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Merged
merged 3 commits into from
Jun 24, 2025
Merged

feat: default database and collection in MetadataDbClient #152

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92ca51e
feat: default database and collection for MetadataDbClient
helen-m-lin Jun 24, 2025
daa9604
docs: update MetadataDbClient examples
helen-m-lin Jun 24, 2025
b3691a3
docs: how to override defaults
helen-m-lin Jun 24, 2025
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13 changes: 5 additions & 8 deletions docs/source/ExamplesDocDBRestApi.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,14 @@ 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
# DATABASE = "metadata_index"
# COLLECTION = "data_assets"

docdb_api_client = MetadataDbClient(
host=API_GATEWAY_HOST,
database=DATABASE,
collection=COLLECTION,
# database=DATABASE,
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It might be better to remove these comments and just make a note above on how to override the fields if needed.

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Updated

# collection=COLLECTION,
)

filter = {"subject.subject_id": "731015"}
Expand Down Expand Up @@ -136,8 +137,6 @@ 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,
Expand All @@ -151,8 +150,6 @@ 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)
Expand Down
9 changes: 5 additions & 4 deletions docs/source/UserGuide.rst
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Expand Up @@ -54,13 +54,14 @@ 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
# DATABASE = "metadata_index"
# COLLECTION = "data_assets"

docdb_api_client = MetadataDbClient(
host=API_GATEWAY_HOST,
database=DATABASE,
collection=COLLECTION,
# database=DATABASE,
# collection=COLLECTION,
)

filter = {"subject.subject_id": "731015"}
Expand Down
30 changes: 30 additions & 0 deletions src/aind_data_access_api/document_db.py
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Expand Up @@ -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,
Expand Down
22 changes: 20 additions & 2 deletions tests/test_document_db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -437,8 +437,6 @@ class TestMetadataDbClient(unittest.TestCase):

example_client_args = {
"host": "example.com/",
"database": "metadata_db",
"collection": "data_assets",
}

example_record_list = [
Expand All @@ -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,
Expand Down