Float Field",
             type=Type.DECIMAL,
@@ -176,7 +180,8 @@ def mock_benchling_schema(
             dropdown_link=None,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "integer_field": Props(
             name="Integer Field",
             type=Type.INTEGER,
@@ -186,7 +191,8 @@ def mock_benchling_schema(
             dropdown_link=None,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "datetime_field": Props(
             name="Datetime Field",
             type=Type.DATE,
@@ -196,7 +202,8 @@ def mock_benchling_schema(
             dropdown_link=None,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "list_dropdown_field": Props(
             name="List Dropdown Field",
             type=Type.DROPDOWN,
@@ -206,7 +213,26 @@ def mock_benchling_schema(
             parent_link=False,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
+        "archived_field": Props(
+            name="Archived Field",
+            type=Type.TEXT,
+            required=False,
+            is_multi=False,
+            _archived=True,
+        ),
+        "wh_name_field_different": Props(
+            name="Different Wh Name Field",
+            type=Type.TEXT,
+            required=False,
+            is_multi=False,
+            parent_link=False,
+            dropdown_link=None,
+            entity_link=None,
+            tooltip=None,
+            _archived=False,
+        ),
     }
     return [(schema_props, fields)]
 
@@ -229,32 +255,51 @@ def mock_benchling_schema_one(
             required=False,
             is_multi=False,
             dropdown_link=mock_benchling_dropdown.__benchling_name__,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "string_field_req": Props(
-            name="String Field Required", type=Type.TEXT, required=True, is_multi=False
-        ).set_archived(False),
+            name="String Field Required",
+            type=Type.TEXT,
+            required=True,
+            is_multi=False,
+            _archived=False,
+        ),
         "string_field_not_req": Props(
             name="String Field Not Required",
             type=Type.TEXT,
             required=False,
             is_multi=False,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "float_field": Props(
-            name="Float Field", type=Type.DECIMAL, required=False, is_multi=False
-        ).set_archived(False),
+            name="Float Field",
+            type=Type.DECIMAL,
+            required=False,
+            is_multi=False,
+            _archived=False,
+        ),
         "integer_field": Props(
-            name="Integer Field", type=Type.INTEGER, required=False, is_multi=False
-        ).set_archived(False),
+            name="Integer Field",
+            type=Type.INTEGER,
+            required=False,
+            is_multi=False,
+            _archived=False,
+        ),
         "datetime_field": Props(
-            name="Datetime Field", type=Type.DATE, required=False, is_multi=False
-        ).set_archived(False),
+            name="Datetime Field",
+            type=Type.DATE,
+            required=False,
+            is_multi=False,
+            _archived=False,
+        ),
         "list_dropdown_field": Props(
             name="List Dropdown Field",
             type=Type.DROPDOWN,
             required=False,
             is_multi=True,
             dropdown_link=mock_benchling_dropdown.__benchling_name__,
-        ).set_archived(False),
+            _archived=False,
+        ),
     }
     return [(schema_props, fields)]
 
@@ -267,7 +312,8 @@ def mock_benchling_schema_archived() -> list[tuple[SchemaProperties, dict[str, P
         prefix="MockEntitySmall",
         entity_type=BenchlingEntityType.CUSTOM_ENTITY,
         naming_strategies=[BenchlingNamingStrategy.NEW_IDS],
-    ).set_archived(True)
+        _archived=True,
+    )
     fields = {
         "string_field_req": Props(
             name="String Field Required",
@@ -278,14 +324,16 @@ def mock_benchling_schema_archived() -> list[tuple[SchemaProperties, dict[str, P
             tooltip=None,
             dropdown_link=None,
             entity_link=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
         "string_field_req_2": Props(
             name="String Field Required 2",
             type=Type.TEXT,
             required=True,
             parent_link=False,
             is_multi=False,
-        ).set_archived(False),
+            _archived=False,
+        ),
     }
     return [(schema_props, fields)]
 
@@ -339,6 +387,20 @@ def mock_benchling_subclass(mock_benchling_dropdown) -> list[type[BaseModel]]:
             is_multi=True,
             dropdown=mock_benchling_dropdown,
         )
+        archived_field: SqlColumn = Column(
+            name="Archived Field",
+            type=Type.TEXT,
+            required=False,
+            is_multi=False,
+            _archived=True,
+        )
+        different_wh_name_field: SqlColumn = Column(
+            name="Different Wh Name Field",
+            type=Type.TEXT,
+            required=False,
+            is_multi=False,
+            _warehouse_name="wh_name_field_different",
+        )
 
         def __init__(
             self,

liminal/tests/test_entity_schema_compare.py

@@ -46,9 +46,10 @@ class TestCompareEntitySchemas:
                 invalid_models["mock_entity_two_wh"][0].op.schema_properties.name
                 == "Mock Entity Two"
             )
-            assert list(invalid_models["mock_entity_two_wh"][0].op.fields.keys()) == [
-                "parent_link_field"
-            ]
+            assert [
+                f.warehouse_name
+                for f in invalid_models["mock_entity_two_wh"][0].op.fields
+            ] == ["parent_link_field"]
             assert isinstance(
                 invalid_models["mock_entity_two_wh"][1].op, UpdateEntitySchema
             )
@@ -152,8 +153,12 @@ class TestCompareEntitySchemas:
                 invalid_models["mock_entity"][0].op, CreateEntitySchemaField
             )
             assert (
-                invalid_models["mock_entity"][0].op.wh_field_name == "string_field_req"
+                invalid_models["mock_entity"][0].op.field_props.warehouse_name
+                == "string_field_req"
             )
+            mock_benchling_subclass[0].get_columns_dict(exclude_base_columns=True)[
+                "string_field_req"
+            ].properties.warehouse_name = None
 
             # Test when the Benchling schema has an extra field compared to the table model
             extra_field = copy.deepcopy(mock_benchling_schema)
@@ -163,7 +168,8 @@ class TestCompareEntitySchemas:
                 required=False,
                 is_multi=False,
                 dropdown_link=None,
-            ).set_archived(False)
+                _archived=False,
+            )
 
             mock_get_benchling_entity_schemas.return_value = extra_field
             invalid_models = compare_entity_schemas(mock_benchling_sdk)
@@ -324,3 +330,14 @@ class TestCompareEntitySchemas:
             assert isinstance(
                 invalid_models["mock_entity"][0].op, ReorderEntitySchemaFields
             )
+
+            # Test when the Benchling schema archived field becomes unarchived
+            benchling_rearchived_field = copy.deepcopy(mock_benchling_schema)
+            benchling_rearchived_field[0][1]["archived_field"].set_archived(False)
+            mock_get_benchling_entity_schemas.return_value = benchling_rearchived_field
+            invalid_models = compare_entity_schemas(mock_benchling_sdk)
+            assert len(invalid_models["mock_entity"]) == 1
+            assert isinstance(
+                invalid_models["mock_entity"][0].op, ArchiveEntitySchemaField
+            )
+            assert invalid_models["mock_entity"][0].op.wh_field_name == "archived_field"

liminal/utils.py

@@ -1,4 +1,6 @@
+import random
 import re
+import string
 from typing import Any
 
 import requests
@@ -7,6 +9,11 @@ from tenacity import retry, retry_if_exception_type, stop_after_attempt, wait_fi
 from liminal.connection.benchling_service import BenchlingService
 
 
+def generate_random_id(length: int = 8) -> str:
+    """Generate a random ID with only lowercase letters."""
+    return "".join(random.choices(string.ascii_lowercase, k=length))
+
+
 def pascalize(input_string: str) -> str:
     return "".join(
         re.sub(r"[\[\]{}():]", "", word).capitalize()
@@ -14,7 +21,9 @@ def pascalize(input_string: str) -> str:
     )
 
 
-def to_snake_case(input_string: str) -> str:
+def to_snake_case(input_string: str | None) -> str:
+    if input_string is None:
+        return ""
     return "_".join(
         re.sub(r"[\[\]{}():]", "", word).lower()
         for word in re.split(r"[ /_\-]", input_string)
@@ -46,9 +55,7 @@ def is_valid_prefix(prefix: str) -> bool:
     It must be contain only alphanumeric characters and underscores, be less than 33 characters, and end with an alphabetic character.
     """
     valid = (
-        all(c.isalnum() or c == "_" for c in prefix)
-        and prefix[-1].isalpha()
-        and len(prefix) <= 32
+        all(c.isalnum() or c == "_" or c == "-" for c in prefix) and len(prefix) <= 32
     )
     if not valid:
         raise ValueError(

{liminal_orm-1.0.6.dist-info → liminal_orm-1.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 1.0.6
+Version: 1.1.1
 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
@@ -10,10 +10,13 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: benchling-sdk (>=1.8.0)
 Requires-Dist: bs4 (>=0.0.2,<0.0.3)
 Requires-Dist: lxml (>=5.3.0,<6.0.0)
-Requires-Dist: pandas (>=1.5.3)
+Requires-Dist: numpy (>=1.23.5,<2.0.0)
+Requires-Dist: pandas (>=1.5.3,<2.0.0)
 Requires-Dist: psycopg2-binary (>=2.9.10,<3.0.0)
 Requires-Dist: pydantic (>=2,<=2.7)
 Requires-Dist: requests (>=2.32.3,<3.0.0)

liminal_orm-1.1.1.dist-info/RECORD

@@ -0,0 +1,61 @@
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+liminal/base/base_dropdown.py,sha256=Unk4l_5Y8rj_eSWYqzFi2BAFSQToQDWW2qdXwiCHTg8,2523
+liminal/base/base_operation.py,sha256=t16LqSPKQPkh1oJtJU1Wr8TPyflILfHqfrRa4Y8ohAM,3089
+liminal/base/base_validation_filters.py,sha256=2Q4QhqDSloZqc313p_fc8dnSw0uMhk_iMtsEtsC_5LQ,536
+liminal/base/compare_operation.py,sha256=hkpv4ewHhxy4dlTPKgJuzBjsAqO6Km7OrrKB44pRA_o,352
+liminal/base/properties/base_field_properties.py,sha256=wSEZI3YlQw2jEAOCE0yemcwYZJJhcfnBXhXZR9YAz6o,4891
+liminal/base/properties/base_schema_properties.py,sha256=IHfSEdghuLtRJvUDCl-Axgf0wgoCj71J134vVTxKWHQ,4425
+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
+liminal/cli/live_test_dropdown_migration.py,sha256=87JwxGD4A5ExjfsEEev9jgBNuldUj4CLoaFwsZ-BjEI,2889
+liminal/cli/live_test_entity_schema_migration.py,sha256=_JawaiJNHkAjIrtwe9_K15OoJSFq_4vaTK5vrmz-b6s,5576
+liminal/connection/__init__.py,sha256=3z4pSANIOkc9mh1Xp763oYQuJZDEh4lauN901PU4vqI,166
+liminal/connection/benchling_connection.py,sha256=a69pIwQX7t0wd6GnI1IwUG3VnNOb4u6vcBINs_V1o-Y,2743
+liminal/connection/benchling_service.py,sha256=lEYCHF1U8nII8Rn3rMBPTffTFiVFjoFeNmX2Kq36-qE,7170
+liminal/dropdowns/api.py,sha256=n5oxi1EhkmpmPpNi1LOI4xcIQmk1C069XFaGP5XSBx8,6959
+liminal/dropdowns/compare.py,sha256=5cz8djtaStozUun_Cp8t_5PVjq-aovme2Qq5J8FXFg4,6829
+liminal/dropdowns/generate_files.py,sha256=IqnBs-IyLsIZE0NUkdB99zd5EAF-1f9CPBeblz-GzJE,2041
+liminal/dropdowns/operations.py,sha256=RKXgwO6NQacao6dqzk6__T1B9s-B2YHLPPUyM-0wf0U,13516
+liminal/dropdowns/utils.py,sha256=1-H7bTszCUeqeRBpiYXjRjreDzhn1Fd1MFwIsrEI-o4,4109
+liminal/entity_schemas/api.py,sha256=Dkd44NGJ4JqRTJLJtPsZ8Qan2owbEYf446A6EuP8iL0,2786
+liminal/entity_schemas/compare.py,sha256=C5qr9amGCKvkV61pa29obN883vSdFzSoiebD7hKEHY4,14128
+liminal/entity_schemas/entity_schema_models.py,sha256=SNScXY3SeF0lhdAXwqKXrrgpCphpLg6s5tU9fO3juB4,5239
+liminal/entity_schemas/generate_files.py,sha256=WQUvK7VZkyVs6u1DNoscVgB9W-slGCDf6ZE62xyd3o4,8572
+liminal/entity_schemas/operations.py,sha256=8uCBTwu-CqjHhy3ImmkKiqzic010GgBynZEEEHct5OI,23017
+liminal/entity_schemas/tag_schema_models.py,sha256=rRCAvpjx7iAiIxOh9MRBrpH603zHbFxKOY7sLgOutnE,16260
+liminal/entity_schemas/utils.py,sha256=X53KNfguWtu7z-tAliBHuCYpSwTqBGgRSGsdR_BU9Vc,4206
+liminal/enums/__init__.py,sha256=jz_c-B_fifatvrYoESlHZ9ljYdz-3rNl0sBazoESiHI,523
+liminal/enums/benchling_api_field_type.py,sha256=0QamSWEMnxZtedZXlh6zNhSRogS9ZqvWskdHHN19xJo,633
+liminal/enums/benchling_entity_type.py,sha256=CXCxJzboEbABLMwxrGIoc8hC73LxoSJXHwJWfPjrjvY,435
+liminal/enums/benchling_field_type.py,sha256=uinDm5Mn_yGK1jlmlRH3NlAlXUzA1guNk8wF6lbUKD4,947
+liminal/enums/benchling_folder_item_type.py,sha256=Jb-YxCvB8O86_qTsfwtLQOkKGjTWGKHFwIKf24eemYk,248
+liminal/enums/benchling_naming_strategy.py,sha256=wG3AfnPOui5Qfc0Fihszm5uKWjuc7gdpI8jptNB5A-w,1201
+liminal/enums/benchling_report_level.py,sha256=HtnSW_yNuRpJ_iQHhzcZudb1Me4QubVg3n9sPSnJiNI,263
+liminal/enums/benchling_sequence_type.py,sha256=TBI4C5c1XKE4ZXqsz1ApDUzy2wR-04u-M3VO_zLikjM,202
+liminal/external/__init__.py,sha256=fXA-WM8eD4q8D0bhnGvRCV-eOzvppnd8d9w6xcH0iLA,991
+liminal/mappers.py,sha256=O9gc95b7JvfaR8xVrn0X1d0Tcs6Iwh-yhBHXhWSX8i0,9616
+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=06qf_7E1Hecucfczpm85rV3ATLDjpCf7y6TUfah5aLM,14450
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+liminal/orm/base_model.py,sha256=8p-JnqBJYjLe3bJxgjhTteecRsxCeonljrAfxk4reFM,10963
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+liminal/orm/mixins.py,sha256=yEeUDF1qEBLP523q8bZra4KtNVK0gwZN9mXJSNe3GEE,4802
+liminal/orm/relationship.py,sha256=Zl4bMHbtDSPx1psGHYnojGGJpA8B8hwcPJdgjB1lmW0,2490
+liminal/orm/schema_properties.py,sha256=UEIIayhiwHw7YexSGoKU9Z7gj57d7_C1CMUv51-HcGk,2158
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+liminal/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+liminal/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+liminal/tests/conftest.py,sha256=1RGiI_h8izLjT9txJ1IkRHYf8yrN_r6yjUn5SI2bxr8,17311
+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=p-9inAZM4GOm4e1cadO191LNsnqceUGGyy0YVIXXxVw,16440
+liminal/utils.py,sha256=vMjSasDnEghwqULDo14joxxJ56G4-9cBsw719nQ8C7g,2798
+liminal/validation/__init__.py,sha256=SBd48xxBMJrBzI48G2RcK056EMlevt5YjmZMkfCWN1I,6924
+liminal_orm-1.1.1.dist-info/LICENSE.md,sha256=oVA877F_D1AV44dpjsv4f-4k690uNGApX1EtzOo3T8U,11353
+liminal_orm-1.1.1.dist-info/METADATA,sha256=-GObmj3sShq8Isn7h2M-6BT-ssmbsSc3UFebxvWEkRE,11313
+liminal_orm-1.1.1.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+liminal_orm-1.1.1.dist-info/entry_points.txt,sha256=atIrU63rrzH81dWC2sjUbFLlc5FWMmYRdMxXEWexIZA,47
+liminal_orm-1.1.1.dist-info/RECORD,,

{liminal_orm-1.0.6.dist-info → liminal_orm-1.1.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.5.1
+Generator: poetry-core 1.9.1
 Root-Is-Purelib: true
 Tag: py3-none-any

liminal_orm-1.0.6.dist-info/RECORD

@@ -1,61 +0,0 @@
-liminal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-liminal/base/base_dropdown.py,sha256=Unk4l_5Y8rj_eSWYqzFi2BAFSQToQDWW2qdXwiCHTg8,2523
-liminal/base/base_operation.py,sha256=Yi0EOyLzXOFjiX4lGZW2mV_uo0lxfyRMs9-6HFVxf1w,3101
-liminal/base/base_validation_filters.py,sha256=2Q4QhqDSloZqc313p_fc8dnSw0uMhk_iMtsEtsC_5LQ,536
-liminal/base/compare_operation.py,sha256=hkpv4ewHhxy4dlTPKgJuzBjsAqO6Km7OrrKB44pRA_o,352
-liminal/base/properties/base_field_properties.py,sha256=V9UlY_geSoOhx_Iwiw2eZ7kDKghYy4Xa5bbGcCOFDk8,4511
-liminal/base/properties/base_schema_properties.py,sha256=fM4wT60yUggT32xS_F8u31bidjBWOS9Xpn0I6FlXZaQ,4335
-liminal/base/str_enum.py,sha256=jF3d-Lo8zsHUe6GsctX2L-TSj92Y3qCYDrTD-saeJoc,210
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