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.

1 files changed, 3 insertions, 2 deletions

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) "