[Integration test] fix after rebase

.github/integration/tests/sda/10_upload_test.sh

@@ -34,7 +34,7 @@ done
 psql -U postgres -h postgres -d sda -At -c "TRUNCATE TABLE sda.files CASCADE;"
 
 if [ "$STORAGETYPE" = "posix" ]; then
-    for file in NA12878.bam NA12878_20k_b37.bam; do
+    for file in NA12878.bam NA12878_20k_b37.bam NA12878.bai NA12878_20k_b37.bai; do
         echo "downloading $file"
         curl -s -L -o /shared/$file "https://github.com/ga4gh/htsget-refserver/raw/main/data/gcp/gatk-test-data/wgs_bam/$file"
         if [ ! -f "$file.c4gh" ]; then

.github/integration/tests/sda/21_cancel_test.sh

@@ -86,11 +86,11 @@ curl -k -u guest:guest "http://rabbitmq:15672/api/exchanges/sda/sda/publish" \
     -d "$ingest_body"
 
 RETRY_TIMES=0
-until [ "$(curl -su guest:guest http://rabbitmq:15672/api/queues/sda/verified/ | jq -r '.messages_ready')" -eq 3 ]; do
-    echo "waiting for verify to complete"
+until [ "$(curl -su guest:guest http://rabbitmq:15672/api/queues/sda/verified/ | jq -r '.messages_ready')" -eq 5 ]; do
+    echo "waiting for verify to complete after re-ingestion"
     RETRY_TIMES=$((RETRY_TIMES + 1))
     if [ "$RETRY_TIMES" -eq 30 ]; then
-        echo "::error::Time out while waiting for verify to complete"
+        echo "::error::Time out while waiting for verify to complete after re-ingestion"
         exit 1
     fi
     sleep 2

.github/integration/tests/sda/30_backup-finalize_test.sh

@@ -4,7 +4,7 @@ set -e
 cd shared || true
 
 i=1
-while [ $i -le 2 ]; do
+while [ $i -le 4 ]; do
     ## get correlation id from upload message
     MSG=$(
         curl -s -X POST \