From 91be84efe80891187a6cbb08bd0b5061ffb2613d Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 7 Aug 2024 12:03:23 -0500
Subject: Make passing SQL_URI to `database_connection` mandatory.

---
 uploader/db_utils.py |  5 ++---
 uploader/dbinsert.py | 22 +++++++++++-----------
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/uploader/db_utils.py b/uploader/db_utils.py
index ef26398..357b3da 100644
--- a/uploader/db_utils.py
+++ b/uploader/db_utils.py
@@ -19,10 +19,9 @@ def parse_db_url(db_url) -> Tuple:
 
 
 @contextlib.contextmanager
-def database_connection(db_url: Optional[str] = None) -> Iterator[mdb.Connection]:
+def database_connection(db_url: str) -> Iterator[mdb.Connection]:
     """function to create db connector"""
-    host, user, passwd, db_name, db_port = parse_db_url(
-        db_url or app.config["SQL_URI"])
+    host, user, passwd, db_name, db_port = parse_db_url(db_url)
     connection = mdb.connect(
         host, user, passwd, db_name, port=(db_port or 3306))
     try:
diff --git a/uploader/dbinsert.py b/uploader/dbinsert.py
index 66b0c41..559dc5e 100644
--- a/uploader/dbinsert.py
+++ b/uploader/dbinsert.py
@@ -41,7 +41,7 @@ def genechips():
             return {**acc, speciesid: (chip,)}
         return {**acc, speciesid: acc[speciesid] + (chip,)}
 
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.execute("SELECT * FROM GeneChip ORDER BY GeneChipName ASC")
             return reduce(__organise_by_species__, cursor.fetchall(), {})
@@ -50,7 +50,7 @@ def genechips():
 
 def platform_by_id(genechipid:int) -> Union[dict, None]:
     "Retrieve the gene platform by id"
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.execute(
                 "SELECT * FROM GeneChip WHERE GeneChipId=%s",
@@ -59,7 +59,7 @@ def platform_by_id(genechipid:int) -> Union[dict, None]:
 
 def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple:
     "Retrieve the studies by the related species and gene platform"
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             query = (
                 "SELECT Species.SpeciesId, ProbeFreeze.* "
@@ -83,7 +83,7 @@ def organise_groups_by_family(acc:dict, group:dict) -> dict:
 
 def tissues() -> tuple:
     "Retrieve type (Tissue) information from the database."
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.execute("SELECT * FROM Tissue ORDER BY Name")
             return tuple(cursor.fetchall())
@@ -158,7 +158,7 @@ def create_study():
         assert form.get("inbredsetid"), "group"
         assert form.get("tissueid"), "type/tissue"
 
-        with database_connection() as conn:
+        with database_connection(app.config["SQL_URI"]) as conn:
             with conn.cursor(cursorclass=DictCursor) as cursor:
                 values = (
                     form["genechipid"],
@@ -190,7 +190,7 @@ def create_study():
 
 def datasets_by_study(studyid:int) -> tuple:
     "Retrieve datasets associated with a study with the ID `studyid`."
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             query = "SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s"
             cursor.execute(query, (studyid,))
@@ -200,7 +200,7 @@ def datasets_by_study(studyid:int) -> tuple:
 
 def averaging_methods() -> tuple:
     "Retrieve averaging methods from database"
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.execute("SELECT * FROM AvgMethod")
             return tuple(cursor.fetchall())
@@ -209,7 +209,7 @@ def averaging_methods() -> tuple:
 
 def dataset_datascales() -> tuple:
     "Retrieve datascales from database"
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor() as cursor:
             cursor.execute(
                 'SELECT DISTINCT DataScale FROM ProbeSetFreeze '
@@ -261,7 +261,7 @@ def create_dataset():
         assert form.get("datasetconfidentiality"), "Dataset confidentiality"
         assert form.get("datasetdatascale"), "Dataset Datascale"
 
-        with database_connection() as conn:
+        with database_connection(app.config["SQL_URI"]) as conn:
             with conn.cursor(cursorclass=DictCursor) as cursor:
                 datasetname = form["datasetname"]
                 cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Name=%s",
@@ -299,7 +299,7 @@ def create_dataset():
 
 def study_by_id(studyid:int) -> Union[dict, None]:
     "Get a study by its Id"
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.execute(
                 "SELECT * FROM ProbeFreeze WHERE Id=%s",
@@ -308,7 +308,7 @@ def study_by_id(studyid:int) -> Union[dict, None]:
 
 def dataset_by_id(datasetid:int) -> Union[dict, None]:
     "Retrieve a dataset by its id"
-    with database_connection() as conn:
+    with database_connection(app.config["SQL_URI"]) as conn:
         with conn.cursor(cursorclass=DictCursor) as cursor:
             cursor.execute(
                 ("SELECT AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.* "
-- 
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