From 153f65439796165e830fc717ad516bb3cb779ca4 Mon Sep 17 00:00:00 2001
From: DavidCroftDKFZ <46788708+DavidCroftDKFZ@users.noreply.github.com>
Date: Fri, 12 Jul 2024 11:07:06 +0200
Subject: [PATCH] Deal with multiple data files, update repos

The check for the presence of data in the TransFAIR updating function
only worked for single CSV files. Tis commit corrects that.

Now also do a git pull on the various repos, to keep things up to date.
---
 bridgehead       | 2 ++
 lib/functions.sh | 8 +++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/bridgehead b/bridgehead
index 1b897b7..33303ef 100755
--- a/bridgehead
+++ b/bridgehead
@@ -89,6 +89,8 @@ case "$ACTION" in
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
 		checkRequirements
+		# Note: changes to "bridgehead" script will only take effect after next start.
+		git pull
                 # Local versions of focus and transfair are needed by EHDS2
                 clone_focus_if_nonexistent ${BASE}/..
                 build_focus ${BASE}/..
diff --git a/lib/functions.sh b/lib/functions.sh
index 03b6868..112e8d6 100644
--- a/lib/functions.sh
+++ b/lib/functions.sh
@@ -282,10 +282,11 @@ function build_transfair() {
 
     # We only take the touble to build transfair if:
     #
-    # 1. There is no data lock file (which means that no ETL has yet been run) and
-    # 2. There is data available.
-    if [ -f ../ecdc/data/*.[cC][sS][vV] ] && [ ! -f ../ecdc/data/lock ]; then
+    # 1. There is data available (any CSV files) and
+    # 2. There is no data lock file (which means that no ETL has yet been run).
+    if ls ../ecdc/data/*.[cC][sS][vV] 1> /dev/null 2>&1 && [ ! -f ../ecdc/data/lock ]; then
         cd $base_dir/transfair
+        git pull
         docker build --progress=plain -t samply/transfair --no-cache .
         cd -
     fi
@@ -295,6 +296,7 @@ function build_focus() {
     local base_dir="$1"
 
     cd $base_dir/focus
+    git pull
     docker build --progress=plain -f DockerfileWithBuild -t samply/focus --no-cache .
     cd -
 }