From 0c6538d458dc8faeacefcf048cedc66e5f93afe5 Mon Sep 17 00:00:00 2001
From: Leonardo Cristella <leonardo.cristella@epfl.ch>
Date: Thu, 13 Aug 2026 15:30:26 +0200
Subject: [PATCH] Add sync_days step to nightly cron before ingest

---
 dj_pipeline/cron_script.sh        | 1 +
 dj_pipeline/docker/cron_common.sh | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/dj_pipeline/cron_script.sh b/dj_pipeline/cron_script.sh
index 71da8a91..2ef4f21e 100755
--- a/dj_pipeline/cron_script.sh
+++ b/dj_pipeline/cron_script.sh
@@ -10,4 +10,5 @@ vr4mice_cron_init
 vr4mice_git_info
 vr4mice_compose_up db client
 
+vr4mice_run_sync_days
 vr4mice_run_cron_scenario local
diff --git a/dj_pipeline/docker/cron_common.sh b/dj_pipeline/docker/cron_common.sh
index 1e714d49..1cc78f2a 100755
--- a/dj_pipeline/docker/cron_common.sh
+++ b/dj_pipeline/docker/cron_common.sh
@@ -67,3 +67,12 @@ vr4mice_run_cron_scenario() {
   fi
   vr4mice_exec_client "${cmd}"
 }
+
+vr4mice_run_sync_days() {
+  # Resync the per-experiment `day` stored in the raw .npy files before ingest, so
+  # (mouse_name, day, attempt) does not collide across dates (the GUI can reset day
+  # to 1). Runs in the client container against /data/data, and must run BEFORE
+  # populate_rig moves the files to processed/.
+  vr4mice_check_env_file ".env" ".env.example"
+  vr4mice_exec_client "${BASE_INSTALL} && set -a && source .env && set +a && python run.py sync_days"
+}