From 0d0b284a76bee863b97c46e8275cd62e02552a93 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 10 Jan 2024 07:16:55 +0300
Subject: Cross-reference genotype data to the dataset.

---
 scripts/rqtl2/install_genotypes.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 63e6113..a555d46 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -106,6 +106,18 @@ def insert_genotype_data(dbconn: mdb.Connection,
             "markerid": row["markerid"]
         } for row in data)
 
+def cross_reference_genotypes(dbconn: mdb.Connection,
+                              datasetid: int,
+                              dataids: tuple[int, ...]) -> int:
+    """Cross-reference the data to the relevant dataset."""
+    with dbconn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "INSERT INTO GenoXRef(GenoFreezeId, GenoId, DataId) "
+            "VALUES(%(datasetid)s, %(markerid)s, %(dataid)s) "
+            "ON DUPLICATE KEY UPDATE GenoFreezeId=GenoFreezeId",
+            tuple({**row, "datasetid": datasetid} for row in dataids))
+        return cursor.rowcount
+
 def install_genotypes(dbconn: mdb.Connection,
                       speciesid: int,
                       populationid: int,
@@ -141,8 +153,9 @@ def install_genotypes(dbconn: mdb.Connection,
                 insert_individuals(dbconn, speciesid, individuals)
                 cross_reference_individuals(
                     dbconn, speciesid, populationid, individuals)
-                _num_rows, data_ids = insert_genotype_data(
+                _num_rows, dataids = insert_genotype_data(
                     dbconn, speciesid, batch, individuals)
+                cross_reference_genotypes(dbconn, datasetid, dataids)
                 count = count + len(batch)
 
             if "gmap" in cdata:
-- 
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