Using bridgehead user for performing git pull

Otherwise problems can arise with authentication.

bbmri/modules/ehds2-compose.yml

@@ -60,7 +60,7 @@ services:
              [ ! -f /app/data/lock ] && \
              ( \
                  echo 'Wait for Blaze to finish initializing' ; \
-                 sleep 300 ; \
+                 sleep 360 ; \
                  echo 'Remove old output files' ; \
                  rm -rf /app/test/* ; \
                  cd /app ; \
@@ -78,5 +78,5 @@ services:
   test-data-loader:
     container_name: test-data-loader
     image: samply/test-data-loader
-    command: sh -c "sleep 400 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"
+    command: sh -c "sleep 420 && echo Listing all resources in FHIR store && blazectl --server http://bridgehead-bbmri-blaze:8080/fhir count-resources && tail -f /dev/null"
 

bridgehead

@@ -88,9 +88,11 @@ case "$ACTION" in
 	start)
 		loadVars
 		hc_send log "Bridgehead $PROJECT startup: Checking requirements ..."
+		chown -R bridgehead ${BASE}
 		checkRequirements
 		# Note: changes to "bridgehead" script will only take effect after next start.
-		git pull
+		su bridgehead -c "git pull"
+		chown -R bridgehead ${BASE}
                 # Local versions of focus and transfair are needed by EHDS2
                 clone_focus_if_nonexistent ${BASE}/..
                 build_focus ${BASE}/..

lib/functions.sh

@@ -258,7 +258,8 @@ function clone_repo_if_nonexistent() {
     cd "$target_dir"
 
     # Checkout the specified branch
-    git checkout "$branch_name"
+    chown -R bridgehead .
+    su bridgehead -c "git checkout $branch_name"
     echo "Checked out branch '$branch_name'."
 
     cd -
@@ -286,8 +287,9 @@ function build_transfair() {
     # 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
+	su bridgehead -c "git pull"
         docker build --progress=plain -t samply/transfair --no-cache .
+        chown -R bridgehead .
         cd -
     fi
 }
@@ -296,8 +298,9 @@ function build_focus() {
     local base_dir="$1"
 
     cd $base_dir/focus
-    git pull
+    su bridgehead -c "git pull"
     docker build --progress=plain -f DockerfileWithBuild -t samply/focus --no-cache .
+    chown -R bridgehead .
     cd -
 }