feat: default database and collection in MetadataDbClient (#152)

* feat: default database and collection for MetadataDbClient

* docs: update MetadataDbClient examples

* docs: how to override defaults

Author: helen-m-lin

docs/source/ExamplesDocDBRestApi.rst

@@ -18,13 +18,12 @@ Count Example 1: Get # of records with a certain subject_id
   from aind_data_access_api.document_db import MetadataDbClient
 
   API_GATEWAY_HOST = "api.allenneuraldynamics.org"
-  DATABASE = "metadata_index"
-  COLLECTION = "data_assets"
+  # Default database and collection names are set in the client
+  # To override the defaults, provide the database and collection
+  # parameters in the constructor
 
   docdb_api_client = MetadataDbClient(
       host=API_GATEWAY_HOST,
-      database=DATABASE,
-      collection=COLLECTION,
   )
 
   filter = {"subject.subject_id": "731015"}
@@ -136,8 +135,6 @@ It's possible to attach a custom Session to retry certain requests errors:
     from aind_data_access_api.document_db import MetadataDbClient
 
     API_GATEWAY_HOST = "api.allenneuraldynamics.org"
-    DATABASE = "metadata_index"
-    COLLECTION = "data_assets"
 
     retry = Retry(
         total=5,
@@ -151,8 +148,6 @@ It's possible to attach a custom Session to retry certain requests errors:
 
     with MetadataDbClient(
         host=API_GATEWAY_HOST,
-        database=DATABASE,
-        collection=COLLECTION,
         session=session,
     ) as docdb_api_client:
         records = docdb_api_client.retrieve_docdb_records(limit=10)

docs/source/UserGuide.rst

@@ -54,13 +54,12 @@ REST API
    from aind_data_access_api.document_db import MetadataDbClient
 
    API_GATEWAY_HOST = "api.allenneuraldynamics.org"
-   DATABASE = "metadata_index"
-   COLLECTION = "data_assets"
+   # Default database and collection names are set in the client
+   # To override the defaults, provide the database and collection
+   # parameters in the constructor
 
    docdb_api_client = MetadataDbClient(
       host=API_GATEWAY_HOST,
-      database=DATABASE,
-      collection=COLLECTION,
    )
 
    filter = {"subject.subject_id": "731015"}

src/aind_data_access_api/document_db.py

@@ -362,6 +362,36 @@ def __exit__(self, exc_type, exc_val, exc_tb):
 class MetadataDbClient(Client):
     """Class to manage reading and writing to metadata db"""
 
+    def __init__(
+        self,
+        host: str,
+        database: str = "metadata_index",
+        collection: str = "data_assets",
+        version: str = "v1",
+        boto: Optional[BotoSession] = None,
+        session: Optional[Session] = None,
+    ):
+        """
+        Instantiate a MetadataDbClient.
+
+        Parameters
+        ----------
+        host : str
+        database : str
+        collection : str
+        version : str
+        boto : Optional[BotoSession]
+        session : Optional[Session]
+        """
+        super().__init__(
+            host=host,
+            database=database,
+            collection=collection,
+            version=version,
+            boto=boto,
+            session=session,
+        )
+
     def retrieve_docdb_records(
         self,
         filter_query: Optional[dict] = None,

tests/test_document_db.py

@@ -437,8 +437,6 @@ class TestMetadataDbClient(unittest.TestCase):
 
     example_client_args = {
         "host": "example.com/",
-        "database": "metadata_db",
-        "collection": "data_assets",
     }
 
     example_record_list = [
@@ -452,6 +450,26 @@ class TestMetadataDbClient(unittest.TestCase):
         for id_num in range(0, 10)
     ]
 
+    def test_metadatadbclient_constructor(self):
+        """Tests class constructor"""
+        client = MetadataDbClient(**self.example_client_args)
+
+        self.assertEqual("example.com", client.host)
+        self.assertEqual("metadata_index", client.database)
+        self.assertEqual("data_assets", client.collection)
+        self.assertEqual("v1", client.version)
+        self.assertEqual(
+            "https://example.com/v1/metadata_index/data_assets",
+            client._base_url,
+        )
+
+        client = MetadataDbClient(**self.example_client_args, version="v2")
+        self.assertEqual("v2", client.version)
+        self.assertEqual(
+            "https://example.com/v2/metadata_index/data_assets",
+            client._base_url,
+        )
+
     @patch("aind_data_access_api.document_db.Client._find_records")
     def test_retrieve_docdb_records(
         self,