Pass connection to `species_by_id` function.

To make `species_by_id` function reusable even outside of the
application context, pass in the database connection instead of
creating the connection inside the function.

1 files changed, 13 insertions, 12 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index ab1c350..2282c8d 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -5,6 +5,7 @@ from typing import Union
 from functools import reduce
 from datetime import datetime
 
+import MySQLdb as mdb
 from redis import Redis
 from MySQLdb.cursors import DictCursor
 from flask import (
@@ -12,7 +13,7 @@ from flask import (
     current_app as app)
 
 from . import jobs
-from .db_utils import database_connection
+from .db_utils import with_db_connection, database_connection
 
 dbinsertbp = Blueprint("dbinsert", __name__)
 
@@ -41,17 +42,16 @@ def species() -> tuple:
 
     return tuple()
 
-def species_by_id(speciesid) -> Union[dict, None]:
+def species_by_id(conn: mdb.Connection, speciesid) -> Union[dict, None]:
     "Retrieve the species from the database by id."
-    with database_connection() as conn:
-        with conn.cursor(cursorclass=DictCursor) as cursor:
-            cursor.execute(
-                (
-                    "SELECT "
-                    "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
-                    "FROM Species WHERE SpeciesId=%s"),
-                (speciesid,))
-            return cursor.fetchone()
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            (
+                "SELECT "
+                "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
+                "FROM Species WHERE SpeciesId=%s"),
+            (speciesid,))
+        return cursor.fetchone()
 
 def genechips():
     "Retrieve the genechip information from the database"
@@ -362,7 +362,8 @@ def final_confirmation():
             filetype=form["filetype"], totallines=form["totallines"],
             species=speciesid, genechipid=genechipid, studyid=studyid,
             datasetid=datasetid, the_species=selected_keys(
-                species_by_id(speciesid), ("SpeciesName", "Name", "MenuName")),
+                with_db_connection(lambda conn: species_by_id(conn, speciesid)),
+                ("SpeciesName", "Name", "MenuName")),
             platform=selected_keys(
                 platform_by_id(genechipid),
                 ("GeneChipName", "Name", "GeoPlatform", "Title", "GO_tree_value")),