liminal-orm 4.0.1__py3-none-any.whl → 4.1.0__py3-none-any.whl

liminal/cli/cli.py

@@ -141,7 +141,7 @@ def generate_files(
 
 @app.command(
     name="current",
-    help="Returns the remote revision_id that your Benchling tenant is currently on. Reads this from the name on the '_liminal_remote' schema.",
+    help="Returns the remote revision_id that your Benchling tenant is currently on. Reads this from the name on the 'liminal_remote' schema.",
 )
 def current(
     benchling_tenant: str = typer.Argument(
@@ -156,7 +156,7 @@ def current(
         remote_revision_id = benchling_service.get_remote_revision_id()
         if current_revision_id is not None:
             warnings.warn(
-                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the '_liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
+                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the 'liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
                 FutureWarning,
             )
         current_revision_id = remote_revision_id
@@ -200,7 +200,7 @@ def revision(
         remote_revision_id = benchling_service.get_remote_revision_id()
         if current_revision_id is not None:
             warnings.warn(
-                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the '_liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
+                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the 'liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
                 FutureWarning,
             )
         current_revision_id = remote_revision_id
@@ -256,7 +256,7 @@ def upgrade(
         remote_revision_id = benchling_service.get_remote_revision_id()
         if current_revision_id is not None:
             warnings.warn(
-                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the '_liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
+                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the 'liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
                 FutureWarning,
             )
         current_revision_id = remote_revision_id
@@ -272,7 +272,7 @@ def upgrade(
             f"[dim red]Set local {benchling_tenant}_CURRENT_REVISION_ID to {upgrade_revision_id} in liminal/env.py"
         )
     print(
-        f"[dim]Set revision_id to {upgrade_revision_id} withinn '_liminal_remote' schema."
+        f"[dim]Set revision_id to {upgrade_revision_id} within 'liminal_remote' schema."
     )
     print("[bold green]Migration complete")
 
@@ -300,7 +300,7 @@ def downgrade(
         remote_revision_id = benchling_service.get_remote_revision_id()
         if current_revision_id is not None:
             warnings.warn(
-                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the '_liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
+                f"Accessing and using the revision_id variable in {LIMINAL_DIR_PATH/'env.py'} is deprecated. Delete the variable set in the env.py file, the revision_id is now stored in your Benchling tenant within the 'liminal_remote' schema. Support for reading/writing the local revision_id will end with the v5 release.",
                 FutureWarning,
             )
         current_revision_id = remote_revision_id
@@ -316,7 +316,7 @@ def downgrade(
             f"[dim red]Set local {benchling_tenant}_CURRENT_REVISION_ID to {downgrade_revision_id} in liminal/env.py"
         )
     print(
-        f"[dim]Set revision_id to {downgrade_revision_id} withinn '_liminal_remote' schema."
+        f"[dim]Set revision_id to {downgrade_revision_id} within 'liminal_remote' schema."
     )
     print("[bold green]Migration complete")
 

liminal/connection/benchling_service.py

@@ -25,10 +25,10 @@ from liminal.enums import (
     BenchlingNamingStrategy,
 )
 
-logger = logging.getLogger(__name__)
+LOGGER = logging.getLogger(__name__)
 logging.getLogger("httpx").setLevel(logging.WARNING)
 
-REMOTE_LIMINAL_SCHEMA_NAME = "_liminal_remote"
+REMOTE_LIMINAL_SCHEMA_NAME = "liminal_remote"
 REMOTE_REVISION_ID_FIELD_WH_NAME = "revision_id"
 
 
@@ -71,7 +71,7 @@ class BenchlingService(Benchling):
             super().__init__(
                 url=url, auth_method=auth_method, retry_strategy=retry_strategy
             )
-            logger.info(f"Tenant {connection.tenant_name}: Connected to Benchling API.")
+            LOGGER.info(f"Tenant {connection.tenant_name}: Connected to Benchling API.")
         self.use_db = use_db
         if use_db:
             if connection.warehouse_connection_string:
@@ -79,7 +79,7 @@ class BenchlingService(Benchling):
                     connection.warehouse_connection_string
                 )
                 configure_mappers()
-                logger.info(
+                LOGGER.info(
                     f"Tenant {connection.tenant_name}: Connected to Benchling read-only Postgres warehouse."
                 )
             else:
@@ -105,7 +105,7 @@ class BenchlingService(Benchling):
                     "Referer": f"https://{connection.tenant_name}.benchling.com/",
                     "Content-Type": "application/json",
                 }
-                logger.info(
+                LOGGER.info(
                     f"Tenant {connection.tenant_name}: Connected to Benchling internal API."
                 )
             else:
@@ -151,7 +151,7 @@ class BenchlingService(Benchling):
 
     def get_remote_revision_id(self) -> str:
         """
-        Uses internal API to to search for the _liminal_remote schema, where the revision_id is stored.
+        Uses internal API to to search for the liminal_remote schema, where the revision_id is stored.
         This schema contains the remote revision_id in the name of the revision_id field.
 
         Returns the remote revision_id stored on the entity.
@@ -180,8 +180,8 @@ class BenchlingService(Benchling):
 
     def upsert_remote_revision_id(self, revision_id: str) -> None:
         """Updates or inserts a remote Liminal schema into your tenant with the given revision_id stored in the name of a field.
-        If the '_liminal_remote' schema is found, check and make sure a field with warehouse_name 'revision_id' is present. If both are present, update the revision_id stored within the name.
-        If no schema is found, create the _liminal_remote entity schema.
+        If the 'liminal_remote' schema is found, check and make sure a field with warehouse_name 'revision_id' is present. If both are present, update the revision_id stored within the name.
+        If no schema is found, create the liminal_remote entity schema.
         Upsert is needed to migrate users from using the CURRENT_REVISION_ID stored in the env.py file smoothly to storing in Benchling itself.
 
         Parameters
@@ -199,20 +199,20 @@ class BenchlingService(Benchling):
         try:
             liminal_schema = TagSchemaModel.get_one(self, REMOTE_LIMINAL_SCHEMA_NAME)
         except Exception:
-            # No _liminal_remote schema found. Create schema.
+            # No liminal_remote schema found. Create schema.
             from liminal.entity_schemas.operations import CreateEntitySchema
 
             CreateEntitySchema(
                 schema_properties=BaseSchemaProperties(
-                    name={REMOTE_LIMINAL_SCHEMA_NAME},
-                    warehouse_name={REMOTE_LIMINAL_SCHEMA_NAME},
-                    prefix={REMOTE_LIMINAL_SCHEMA_NAME},
+                    name=REMOTE_LIMINAL_SCHEMA_NAME,
+                    warehouse_name=REMOTE_LIMINAL_SCHEMA_NAME,
+                    prefix=REMOTE_LIMINAL_SCHEMA_NAME,
                     entity_type=BenchlingEntityType.CUSTOM_ENTITY,
                     naming_strategies={BenchlingNamingStrategy.NEW_IDS},
                 ),
                 fields=[
                     BaseFieldProperties(
-                        name={revision_id},
+                        name=revision_id,
                         warehouse_name=REMOTE_REVISION_ID_FIELD_WH_NAME,
                         type=BenchlingFieldType.TEXT,
                         parent_link=False,
@@ -221,14 +221,18 @@ class BenchlingService(Benchling):
                     )
                 ],
             ).execute(self)
-        # _liminal_remote schema found. Check if revision_id field exists on it.
+            LOGGER.warning(
+                f"Created {REMOTE_LIMINAL_SCHEMA_NAME} schema for tracking the remote revision id. Please delete the revision_id variable tracked in your env.py to complete the migration to tracking the tenant revision_id in Benchling instead of locally."
+            )
+            return
+        # liminal_remote schema found. Check if revision_id field exists on it.
         revision_id_fields = [
             f
             for f in liminal_schema.fields
             if f.systemName == REMOTE_REVISION_ID_FIELD_WH_NAME
         ]
         if len(revision_id_fields) == 1:
-            # _liminal_remote schema found, revision_id field found. Update revision_id field on it with given revision_id.
+            # liminal_remote schema found, revision_id field found. Update revision_id field on it with given revision_id.
             from liminal.entity_schemas.operations import UpdateEntitySchemaField
 
             revision_id_field = revision_id_fields[0]

liminal/entity_schemas/utils.py

@@ -33,7 +33,7 @@ def get_converted_tag_schemas(
         if include_archived
         else [s for s in all_schemas if not s.archiveRecord]
     )
-    all_schemas = [s for s in all_schemas if s.sqlIdentifier != "_liminal_remote"]
+    all_schemas = [s for s in all_schemas if s.sqlIdentifier != "liminal_remote"]
     return [
         convert_tag_schema_to_internal_schema(
             tag_schema, dropdowns_map, unit_id_to_name_map, include_archived

liminal/enums/benchling_api_field_type.py

@@ -18,3 +18,5 @@ class BenchlingAPIFieldType(StrEnum):
     SELECTOR = "ft_selector"
     STORABLE_LINK = "ft_storable_link"
     STRING = "ft_string"
+    JSON = "ft_json"
+    BOOLEAN = "ft_boolean"

liminal/enums/benchling_field_type.py

@@ -21,6 +21,8 @@ class BenchlingFieldType(StrEnum):
     MIXTURE_LINK = "mixture_link"
     STORAGE_LINK = "storage_link"
     TEXT = "text"
+    JSON = "json"
+    BOOLEAN = "boolean"
 
     @classmethod
     def get_non_multi_select_types(cls) -> list[str]:

liminal/mappers.py

@@ -1,7 +1,7 @@
 from datetime import datetime
 from typing import Any
 
-from sqlalchemy import JSON, DateTime, Float, Integer, String
+from sqlalchemy import JSON, DateTime, Float, Integer, String, Boolean
 from sqlalchemy.sql.type_api import TypeEngine
 
 from liminal.enums import (
@@ -32,6 +32,8 @@ def convert_benchling_type_to_python_type(benchling_type: BenchlingFieldType) ->
         BenchlingFieldType.STORAGE_LINK: str,
         BenchlingFieldType.PART_LINK: str,
         BenchlingFieldType.TEXT: str,
+        BenchlingFieldType.JSON: dict[str, Any],
+        BenchlingFieldType.BOOLEAN: bool,
     }
     if benchling_type in benchling_to_python_type_map:
         return benchling_to_python_type_map[benchling_type]
@@ -60,6 +62,8 @@ def convert_benchling_type_to_sql_alchemy_type(
         BenchlingFieldType.PART_LINK: String,
         BenchlingFieldType.MIXTURE_LINK: String,
         BenchlingFieldType.TEXT: String,
+        BenchlingFieldType.JSON: JSON,
+        BenchlingFieldType.BOOLEAN: Boolean,
     }
     if benchling_type in benchling_to_sql_alchemy_type_map:
         return benchling_to_sql_alchemy_type_map[benchling_type]
@@ -103,6 +107,8 @@ def convert_field_type_to_api_field_type(
         BenchlingFieldType.DROPDOWN: (BenchlingAPIFieldType.SELECTOR, None),
         BenchlingFieldType.STORAGE_LINK: (BenchlingAPIFieldType.STORABLE_LINK, None),
         BenchlingFieldType.TEXT: (BenchlingAPIFieldType.STRING, None),
+        BenchlingFieldType.JSON: (BenchlingAPIFieldType.JSON, None),
+        BenchlingFieldType.BOOLEAN: (BenchlingAPIFieldType.BOOLEAN, None),
     }
     if field_type in conversion_map:
         return conversion_map[field_type]
@@ -147,6 +153,8 @@ def convert_api_field_type_to_field_type(
         (BenchlingAPIFieldType.SELECTOR, None): BenchlingFieldType.DROPDOWN,
         (BenchlingAPIFieldType.STORABLE_LINK, None): BenchlingFieldType.STORAGE_LINK,
         (BenchlingAPIFieldType.STRING, None): BenchlingFieldType.TEXT,
+        (BenchlingAPIFieldType.JSON, None): BenchlingFieldType.JSON,
+        (BenchlingAPIFieldType.BOOLEAN, None): BenchlingFieldType.BOOLEAN,
     }
     if (field_type, folder_item_type) in conversion_map:
         return conversion_map[(field_type, folder_item_type)]

{liminal_orm-4.0.1.dist-info → liminal_orm-4.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 4.0.1
+Version: 4.1.0
 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-4.0.1.dist-info → liminal_orm-4.1.0.dist-info}/RECORD

@@ -9,14 +9,14 @@ liminal/base/properties/base_field_properties.py,sha256=2I3L8mhoxOD1nzEAzwWJzUFe
 liminal/base/properties/base_name_template.py,sha256=AOtaW4QEDRC-mjZOZk6jgc_mopUMsHS2Fj6VVsO07WY,3150
 liminal/base/properties/base_schema_properties.py,sha256=jm7dG218gzHITOPdnILY4BUnOCW-KA8yiQjgz5FgQUI,5906
 liminal/base/str_enum.py,sha256=jF3d-Lo8zsHUe6GsctX2L-TSj92Y3qCYDrTD-saeJoc,210
-liminal/cli/cli.py,sha256=dqEnoIzz72YwzNiLacD7g_uE8nUtjkhksapODXQJvfo,14587
+liminal/cli/cli.py,sha256=mh86uHRL7pidrtxHVzxgdcvRCVZjPYumLbkDc_aJXYM,14578
 liminal/cli/controller.py,sha256=2eRP-SDapjDsTYaipxhQyXwBYKtoJcbKNbd4rZCQNlk,11501
 liminal/cli/live_test_dropdown_migration.py,sha256=XLeFZaR4acLOQ6LmTMWjZHIIUnB6ysZMUu6kaSRcQiA,2913
 liminal/cli/live_test_entity_schema_migration.py,sha256=_JawaiJNHkAjIrtwe9_K15OoJSFq_4vaTK5vrmz-b6s,5576
 liminal/cli/utils.py,sha256=zaUkNW0P3ZU2qgtSbIwW6pE7DSlrrijv8NG7v21_5xw,4588
 liminal/connection/__init__.py,sha256=60SyUzDxiTv9wn7cNyoqB4b9BuI3E6susqanYGvLnG8,212
 liminal/connection/benchling_connection.py,sha256=PLiaI4v9EcJDNBEO5ZF3jERuI6AYo8NAYpqPYLxVYdQ,3237
-liminal/connection/benchling_service.py,sha256=1SWieCH5mTlNgx0C_XG75lhVJBfvoDlN4-4-yAdTbSw,12123
+liminal/connection/benchling_service.py,sha256=gpZLGd7SwqyddWHLSoAd6PBxGqjdfQKYWhtVdpFnMeU,12425
 liminal/dropdowns/api.py,sha256=n5oxi1EhkmpmPpNi1LOI4xcIQmk1C069XFaGP5XSBx8,6959
 liminal/dropdowns/compare.py,sha256=-UbCkeTKx3THwvjMTUubyYVXBkhmvyhEKzwrIzBkthY,7141
 liminal/dropdowns/generate_files.py,sha256=zErD1jbbQxc5MpCPhgMnlXapyZ90S_0epE7FZD-sx4s,2519
@@ -28,18 +28,18 @@ liminal/entity_schemas/entity_schema_models.py,sha256=v5A1ELaiuBnUSl1HkUNAeMuIRQ
 liminal/entity_schemas/generate_files.py,sha256=j8JcGzbERCFdL85Xd5ljeH1O7S7l2ffsRxMwoaobzM4,10548
 liminal/entity_schemas/operations.py,sha256=mIMPvr9-eFaM603eOGn4PHfl7RblDpOzRtktBwqd5vQ,27189
 liminal/entity_schemas/tag_schema_models.py,sha256=HCtiJPMsPksX3wOBpfDdyIElNH3XybM7w25OUpIYoWM,24242
-liminal/entity_schemas/utils.py,sha256=ngWqBq9RKVjHAODok85yeuReHXaqmrexHiSmyVx30Vg,6244
+liminal/entity_schemas/utils.py,sha256=voy5_dTvjdLO6K3c5ACr3ayUEL3BsUbZImIgLfIk9fs,6243
 liminal/enums/__init__.py,sha256=-szuqAwMED4ai0NaPVUfgihQJAJ27wPu_nDnj4cEgTk,518
-liminal/enums/benchling_api_field_type.py,sha256=0QamSWEMnxZtedZXlh6zNhSRogS9ZqvWskdHHN19xJo,633
+liminal/enums/benchling_api_field_type.py,sha256=jwp6txwPo_n1AU8oyl7vR7LnakVpxPPicGS1krwsvVE,681
 liminal/enums/benchling_entity_type.py,sha256=H_6ZlHJsiVNMpezPBrNKo2eP0pDrt--HU-P7PgznaMA,846
-liminal/enums/benchling_field_type.py,sha256=kKbLR6_gTP3qI-bNOWDO3csfOXI50Y6p6buQH7cQqUg,1194
+liminal/enums/benchling_field_type.py,sha256=mPRMAucNpR4dE75Dh9S-6GobiU9SifO0XK6DSzQrx1w,1236
 liminal/enums/benchling_folder_item_type.py,sha256=Jb-YxCvB8O86_qTsfwtLQOkKGjTWGKHFwIKf24eemYk,248
 liminal/enums/benchling_naming_strategy.py,sha256=jmaR-Vfj3MWhna8tANBNjAgYUyoQ5wMbz1AIy2bv6Zk,1258
 liminal/enums/benchling_sequence_type.py,sha256=TBI4C5c1XKE4ZXqsz1ApDUzy2wR-04u-M3VO_zLikjM,202
 liminal/enums/name_template_part_type.py,sha256=Z3Zv5PpzoUrIj_EvwPVgDDkY2G0kO-wE3-ZvEvnv86M,507
 liminal/enums/sequence_constraint.py,sha256=CT3msm8qzJpcivfbQZ3NOWNRsedH4mSlfhzvQBLrHWA,407
 liminal/external/__init__.py,sha256=EundQBe68_ZIhcsuSOhc-CznzYauNDYlNG1CjRDui_Y,1348
-liminal/mappers.py,sha256=TgPMQsLrESAI6D7KBl0UoBBpnxYgcgGOT7a2faWsuhY,9587
+liminal/mappers.py,sha256=UYj8xqse1wXXkGedaqnGo6hkbOT9lntbQmju105MfaM,10059
 liminal/migrate/components.py,sha256=bzt-5eJbhWVNs_zk9WieKmTkGgQrn58sm9GOuHUlM3Q,3526
 liminal/migrate/revision.py,sha256=KppU0u-d0JsfPsXsmncxy9Q_XBJyf-o4e16wNZAJODM,7774
 liminal/migrate/revisions_timeline.py,sha256=FSKzjUnZwnD3v2o7qoilBUkmKmJVvLVqozo25WnTo-w,14456
@@ -70,8 +70,8 @@ liminal/unit_dictionary/utils.py,sha256=o3K06Yyt33iIUSMHPT8f1vSuUSgWjZLf51p78lx4
 liminal/utils.py,sha256=Eu_o5qfx1Thy26UaDOL-QnrB67FeJf3kOrTavGNRSo0,3248
 liminal/validation/__init__.py,sha256=NsjzmivSRwGki1k9ykJgjtcYNcILR_PHSf6RkI1w2n0,5290
 liminal/validation/validation_severity.py,sha256=ib03PTZCQHcbBDc01v4gJF53YtA-ANY6QSFnhTV-FbU,259
-liminal_orm-4.0.1.dist-info/LICENSE.md,sha256=oVA877F_D1AV44dpjsv4f-4k690uNGApX1EtzOo3T8U,11353
-liminal_orm-4.0.1.dist-info/METADATA,sha256=kC2TXuXpSa0_WrnCid8_TAdiiV_ZxJgJaF3K3iTPk4Y,10989
-liminal_orm-4.0.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-liminal_orm-4.0.1.dist-info/entry_points.txt,sha256=atIrU63rrzH81dWC2sjUbFLlc5FWMmYRdMxXEWexIZA,47
-liminal_orm-4.0.1.dist-info/RECORD,,
+liminal_orm-4.1.0.dist-info/LICENSE.md,sha256=oVA877F_D1AV44dpjsv4f-4k690uNGApX1EtzOo3T8U,11353
+liminal_orm-4.1.0.dist-info/METADATA,sha256=py9yzLxXw5qJLAT3U_YW5zlsfuF2H5ceDnaNTLyk9Kc,10989
+liminal_orm-4.1.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+liminal_orm-4.1.0.dist-info/entry_points.txt,sha256=atIrU63rrzH81dWC2sjUbFLlc5FWMmYRdMxXEWexIZA,47
+liminal_orm-4.1.0.dist-info/RECORD,,