From 8e4e15ae62989f07d3ca8512165ba2a93c42aa94 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 12 Apr 2024 09:17:49 +0300
Subject: Consistently check for possibly non-existent data

The "geno-dataset", "tissue", "pheno-study" and "pheno-dataset" data
"objects" might not exist for a particular uploaded bundle, so we
check in a consistent manner to ensure they are provided when needed.
---
 qc_app/db/datasets.py | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

(limited to 'qc_app/db/datasets.py')

diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 448db18..b56dcf5 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -18,12 +18,12 @@ def geno_datasets_by_species_and_population(
             {"sid": speciesid, "pid": populationid})
         return tuple(dict(row) for row in cursor.fetchall())
 
-def geno_dataset_by_id(conn: mdb.Connection, dataset_id: int) -> dict:
+def geno_dataset_by_id(conn: mdb.Connection, dataset_id) -> Optional[dict]:
     """Retrieve genotype dataset by ID"""
     with conn.cursor(cursorclass=DictCursor) as cursor:
-        cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
-                       (dataset_id,))
-        return dict(cursor.fetchone())
+        cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s", (dataset_id,))
+        _dataset = cursor.fetchone()
+        return dict(_dataset) if bool(_dataset) else None
 
 def probeset_studies_by_species_and_population(
         conn: mdb.Connection,
@@ -46,12 +46,12 @@ def probeset_datasets_by_study(conn: mdb.Connection,
                        (studyid,))
         return tuple(dict(row) for row in cursor.fetchall())
 
-def probeset_study_by_id(conn: mdb.Connection, studyid: int) -> dict:
+def probeset_study_by_id(conn: mdb.Connection, studyid) -> Optional[dict]:
     """Retrieve ProbeSet study by ID"""
     with conn.cursor(cursorclass=DictCursor) as cursor:
-        cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s",
-                       (studyid,))
-        return dict(cursor.fetchone())
+        cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s", (studyid,))
+        _study = cursor.fetchone()
+        return dict(_study) if bool(_study) else None
 
 def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
                           populationid: int,
@@ -120,12 +120,10 @@ def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-argu
             dataset)
         return {**dataset, "datasetid": cursor.lastrowid}
 
-def probeset_dataset_by_id(
-        conn: mdb.Connection, datasetid: int) -> Optional[dict]:
+def probeset_dataset_by_id(conn: mdb.Connection, datasetid) -> Optional[dict]:
     """Fetch a ProbeSet dataset by its ID"""
     with conn.cursor(cursorclass=DictCursor) as cursor:
-        cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Id=%s",
-                       (datasetid,))
+        cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Id=%s", (datasetid,))
         result = cursor.fetchone()
         if bool(result):
             return dict(result)
-- 
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