liminal-orm 4.5.0__tar.gz → 4.6.0__tar.gz

{liminal_orm-4.5.0 → liminal_orm-4.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: liminal-orm
-Version: 4.5.0
+Version: 4.6.0
 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-4.5.0 → liminal_orm-4.6.0}/liminal/connection/benchling_service.py

@@ -2,11 +2,12 @@ import asyncio
 import logging
 import os
 from typing import Any
+from urllib.parse import urlparse
 
-from playwright.async_api import async_playwright
+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
@@ -54,6 +55,10 @@ 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__(
@@ -62,6 +67,7 @@ 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
@@ -76,7 +82,10 @@ 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
@@ -96,28 +105,23 @@ class BenchlingService(Benchling):
         self.use_internal_api = use_internal_api
         if use_internal_api:
             try:
-                authenticated_session = asyncio.get_event_loop().run_until_complete(
-                    self.autogenerate_auth(
-                        connection.tenant_name,
-                        connection.internal_api_admin_email,
-                        connection.internal_api_admin_password,
-                        connection.playwright_data_dir,
-                    )
+                authenticated_session, csrf_token = self.autogenerate_auth(
+                    connection.tenant_name,
+                    connection.internal_api_admin_email,
+                    connection.internal_api_admin_password,
+                    connection.playwright_data_dir,
                 )
             except SSODisabledError as e:
                 raise SSODisabledError(
                     f"{e} Please provide `internal_api_admin_email` and `internal_api_admin_password` in your BenchlingConnection."
                 )
-            except RuntimeError as e:
-                raise RuntimeError(
-                    f"{e}. If you are running this in a Jupyter notebook, use `nest_asyncio.apply()` to allow the async playwright login to run."
-                )
             self.custom_post_cookies = {
                 "session": authenticated_session,
             }
             self.custom_post_headers = {
                 "Referer": f"https://{connection.tenant_name}.benchling.com/",
                 "Content-Type": "application/json",
+                "x-csrftoken": csrf_token,
             }
             LOGGER.info(
                 f"Tenant {connection.tenant_name}: Connected to Benchling internal API."
@@ -260,14 +264,14 @@ class BenchlingService(Benchling):
             )
 
     @classmethod
-    async def autogenerate_auth(
+    def autogenerate_auth(
         cls,
         benchling_tenant: str,
         email: str | None = None,
         password: str | None = None,
         playwright_data_dir: str | None = None,
-    ) -> str:
-        """Logs in to Benchling using the admin email and password or playwright and returns the session cookie.
+    ) -> tuple[str, str]:
+        """Logs in to Benchling using the admin email and password or playwright and returns the session cookie and CSRF token.
         If email and password are not passed in or if SSO is set to required on the Benchling tenant, playwright is used to log in.
         Otherwise, the admin email and password are used to log in."""
         with requests.Session() as session:
@@ -291,9 +295,16 @@ class BenchlingService(Benchling):
                         f"admin_email and admin_password not provided when sso is turned off for Benchling tenant {benchling_tenant}."
                     )
             if signin_page.status_code == 302:
-                return await cls.get_authenticated_session_sso_login_playwright(
-                    benchling_tenant, playwright_data_dir
-                )
+                try:
+                    return asyncio.get_event_loop().run_until_complete(
+                        cls.get_authenticated_session_sso_login_playwright(
+                            benchling_tenant, playwright_data_dir
+                        )
+                    )
+                except RuntimeError as e:
+                    raise RuntimeError(
+                        f"{e}. If you are running this in a Jupyter notebook, use `nest_asyncio.apply()` to allow the async playwright login to run."
+                    )
             else:
                 raise ValueError(
                     f"Unexpected response: Status code {signin_page.status_code}: {signin_page.text}"
@@ -302,8 +313,8 @@ class BenchlingService(Benchling):
     @classmethod
     async def get_authenticated_session_sso_login_playwright(
         cls, benchling_tenant: str, playwright_data_dir: str | None = None
-    ) -> str:
-        """Logs in to Benchling using playwright and returns the session cookie.
+    ) -> tuple[str, str]:
+        """Logs in to Benchling using playwright and returns the session cookie and CSRF token.
         This can be used when SSO is enabled and required on the Benchling tenant."""
         LOGGER.info(f"Log into your {benchling_tenant} Benchling tenant...")
         async with async_playwright() as playwright:
@@ -319,6 +330,15 @@ class BenchlingService(Benchling):
                 )
                 context = await browser.new_context()
             page = await context.new_page()
+
+            headers = {}
+
+            async def async_get_request_headers(request: Request) -> None:
+                if urlparse(request.url).netloc == f"{benchling_tenant}.benchling.com":
+                    headers.update(await request.all_headers())
+
+            page.on("request", async_get_request_headers)
+
             try:
                 await page.goto(f"https://{benchling_tenant}.benchling.com")
             except Exception:
@@ -340,7 +360,10 @@ class BenchlingService(Benchling):
             )
             if not session_cookie:
                 raise ValueError("No session cookie found.")
-            return session_cookie
+            csrf_token = headers.get("x-csrftoken", None)
+            if not csrf_token:
+                raise ValueError("No CSRF token found.")
+            return session_cookie, csrf_token
 
     @classmethod
     @retry(
@@ -351,8 +374,8 @@ class BenchlingService(Benchling):
     )
     def get_authenticated_session_benchling_admin_login(
         cls, benchling_tenant: str, email: str, password: str
-    ) -> str:
-        """Logs in to Benchling using the admin email and password and returns the session cookie.
+    ) -> tuple[str, str]:
+        """Logs in to Benchling using the admin email and password and returns the session cookie and CSRF token.
         This can be used when SSO is disabled or optional on the Benchling tenant."""
         with requests.Session() as session:
             homepage = session.get(f"https://{benchling_tenant}.benchling.com/signin")
@@ -384,5 +407,6 @@ class BenchlingService(Benchling):
         return (
             signin_response.headers["Set-Cookie"]
             .split("; Secure")[0]
-            .removeprefix("session=")
+            .removeprefix("session="),
+            csrf_token,
         )

liminal_orm-4.6.0/liminal/entity_schemas/api_v3.py

@@ -0,0 +1,160 @@
+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-4.6.0/liminal/entity_schemas/entity_schema_models_v3.py

@@ -0,0 +1,86 @@
+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-4.6.0/liminal/enums/benchling_api_entity_type.py

@@ -0,0 +1,18 @@
+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"

liminal_orm-4.6.0/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-4.5.0 → liminal_orm-4.6.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "liminal-orm"
-version = "4.5.0"
+version = "4.6.0"
 description = "An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync."
 authors = [{ name = "DynoTx Open Source", email = "opensource@dynotx.com" }]
 requires-python = ">=3.9,<4"

liminal_orm-4.5.0/liminal/.gitignore

@@ -1 +0,0 @@
-*

liminal_orm-4.5.0/liminal/CACHEDIR.TAG

@@ -1 +0,0 @@
-Signature: 8a477f597d28d172789f06886806bc55

liminal_orm-4.5.0/liminal/pyvenv.cfg

@@ -1,5 +0,0 @@
-home = /Users/nirmitdamania/.local/share/uv/python/cpython-3.10.8-macos-aarch64-none/bin
-implementation = CPython
-uv = 0.8.9
-version_info = 3.10.8
-include-system-site-packages = false

liminal_orm-4.5.0/liminal/share/jupyter/kernels/python3/kernel.json

@@ -1,14 +0,0 @@
-{
- "argv": [
-  "python",
-  "-m",
-  "ipykernel_launcher",
-  "-f",
-  "{connection_file}"
- ],
- "display_name": "Python 3 (ipykernel)",
- "language": "python",
- "metadata": {
-  "debugger": true
- }
-}

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liminal_orm-4.5.0/liminal/share/man/man1/ipython.1

@@ -1,60 +0,0 @@
-.\"                                      Hey, EMACS: -*- nroff -*-
-.\" First parameter, NAME, should be all caps
-.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
-.\" other parameters are allowed: see man(7), man(1)
-.TH IPYTHON 1 "July 15, 2011"
-.\" Please adjust this date whenever revising the manpage.
-.\"
-.\" Some roff macros, for reference:
-.\" .nh        disable hyphenation
-.\" .hy        enable hyphenation
-.\" .ad l      left justify
-.\" .ad b      justify to both left and right margins
-.\" .nf        disable filling
-.\" .fi        enable filling
-.\" .br        insert line break
-.\" .sp <n>    insert n+1 empty lines
-.\" for manpage-specific macros, see man(7) and groff_man(7)
-.\" .SH        section heading
-.\" .SS        secondary section heading
-.\"
-.\"
-.\" To preview this page as plain text: nroff -man ipython.1
-.\"
-.SH NAME
-ipython \- Tools for Interactive Computing in Python.
-.SH SYNOPSIS
-.B ipython
-.RI [ options ] " files" ...
-
-.B ipython subcommand
-.RI [ options ] ...
-
-.SH DESCRIPTION
-An interactive Python shell with automatic history (input and output), dynamic
-object introspection, easier configuration, command completion, access to the
-system shell, integration with numerical and scientific computing tools,
-web notebook, Qt console, and more.
-
-For more information on how to use IPython, see 'ipython \-\-help',
-or 'ipython \-\-help\-all' for all available command\(hyline options.
-
-.SH "ENVIRONMENT VARIABLES"
-.sp
-.PP
-\fIIPYTHONDIR\fR
-.RS 4
-This is the location where IPython stores all its configuration files.  The default
-is $HOME/.ipython if IPYTHONDIR is not defined.
-
-You can see the computed value of IPYTHONDIR with `ipython locate`.
-
-.SH FILES
-
-IPython uses various configuration files stored in profiles within IPYTHONDIR.
-To generate the default configuration files and start configuring IPython,
-do 'ipython profile create', and edit '*_config.py' files located in
-IPYTHONDIR/profile_default.
-
-.SH AUTHORS
-IPython is written by the IPython Development Team <https://github.com/ipython/ipython>.