cx_Oracle -> oracledb

UCLOrengoGroup · Jan 24, 2024 · a7717e1 · a7717e1
1 parent 235ebef
commit a7717e1
Show file tree

Hide file tree

Showing 4 changed files with 9 additions and 11 deletions.
diff --git a/cath_alphaflow/db_utils.py b/cath_alphaflow/db_utils.py
@@ -1,5 +1,5 @@
 import logging
-import cx_Oracle
+import oracledb as Oracle
 
 from cath_alphaflow.settings import get_default_settings
 from cath_alphaflow.predicted_domain_provider import OraclePredictedCathDomainProvider
@@ -15,7 +15,7 @@
 DEFAULT_PASSWORD = config.ORACLE_DB_PASSWORD
 
 
-class OraDB(OraclePredictedCathDomainProvider, cx_Oracle.Connection):
+class OraDB(OraclePredictedCathDomainProvider, Oracle.Connection):
     def __init__(
         self,
         host=DEFAULT_HOST,
@@ -24,8 +24,8 @@ def __init__(
         user=DEFAULT_USER,
         password=DEFAULT_PASSWORD,
     ):
-        self._dsn = cx_Oracle.makedsn(host, port, sid=sid)
-        self._conn = cx_Oracle.connect(user=user, password=password, dsn=self._dsn)
+        self._dsn = Oracle.makedsn(host, port, sid=sid)
+        self._conn = Oracle.connect(user=user, password=password, dsn=self._dsn)
 
     @property
     def conn(self):

diff --git a/setup.py b/setup.py
@@ -34,7 +34,7 @@ def get_long_description():
     install_requires=[
         "click",
         "google-cloud-storage",
-        "cx_oracle",
+        "oracledb",
         "prettyconf",
         "biopython",
         "pdb-tools",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,7 +1,7 @@
 from cath_alphaflow import settings
 import logging
 import pytest
-import cx_Oracle
+import oracledb as Oracle
 
 from click.testing import CliRunner
 
@@ -97,7 +97,7 @@ def mock_connection(monkeypatch):
     def mock_connect(*args, **kwargs):
         return MockConnect()
 
-    monkeypatch.setattr(cx_Oracle, "connect", mock_connect)
+    monkeypatch.setattr(Oracle, "connect", mock_connect)
 
 
 @pytest.fixture

diff --git a/tests/test_db_utils.py b/tests/test_db_utils.py
@@ -1,7 +1,7 @@
 from unittest import mock
 import logging
 
-import cx_Oracle
+import oracledb
 
 from cath_alphaflow.db_utils import OraDB
 from cath_alphaflow.settings import get_default_settings
@@ -17,9 +17,8 @@ def test_mock_query(create_mock_query):
     assert rows == expected_rows
 
 
-@mock.patch.object(cx_Oracle, "connect")
+@mock.patch.object(oracledb, "connect")
 def test_mock_connection(mock_connect, mock_settings):
-
     settings = get_default_settings()
 
     OraDB()
@@ -37,7 +36,6 @@ def test_mock_connection(mock_connect, mock_settings):
 
 
 def test_yieldall(create_mock_query):
-
     mock_rows = [
         {"cath_code": "1", "description": "Mainly Alpha"},
         {"cath_code": "2", "description": "Mainly Beta"},