From 4f2934d16a6dba52a7676fab48acc41e59b5bf29 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 10 Jan 2024 06:48:23 +0300
Subject: Insert any new individuals/samples into the database.

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

(limited to 'scripts/rqtl2')

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 88f776b..3016f1f 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -35,6 +35,19 @@ def insert_markers(dbconn: mdb.Connection,
             tuple({"speciesid": speciesid, "marker": marker}
                   for marker in markers))
         return cursor.rowcount
+
+def insert_individuals(dbconn: mdb.Connection,
+                       speciesid: int,
+                       individuals: tuple[str, ...]) -> int:
+    """Insert individuals/samples into the database."""
+    with dbconn.cursor() as cursor:
+        cursor.executemany(
+            "INSERT INTO Strain(Name, Name2, SpeciesId) "
+            "VALUES(%(id)s, %(id)s, %(speciesid)s) "
+            "ON DUPLICATE KEY UPDATE Name=Name",
+            tuple({"speciesid": speciesid, "id": individual}
+                  for individual in individuals))
+        return cursor.rowcount
         # TODO: Install geno data: GenoData
         return cursor.rowcount
 
@@ -69,6 +82,8 @@ def install_genotypes(dbconn: mdb.Connection,
                     dbconn,
                     speciesid,
                     tuple(key for key in batch[0].keys() if key != "id"))
+                individuals = tuple(row["id"] for row in batch)
+                insert_individuals(dbconn, speciesid, individuals)
                 count = count + len(batch)
 
             if "gmap" in cdata:
-- 
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