add ability to directly connect to mongo with pymongo.MongoClient

README.md

@@ -66,6 +66,7 @@ including:
 LinkML-Store is designed to work with multiple backends, giving a common abstraction layer
 
 * [MongoDB](https://linkml.io/linkml-store/how-to/Use-MongoDB.html)
+  * Supports using existing MongoClient instances directly
 * [DuckDB](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)
 * [Solr](https://linkml.io/linkml-store/how-to/Query-Solr-using-CLI.html)
 * [Neo4j](https://linkml.io/linkml-store/how-to/Use-Neo4j.html)

docs/how-to/Use-MongoDB.ipynb

@@ -51,21 +51,17 @@
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "Next we'll attach to a MongoDB instance. this assumes you have one running already."
-   ],
+   "source": "Next we'll attach to a MongoDB instance. this assumes you have one running already.\n\nYou can connect in two ways:\n1. Using a connection string\n2. Using an existing MongoClient instance\n\n### Connection using a string",
    "metadata": {
     "collapsed": false
    },
-   "id": "470f1cb70bf3641b"
+   "id": "470f1cb70bf3641b",
+   "outputs": []
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
    "outputs": [],
-   "source": [
-    "db = client.attach_database(\"mongodb://localhost:27017\", \"test\")"
-   ],
+   "source": "db = client.attach_database(\"mongodb://localhost:27017\", \"test\")",
    "metadata": {
     "collapsed": false,
     "ExecuteTime": {
@@ -100,22 +96,26 @@
    },
    "id": "cb437a6dd0f73ec8"
   },
+  {
+   "cell_type": "markdown",
+   "source": "### Connection using an existing MongoClient\n\nIf you already have a MongoClient instance (for example, from an existing application), you can use it directly without having to create a new connection:",
+   "metadata": {}
+  },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "outputs": [
-    {
-     "data": {
-      "text/plain": "'{\"handle\":\"mongodb://localhost:27017\",\"alias\":\"test\",\"schema_location\":null,\"schema_dict\":null,\"collections\":{},\"recreate_if_exists\":false,\"collection_type_slot\":null,\"searchable_slots\":null,\"ensure_referential_integrity\":false}'"
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "db.metadata.model_dump_json()"
-   ],
+   "source": "# Now let's connect using an existing MongoClient\nfrom pymongo import MongoClient\n\n# Create a MongoClient instance directly\nmongo_client = MongoClient(\"mongodb://localhost:27017/\")\n\n# Use the existing client with linkml-store\ndb2 = client.attach_mongodb_client(\n    mongo_client=mongo_client,\n    db_name=\"test2\",\n    alias=\"direct_mongo\"\n)\n\nprint(f\"DB Handle: {db2.handle}\")\nprint(f\"DB Alias: {db2.alias}\")\nprint(f\"DB Name: {db2._db_name}\")",
+   "metadata": {},
+   "outputs": []
+  },
+  {
+   "cell_type": "markdown",
+   "source": "This approach is particularly useful when:\n1. You already have a MongoClient configured in your application\n2. You need special authentication or connection settings\n3. You want to reuse an existing connection pool\n\nFor the rest of this tutorial, we'll continue using the first database (`db`), but all operations work the same on both connection types.",
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": "db.metadata.model_dump_json()",
    "metadata": {
     "collapsed": false,
     "ExecuteTime": {
@@ -594,4 +594,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}