liminal-orm 4.5.1__tar.gz → 4.6.1__tar.gz

{liminal_orm-4.5.1 → liminal_orm-4.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: liminal-orm
-Version: 4.5.1
+Version: 4.6.1
 Summary: An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync.
 Project-URL: Homepage, https://github.com/dynotx/liminal-orm
 Project-URL: Repository, https://github.com/dynotx/liminal-orm

{liminal_orm-4.5.1 → liminal_orm-4.6.1}/liminal/connection/benchling_service.py

@@ -7,7 +7,7 @@ from urllib.parse import urlparse
 from playwright.async_api import async_playwright, Request
 import requests
 from benchling_sdk.auth.client_credentials_oauth2 import ClientCredentialsOAuth2
-from benchling_sdk.benchling import Benchling
+from benchling_sdk.benchling import Benchling, BenchlingApiClientDecorator
 from benchling_sdk.helpers.retry_helpers import RetryStrategy
 from bs4 import BeautifulSoup
 from sqlalchemy import create_engine
@@ -43,7 +43,6 @@ class SSODisabledError(ValueError):
 class BenchlingService(Benchling):
     """
     Class that creates a connection object that can be used to connect to Benchling's API, database, or internal API.
-    This inherits from LiminalBenchlingService, which takes in credentials and connects the specified services.
 
     Parameters
     ----------
@@ -55,6 +54,10 @@ class BenchlingService(Benchling):
         Whether to connect to the Benchling Postgres database. Requires warehouse_connection_string from the connection object.
     use_internal_api: bool = False
         Whether to connect to the Benchling internal API. Requires internal_api_admin_email and internal_api_admin_password from the connection object.
+    client_decorator: BenchlingApiClientDecorator | None = None
+        An optional function that receives the default BenchlingApiClient and returns a
+        customized one. Forwarded to the Benchling SDK. A common use is raising the HTTP
+        timeout, which otherwise defaults to 10 seconds: ``lambda c: c.with_timeout(60)``.
     """
 
     def __init__(
@@ -63,6 +66,7 @@ class BenchlingService(Benchling):
         use_api: bool = True,
         use_db: bool = False,
         use_internal_api: bool = False,
+        client_decorator: BenchlingApiClientDecorator | None = None,
     ) -> None:
         self.connection = connection
         self._session: Session | None = None
@@ -77,7 +81,10 @@ class BenchlingService(Benchling):
             )
             url = f"https://{connection.tenant_name}.benchling.com"
             super().__init__(
-                url=url, auth_method=auth_method, retry_strategy=retry_strategy
+                url=url,
+                auth_method=auth_method,
+                retry_strategy=retry_strategy,
+                client_decorator=client_decorator,
             )
             LOGGER.info(f"Tenant {connection.tenant_name}: Connected to Benchling API.")
         self.use_db = use_db

liminal_orm-4.6.1/liminal/tests/test_benchling_service.py

@@ -0,0 +1,34 @@
+from typing import cast
+
+from benchling_api_client.v2.benchling_client import BenchlingApiClient
+
+from liminal.connection.benchling_connection import BenchlingConnection
+from liminal.connection.benchling_service import BenchlingService
+
+# The Benchling SDK defaults the per-request HTTP timeout to 10 seconds.
+SDK_DEFAULT_TIMEOUT_SECONDS = 10
+
+
+def _connection() -> BenchlingConnection:
+    return BenchlingConnection(
+        tenant_name="test-tenant",
+        api_client_id="test-id",
+        api_client_secret="test-secret",
+    )
+
+
+class TestBenchlingServiceClientDecorator:
+    def test_default_timeout_is_sdk_default(self) -> None:
+        service = BenchlingService(_connection(), use_db=False)
+        assert service._client.get_timeout() == SDK_DEFAULT_TIMEOUT_SECONDS
+
+    def test_client_decorator_is_forwarded_to_sdk(self) -> None:
+        def raise_timeout(client: BenchlingApiClient) -> BenchlingApiClient:
+            # with_timeout is typed to return the base Client but preserves the subclass.
+            return cast(BenchlingApiClient, client.with_timeout(60))
+
+        service = BenchlingService(
+            _connection(), use_db=False, client_decorator=raise_timeout
+        )
+
+        assert service._client.get_timeout() == 60

{liminal_orm-4.5.1 → liminal_orm-4.6.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "liminal-orm"
-version = "4.5.1"
+version = "4.6.1"
 description = "An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync."
 authors = [{ name = "DynoTx Open Source", email = "opensource@dynotx.com" }]
 requires-python = ">=3.9,<4"

liminal_orm-4.5.1/liminal/entity_schemas/api_v3.py

@@ -1,160 +0,0 @@
-import json
-from typing import Any
-
-import requests
-
-from liminal.connection import BenchlingService
-from liminal.enums.benchling_api_entity_type import BenchlingAPIEntityType
-from liminal.utils import await_queued_response
-
-
-def create_entity_schema(
-    benchling_service: BenchlingService,
-    api_entity_type: BenchlingAPIEntityType,
-    payload: dict[str, Any],
-) -> dict[str, Any]:
-    """
-    Create a new entity schema.
-    """
-    response = benchling_service.api.post_response(
-        url=f"/api/v3-alpha/benchling/{api_entity_type.value}", body=payload
-    )
-    if not (200 <= response.status_code < 300):
-        raise Exception("Failed to create entity schema:", response.content)
-    return json.loads(response.content)
-
-
-def get_entity_schema(
-    benchling_service: BenchlingService,
-    api_entity_type: BenchlingAPIEntityType,
-    entity_schema_id: str,
-) -> dict[str, Any]:
-    """
-    Get an entity schema.
-    """
-    response = benchling_service.api.get_response(
-        url=f"/api/v3-alpha/benchling/{api_entity_type.value}/{entity_schema_id}"
-    )
-    if not (200 <= response.status_code < 300):
-        raise Exception("Failed to get entity schema:", response.content)
-    return json.loads(response.content)
-
-
-def list_entity_schemas(
-    benchling_service: BenchlingService,
-) -> dict[str, Any]:
-    """
-    List all entity schemas.
-    """
-    response = benchling_service.api.get_response(
-        url="/api/v3-alpha/benchling/entity-schema/items"
-    )
-    if not (200 <= response.status_code < 300):
-        raise Exception("Failed to get entity schema:", response.content)
-    return json.loads(response.content)
-
-
-def get_entity_schema_field_definitions(
-    benchling_service: BenchlingService,
-    api_entity_type: BenchlingAPIEntityType,
-    entity_schema_id: str,
-) -> dict[str, Any]:
-    """
-    Get the field definitions for an entity schema.
-    """
-    response = benchling_service.api.get_response(
-        url=f"/api/v3-alpha/benchling/{api_entity_type.value}/{entity_schema_id}/field-definitions/items"
-    )
-    if not (200 <= response.status_code < 300):
-        raise Exception("Failed to get entity schema:", response.content)
-    return json.loads(response.content)
-
-
-def get_entity_schema_fieldsets(
-    benchling_service: BenchlingService,
-    api_entity_type: BenchlingAPIEntityType,
-    entity_schema_id: str,
-) -> dict[str, Any]:
-    """
-    Get the fieldsets for an entity schema.
-    """
-    response = benchling_service.api.get_response(
-        url=f"/api/v3-alpha/benchling/{api_entity_type.value}/{entity_schema_id}/fieldsets/items"
-    )
-    if not (200 <= response.status_code < 300):
-        raise Exception("Failed to get entity schema:", response.content)
-    return json.loads(response.content)
-
-
-# def archive_tag_schemas(
-#     benchling_service: BenchlingService, entity_schema_ids: list[str]
-# ) -> dict[str, Any]:
-#     """
-#     Archive a list of entity schema ids.
-#     """
-#     with requests.Session() as session:
-#         response = session.post(
-#             f"https://{benchling_service.benchling_tenant}.benchling.com/1/api/tag-schemas:bulk-archive",
-#             data=json.dumps({"ids": entity_schema_ids, "purpose": "Made in error"}),
-#             headers=benchling_service.custom_post_headers,
-#             cookies=benchling_service.custom_post_cookies,
-#         )
-#         if not response.ok:
-#             raise Exception("Failed to archive tag schemas:", response.content)
-#         return response.json()
-
-
-# def unarchive_tag_schemas(
-#     benchling_service: BenchlingService, entity_schema_ids: list[str]
-# ) -> dict[str, Any]:
-#     """
-#     Unarchive a list of entity schema ids.
-#     """
-#     with requests.Session() as session:
-#         response = session.post(
-#             f"https://{benchling_service.benchling_tenant}.benchling.com/1/api/tag-schemas:bulk-unarchive",
-#             data=json.dumps({"ids": entity_schema_ids}),
-#             headers=benchling_service.custom_post_headers,
-#             cookies=benchling_service.custom_post_cookies,
-#         )
-#         if not response.ok:
-#             raise Exception("Failed to unarchive tag schemas:", response.content)
-#         return response.json()
-
-
-# def update_tag_schema(
-#     benchling_service: BenchlingService, entity_schema_id: str, payload: dict[str, Any]
-# ) -> dict[str, Any]:
-#     """
-#     Update the tag schema with a new field.
-#     """
-#     with requests.Session() as session:
-#         queued_response = session.post(
-#             f"https://{benchling_service.benchling_tenant}.benchling.com/1/api/tag-schemas/{entity_schema_id}/actions/update",
-#             data=json.dumps(payload),
-#             headers=benchling_service.custom_post_headers,
-#             cookies=benchling_service.custom_post_cookies,
-#         )
-#         if not queued_response.ok:
-#             raise Exception("Failed to update tag schema:", queued_response.content)
-#         return await_queued_response(
-#             queued_response.json()["status_url"], benchling_service
-#         )
-
-
-# def set_tag_schema_name_template(
-#     benchling_service: BenchlingService, entity_schema_id: str, payload: dict[str, Any]
-# ) -> dict[str, Any]:
-#     """
-#     Update the tag schema name template. Must be in a separate endpoint compared to update_tag_schema.
-#     """
-#     with requests.Session() as session:
-#         response = session.post(
-#             f"https://{benchling_service.benchling_tenant}.benchling.com/1/api/tag-schemas/{entity_schema_id}/actions/set-name-template",
-#             data=json.dumps(payload),
-#             headers=benchling_service.custom_post_headers,
-#             cookies=benchling_service.custom_post_cookies,
-#         )
-#         if not response.ok:
-#             raise Exception("Failed to set tag schema name template:", response.content)
-#         return response.json()

liminal_orm-4.5.1/liminal/entity_schemas/entity_schema_models_v3.py

@@ -1,86 +0,0 @@
-from __future__ import annotations
-
-from typing import Any
-
-from pydantic import BaseModel, ConfigDict, Field
-from liminal.connection import BenchlingService
-
-
-class EntitySchemaOrganizationRefV2(BaseModel):
-    id: str
-
-
-class EntitySchemaConstraintV2(BaseModel):
-    fieldDefinitionNames: list[str] = Field(default_factory=list)
-    hasUniqueResidues: bool | None = None
-
-
-class FieldDefinitionLinkRefV2(BaseModel):
-    id: str
-
-
-class EntitySchemaFieldDefinitionV2(BaseModel):
-    id: str
-    name: str
-    archived: bool
-    systemName: str
-    isMulti: bool | None = None
-    isRequired: bool
-    derivationType: str
-    isParent: bool | None = None
-    archiveReason: str | None = None
-    description: str | None = None
-    linkDefinition: FieldDefinitionLinkRefV2 | None = None
-    __typename: str | None = None
-
-
-class EntitySchemaModelV2(BaseModel):
-    """Pydantic model for Benchling entity schema API payloads (e.g. RnaSequenceSchema)."""
-
-    model_config = ConfigDict(extra="ignore")
-
-    id: str
-    fieldDefinitions: str
-    fields: list[EntitySchemaFieldDefinitionV2] = Field(default_factory=list)
-    systemName: str
-    itemIdPrefix: str
-    containableType: str
-    fieldsets: str
-    systemCategories: list[Any] = Field(default_factory=list)
-    organization: EntitySchemaOrganizationRefV2
-    modifiedAt: str
-    includeRegistryIdInChips: bool | None = None
-    useRegistryIdForItemDisplayLabel: bool | None = None
-    availableRegistrationNamingOptions: list[str] = Field(default_factory=list)
-    archived: bool | None = None
-    name: str
-    description: str | None = None
-    showResidues: bool | None = None
-    createdAt: str
-    constraint: EntitySchemaConstraintV2 | None = None
-    archiveReason: str | None = None
-    __typename: str | None = None
-
-    @classmethod
-    def get_one(
-        cls,
-        benchling_service: BenchlingService,
-        wh_schema_name: str,
-        schemas_data: list[dict[str, Any]] | None = None,
-    ) -> EntitySchemaModelV2:
-        if schemas_data is None:
-            schemas_data = cls.get_all_json(benchling_service)
-        schema = next(
-            (
-                schema
-                for schema in schemas_data
-                if schema["sqlIdentifier"] == wh_schema_name
-                and schema["registryId"] == benchling_service.registry_id
-            ),
-            None,
-        )
-        if schema is None:
-            raise ValueError(
-                f"Schema {wh_schema_name} not found in Benchling {benchling_service.benchling_tenant}."
-            )
-        return cls.model_validate(schema)

liminal_orm-4.5.1/liminal/enums/benchling_api_entity_type.py

@@ -1,18 +0,0 @@
-from liminal.base.str_enum import StrEnum
-
-
-class BenchlingAPIEntityType(StrEnum):
-    """This enum represents the different types a Benchling field can have on an entity schema.
-    These are ONLY USED FOR THE INTERNAL BENCHLING API."""
-
-    CUSTOM_ENTITY_SCHEMA = "custom-entity-schema"
-    AA_SEQUENCE_SCHEMA = "aa-sequence-schema"
-    DNA_OLIGO_SCHEMA = "dna-oligo-schema"
-    DNA_SEQUENCE_SCHEMA = "dna-sequence-schema"
-    OLIGO_CONJUGATE_SCHEMA = "oligo-conjugate-schema"
-    OLIGO_DUPLEX_SCHEMA = "oligo-duplex-schema"
-    RNA_OLIGO_SCHEMA = "rna-oligo-schema"
-    RNA_SEQUENCE_SCHEMA = "rna-sequence-schema"
-    MIXTURE_SCHEMA = "mixture-schema"
-    MOLECULE_SCHEMA = "molecule-schema"
-    EQUIPMENT_SCHEMA = "equipment-schema"