Ignore any optional files that are not provided.

1 files changed, 20 insertions, 17 deletions

diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py
index 5ce37f3..08ee558 100644
--- a/scripts/load_phenotypes_to_db.py
+++ b/scripts/load_phenotypes_to_db.py
@@ -410,23 +410,26 @@ def load_data(conn: mysqldb.Connection, job: dict) -> int:
         conn, tuple(dataidmap.values()))
     # 5. If standard errors and N exist, save them too
     #    (use IDs returned in `3. b.` above).
-    logger.info("Saving new phenotypes standard errors.")
-    _num_se_rows = save_phenotypes_se(conn=conn,
-                                      dataidmap=dataidmap,
-                                      pheno_name2id=pheno_name2id,
-                                      samples=samples,
-                                      control_data=_control_data,
-                                      filesdir=_outdir)
-    logger.info("Saved %s new phenotype standard error rows.", _num_se_rows)
-
-    logger.info("Saving new phenotypes sample counts.")
-    _num_n_rows = save_phenotypes_n(conn=conn,
-                                    dataidmap=dataidmap,
-                                    pheno_name2id=pheno_name2id,
-                                    samples=samples,
-                                    control_data=_control_data,
-                                    filesdir=_outdir)
-    logger.info("Saved %s new phenotype sample counts rows.", _num_n_rows)
+    if _control_data.get("phenose"):
+        logger.info("Saving new phenotypes standard errors.")
+        _num_se_rows = save_phenotypes_se(conn=conn,
+                                          dataidmap=dataidmap,
+                                          pheno_name2id=pheno_name2id,
+                                          samples=samples,
+                                          control_data=_control_data,
+                                          filesdir=_outdir)
+        logger.info("Saved %s new phenotype standard error rows.", _num_se_rows)
+
+    if _control_data.get("phenonum"):
+        logger.info("Saving new phenotypes sample counts.")
+        _num_n_rows = save_phenotypes_n(conn=conn,
+                                        dataidmap=dataidmap,
+                                        pheno_name2id=pheno_name2id,
+                                        samples=samples,
+                                        control_data=_control_data,
+                                        filesdir=_outdir)
+        logger.info("Saved %s new phenotype sample counts rows.", _num_n_rows)
+
     return (_species, _population, _dataset, _xrefs)