Merge pull request #11 from nipreps/codex/create-crontab-script-for-daily-database-backup

Improve MongoDB backup secret handling

Author: oesteban

README.md

@@ -51,3 +51,14 @@ Make it executable before scheduling it with `cron`:
 ```bash
 chmod +x scripts/backup_mongodb.sh
 ```
+Store `DBNAME` (and optional credentials) in environment variables rather than
+editing the script.  You may create a file named `~/.mongodb_backup_env` with
+content like:
+
+```bash
+export DBNAME="fmriprep_stats"
+# export MONGO_USER=myuser
+# export MONGO_PASS=mypassword
+```
+
+The backup script will source this file if present.

scripts/backup_mongodb.sh

@@ -2,11 +2,20 @@
 # scripts/backup_mongodb.sh
 # Backup MongoDB database, ensuring mongod is running.
 
+set -euo pipefail
+
+# Optionally source credentials from ~/.mongodb_backup_env
+ENV_FILE="$HOME/.mongodb_backup_env"
+if [ -f "$ENV_FILE" ]; then
+    # shellcheck disable=SC1090
+    source "$ENV_FILE"
+fi
+
+# DBNAME is required; credentials are optional
+: "${DBNAME:?Set DBNAME, e.g., export DBNAME=your_db}"
+
 DATE=$(date +%Y-%m-%d)
-BACKUP_DIR="$HOME/Dropbox/backups"
-DBNAME="DBNAME"
-USERNAME="USERNAME"
-PASSWORD="PASSWORD"
+BACKUP_DIR="$HOME/Dropbox/fmriprep_stats"
 BACKUP_PATH="$BACKUP_DIR/db_backup_${DATE}"
 
 mkdir -p "$BACKUP_DIR"
@@ -27,8 +36,17 @@ else
     started_mongod=true
 fi
 
+# Build mongodump options
+dump_opts=(--db "$DBNAME" --out "$BACKUP_PATH")
+if [ -n "${MONGO_USER:-}" ]; then
+    dump_opts+=(--username "$MONGO_USER")
+fi
+if [ -n "${MONGO_PASS:-}" ]; then
+    dump_opts+=(--password "$MONGO_PASS")
+fi
+
 # Dump the database
-mongodump --db "$DBNAME" --username "$USERNAME" --password "$PASSWORD" --out "$BACKUP_PATH"
+mongodump "${dump_opts[@]}"
 
 # Stop mongod if we started it
 if [ "$started_mongod" = true ]; then