liminal-orm 4.0.0__tar.gz → 4.1.0__tar.gz

{liminal_orm-4.0.0 → liminal_orm-4.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 4.0.0
+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-4.0.0 → liminal_orm-4.1.0}/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_orm-4.0.0 → liminal_orm-4.1.0}/liminal/connection/benchling_service.py

@@ -25,9 +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"
 
 
@@ -70,7 +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:
@@ -78,7 +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:
@@ -104,7 +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:
@@ -150,7 +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.
@@ -179,8 +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
@@ -198,20 +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,
@@ -220,14 +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_orm-4.0.0 → liminal_orm-4.1.0}/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_orm-4.0.0 → liminal_orm-4.1.0}/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_orm-4.0.0 → liminal_orm-4.1.0}/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_orm-4.0.0 → liminal_orm-4.1.0}/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-4.0.0 → liminal_orm-4.1.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "liminal-orm"
-version = "4.0.0"
+version = "4.1.0"
 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"