From 88a8bc0b458f079e93757057080f1ec0dc842fd8 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 11 Jan 2024 02:26:46 +0300
Subject: Cleanup linting and typing errors.

---
 scripts/rqtl2/install_genotypes.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

(limited to 'scripts')

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 3b9e987..5c3da85 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -57,8 +57,9 @@ def cross_reference_individuals(dbconn: mdb.Connection,
     """Cross reference any inserted individuals."""
     with dbconn.cursor(cursorclass=DictCursor) as cursor:
         paramstr = ", ".join(["%s"] * len(individuals))
-        cursor.execute(f"SELECT Id FROM Strain WHERE Name IN ({paramstr})",
-                       individuals)
+        cursor.execute("SELECT Id FROM Strain "
+                       f"WHERE SpeciesId=%s AND Name IN ({paramstr})",
+                       (speciesid,) + individuals)
         ids = ({"popid": populationid, "indid": row["Id"]}
                for row in cursor.fetchall())
         cursor.executemany(
@@ -71,7 +72,8 @@ def cross_reference_individuals(dbconn: mdb.Connection,
 def insert_genotype_data(dbconn: mdb.Connection,
                          speciesid: int,
                          genotypes: tuple[dict, ...],
-                         individuals: tuple[str, ...]) -> tuple[int, tuple[int, ...]]:
+                         individuals: tuple[str, ...]) -> tuple[
+                             int, tuple[dict, ...]]:
     """Insert the genotype data values into the database."""
     with dbconn.cursor(cursorclass=DictCursor) as cursor:
         paramstr = ", ".join(["%s"] * len(individuals))
@@ -108,7 +110,7 @@ def insert_genotype_data(dbconn: mdb.Connection,
 
 def cross_reference_genotypes(dbconn: mdb.Connection,
                               datasetid: int,
-                              dataids: tuple[int, ...]) -> int:
+                              dataids: tuple[dict, ...]) -> int:
     """Cross-reference the data to the relevant dataset."""
     with dbconn.cursor(cursorclass=DictCursor) as cursor:
         cursor.execute(
@@ -155,6 +157,7 @@ def install_genotypes(dbconn: mdb.Connection,
                 cross_reference_genotypes(dbconn, datasetid, dataids)
                 count = count + len(batch)
 
+            cdata = rqtl2.control_data(zfile)
             if "gmap" in cdata:
                 logger.info("Loading genetic mapping info.")
                 # TODO: load gmap files
@@ -167,7 +170,8 @@ def install_genotypes(dbconn: mdb.Connection,
         except rqtl2.InvalidFormat as exc:
             logger.error(str(exc))
             logger.info("There are no genotypes to load.")
-        except Exception as _exc:
+        except Exception as _exc:# pylint: disable=[broad-except]
+            # Narrow this exception with time.
             logger.error("Failing with exception: %s", traceback.format_exc())
             return 3
 
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