From 0b8bd607645bf32e1713841e4c68dbc7ea60c0a2 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 16 Jan 2024 06:52:49 +0300
Subject: Filter out items with values of `None`.

The ProbeSetData table does not allow `NULL` for the `value` column
for good reason - if there is no value, just don't have a record for
that particular sample.
---
 scripts/rqtl2/install_phenos.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'scripts/rqtl2')

diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index 4fdf428..5c25866 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -54,12 +54,13 @@ def insert_probeset_data(dbconn: mdb.Connection,
         data = tuple(
             {**row, "psdid": lastid + idx}
             for idx, row in enumerate(
-                    ({
+                    (item for item in ({
                         "sampleid": sampleids[innerrow["id"]],
                         "value": innerrow[pheno],
                         "pheno": pheno
                     } for innerrow in phenos for pheno in
-                     (key for key in innerrow.keys() if key != "id")),
+                      (key for key in innerrow.keys() if key != "id"))
+                     if item["value"] is not None),
                     start=1))
         cursor.executemany(
             "INSERT INTO ProbeSetData(Id, StrainId, value) "
-- 
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