From ece7a615b2c13dedc1c3cdca06f92f714023a5b4 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 19 May 2025 10:48:21 -0500
Subject: Rework order of execution of potential steps.

---
 scripts/load_phenotypes_to_db.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py
index 378497f..d31ade6 100644
--- a/scripts/load_phenotypes_to_db.py
+++ b/scripts/load_phenotypes_to_db.py
@@ -139,16 +139,16 @@ def load_data(conn, job):
     #    b. Save all the data items (DataIds are vibes), return new IDs
     data = save_phenotypes_data(
         cursor, dataidmap, samples, , _control_data["pheno"])
-    #    c. If standard errors and N exist, save them too
-    #       (use IDs returned in `b` above).
+    # 4. Cross-reference Phenotype, Publication, and PublishData in PublishXRef
+    xrefs = cross_reference_phenotypes_publications_and_data(
+        cursor, __merge_map_with_publications__(dataidmap))
+    # 5. If standard errors and N exist, save them too
+    #    (use IDs returned in `3. b.` above).
     data_se = save_phenotypes_data(
         cursor, dataidmap, samples, , _control_data["phenose"])
     data_n = save_phenotypes_n(
         cursor, dataidmap, samples, , _control_data["phenonum"])
-    # 4. Cross-reference Phenotype, Publication, and PublishData in PublishXRef
-    xrefs = cross_reference_phenotypes_publications_and_data(
-        cursor, __merge_map_with_publications__(dataidmap))
-    # 5. If entirely new data, update authorisations (break this down)
+    # 6. If entirely new data, update authorisations (break this down)
     update_auth(_user, _species, _population, _dataset, _phenos)
     return 0
 
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