From 6b983ebbc146673760a4bb742fcb6fb7d10f4d80 Mon Sep 17 00:00:00 2001
From: Keith James <kdj@sanger.ac.uk>
Date: Mon, 23 Sep 2024 12:22:36 +0100
Subject: [PATCH] Fix id parameter showing builtin "id"

Fix docstrings with single rather than triple quotes.
---
 src/npg_notify/db/mlwh.py                | 16 ++++++++--------
 src/npg_notify/porch_wrapper/qc_state.py |  2 +-
 tests/test_retrieve_contacts.py          |  4 ++--
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/npg_notify/db/mlwh.py b/src/npg_notify/db/mlwh.py
index 603c800..bc9a454 100644
--- a/src/npg_notify/db/mlwh.py
+++ b/src/npg_notify/db/mlwh.py
@@ -18,7 +18,7 @@
 # You should have received a copy of the GNU General Public License along with
 # this program. If not, see <http://www.gnu.org/licenses/>.
 
-from sqlalchemy import ForeignKey, Integer, String, UniqueConstraint, select
+from sqlalchemy import DateTime, ForeignKey, Integer, String, UniqueConstraint, select
 from sqlalchemy.exc import NoResultFound
 from sqlalchemy.orm import (
     DeclarativeBase,
@@ -46,7 +46,7 @@ class Base(DeclarativeBase):
 
 
 class Study(Base):
-    "A representation for the 'study' table."
+    """A representation for the 'study' table."""
 
     __tablename__ = "study"
 
@@ -89,7 +89,7 @@ def contacts(self) -> list[str]:
 
 
 class StudyUser(Base):
-    "A representation for the 'study_users' table."
+    """A representation for the 'study_users' table."""
 
     __tablename__ = "study_users"
 
@@ -111,18 +111,18 @@ def __repr__(self):
 
 
 class StudyNotFoundError(Exception):
-    "An error to use when a study does not exist in mlwh."
+    """An error to use when a study does not exist in mlwh."""
 
     pass
 
 
-def get_study_contacts(session: Session, id: str) -> list[str]:
+def get_study_contacts(session: Session, study_id: str) -> list[str]:
     """Retrieves emails of study contacts from the mlwh database.
 
     Args:
       session:
         sqlalchemy.orm.Session object
-      id:
+      study_id:
         String study ID.
 
     Returns:
@@ -136,13 +136,13 @@ def get_study_contacts(session: Session, id: str) -> list[str]:
     """
     try:
         contacts = (
-            session.execute(select(Study).where(Study.id_study_lims == id))
+            session.execute(select(Study).where(Study.id_study_lims == study_id))
             .scalar_one()
             .contacts()
         )
     except NoResultFound:
         raise StudyNotFoundError(
-            f"Study with ID {id} is not found in ml warehouse"
+            f"Study with ID {study_id} is not found in ml warehouse"
         )
 
     return contacts
diff --git a/src/npg_notify/porch_wrapper/qc_state.py b/src/npg_notify/porch_wrapper/qc_state.py
index 0c30869..041e4b2 100644
--- a/src/npg_notify/porch_wrapper/qc_state.py
+++ b/src/npg_notify/porch_wrapper/qc_state.py
@@ -267,7 +267,7 @@ def process_task(conf_file_path) -> bool:
         ) as session:
             for study_id in study_ids:
                 contacts_per_study[study_id] = get_study_contacts(
-                    session=session, id=study_id
+                    session=session, study_id=study_id
                 )
 
     except Exception as err:
diff --git a/tests/test_retrieve_contacts.py b/tests/test_retrieve_contacts.py
index 03067d7..42dc826 100644
--- a/tests/test_retrieve_contacts.py
+++ b/tests/test_retrieve_contacts.py
@@ -9,8 +9,8 @@ def test_retrieving_study_contacts(mlwh_test_session):
     ):
         get_study_contacts(mlwh_test_session, "666")
 
-    for id in ["2", "5", "4"]:
-        assert get_study_contacts(mlwh_test_session, id) == []
+    for study_id in ["2", "5", "4"]:
+        assert get_study_contacts(mlwh_test_session, study_id) == []
 
     users = ["owner", "user1", "user2", "user3"]
     assert get_study_contacts(mlwh_test_session, "3") == [