liminal-orm 1.0.5__py3-none-any.whl → 1.1.0__py3-none-any.whl

liminal/orm/mixins.py

@@ -87,3 +87,12 @@ class MixtureMixin:
     project_id = SqlColumn("project_id$", String, nullable=True)
     type = SqlColumn("type$", String, nullable=True)
     validation_status = SqlColumn("validation_status$", String, nullable=True)
+
+
+class MoleculeMixin:
+    canonical_smiles = SqlColumn("canonical_smiles$", String, nullable=True)
+    file_registry_id = SqlColumn("file_registry_id$", String, nullable=True)
+    is_registered = SqlColumn("is_registered$", Boolean, nullable=True)
+    project_id = SqlColumn("project_id$", String, nullable=True)
+    type = SqlColumn("type$", String, nullable=True)
+    validation_status = SqlColumn("validation_status$", String, nullable=True)

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 +213,8 @@ def mock_benchling_schema(
             parent_link=False,
             entity_link=None,
             tooltip=None,
-        ).set_archived(False),
+            _archived=False,
+        ),
     }
     return [(schema_props, fields)]
 
@@ -229,32 +237,51 @@ 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 +294,8 @@ 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 +306,16 @@ 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)]
 

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)

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-1.0.5.dist-info → liminal_orm-1.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 1.0.5
+Version: 1.1.0
 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
@@ -13,7 +13,9 @@ Classifier: Programming Language :: Python :: 3.11
 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)
 Requires-Dist: rich (>=13.9.2,<14.0.0)
@@ -27,7 +29,12 @@ Description-Content-Type: text/markdown
 
 # [Liminal ORM](#liminal-orm)
 
-Liminal ORM<sup>1</sup> is an open-source Python package that builds on [Benchling's](https://www.benchling.com/) LIMS<sup>2</sup> platform and provides a simple, code-first approach for synchronizing and managing your Benchling schemas. Check out the [**full documentation here**](https://dynotx.github.io/liminal-orm/)!
+[![PyPI version](https://img.shields.io/pypi/v/liminal-orm.svg)](https://pypi.org/project/liminal-orm/)
+[![License](https://img.shields.io/github/license/dynotx/liminal-orm)](https://github.com/dynotx/liminal-orm/blob/main/LICENSE.md)
+[![CI](https://github.com/dynotx/liminal-orm/actions/workflows/liminal.yml/badge.svg)](https://github.com/dynotx/liminal-orm/actions/workflows/liminal.yml)
+[![Downloads](https://static.pepy.tech/personalized-badge/liminal-orm?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Downloads)](https://pepy.tech/project/liminal-orm)
+
+Liminal ORM<sup>1</sup> is an open-source Python package that builds on [Benchling's](https://www.benchling.com/) LIMS<sup>2</sup> platform and provides a simple, code-first approach for synchronizing and managing your Benchling schemas. Check out the [**full documentation here**](https://dynotx.github.io/liminal-orm/) and join our [**Slack community here**](https://join.slack.com/t/liminalorm/shared_invite/zt-2ujrp07s3-bctook4e~cAjn1LgOLVY~Q)!
 
 Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalchemy/sqlalchemy) along with a schema migration service inspired by [Alembic](https://alembic.sqlalchemy.org/en/latest/). This allows you to define your Benchling schemas in code and create a *single source of truth* that synchronizes between your upstream Benchling tenant(s) and downstream dependencies. By creating a standard interface and through using one-line CLI<sup>3</sup> commands, Liminal enables a code-first approach for managing Benchling tenants and accessing Benchling data. With the schemas defined in code, you can also take advantage of the additional capabilities that the Liminal toolkit provides. This includes:
 
@@ -38,10 +45,10 @@ Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalche
 - CI/CD integration with GitHub Actions to ensure that your Benchling schemas and code are always in sync.
 - And more based on community contributions/feedback :)
 
-Benchling is an industry standard cloud platform for life sciences R&D. Liminal builds on top of Benchling's platform and assumes that you already have a Benchling tenant set up and have (or have access to) an admin user account. If not, learn more about getting started with Benchling [here](https://www.benchling.com/explore-benchling)!
-
 If you are a Benchling user, try out Liminal by following the [**Quick Start Guide**](https://dynotx.github.io/liminal-orm/getting-started/prerequisites/)! Reach out in the [Discussions](https://github.com/dynotx/liminal-orm/discussions) forum with any questions or to simply introduce yourself! If there is something blocking you from using Liminal or you're having trouble setting Liminal up, please share in [Issues](https://github.com/dynotx/liminal-orm/issues) or reach out directly (contact information below). You can expect responses within 48 hours :)
 
+Benchling is an industry standard cloud platform for life sciences R&D. Liminal builds on top of Benchling's platform and assumes that you already have a Benchling tenant set up and have (or have access to) an admin user account. If not, learn more about getting started with Benchling [here](https://www.benchling.com/explore-benchling)!
+
 Nirmit Damania is the creator and current maintainer of Liminal (I post Liminal updates to [Discussions](https://github.com/dynotx/liminal-orm/discussions) and my [LinkedIn](https://www.linkedin.com/in/nirmit-damania/)). Most importantly, **you** have the ability to influence the future of Liminal! Any feedback, positive or negative, is highly encouraged and will be used to steer the direction of Liminal. Refer to the [Contributing guide](https://github.com/dynotx/liminal-orm/blob/main/CONTRIBUTING.md) to learn more about how you can contribute to Liminal.
 
 ⭐️ Leave a star on the repo to spread the word!

liminal_orm-1.1.0.dist-info/RECORD

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