add ability to directly connect to mongo with pymongo.MongoClient

[sierra-moxon]

useful when instantiating a linkml_store.Client class with an existing mongodb connection, e.g. from an external job like Jenkins or Dagster

fixes #55

[hyperlint-ai]

PR Change Summary

Added support for directly connecting to MongoDB using existing MongoClient instances, enhancing the functionality of the linkml_store.Client class.

• Enabled direct connection to MongoDB with pymongo.MongoClient
• Updated documentation to reflect new MongoClient support
• Improved integration with external job systems like Jenkins and Dagster

Modified Files

• README.md

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[Copilot]

Pull Request Overview

This PR adds support for attaching existing pymongo.MongoClient instances directly to a Client, alongside existing connection‐string workflows.

• Introduces attach_native_connection and attach_mongodb_client methods in Client
• Updates MongoDBDatabase to accept a mongo_client and override database name
• Adds tests and documentation for direct MongoClient usage

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_api/test_mongodb_client.py	New tests for attach_mongodb_client and attach_native_connection
src/linkml_store/api/stores/mongodb/mongodb_database.py	Extended __init__ to accept mongo_client and db_name
src/linkml_store/api/client.py	Added attach_native_connection and attach_mongodb_client
docs/how-to/Use-MongoDB.ipynb	Tutorial updated with existing MongoClient examples
README.md	Added feature note about direct MongoClient support

Comments suppressed due to low confidence (4)

tests/test_api/test_mongodb_client.py:27

• [nitpick] Remove the duplicated # Setup comment on this line to avoid confusion and keep the setup section concise.

#    # Setup

docs/how-to/Use-MongoDB.ipynb:54

• Notebook cells expect source as a list of strings, not a single string. Wrap each line (including newlines) as elements in an array to conform with the IPython notebook spec.

"source": "Next we'll attach to a MongoDB instance..."

src/linkml_store/api/stores/mongodb/mongodb_database.py:51

• Indentation here is incorrect and will cause a SyntaxError. Align this if handle is None: with the other statements in the if mongo_client is not None: block (remove the extra spaces).

                if handle is None:

src/linkml_store/api/client.py:282

• The code uses importlib.import_module but importlib is not imported. Add import importlib at the top of the file.

module = importlib.import_module(module_path)