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Merged
merged 4 commits into from
Jun 20, 2025
Merged

Improve MongoDB backup secret handling #11

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118f2a5
Improve secret handling for MongoDB backups
oesteban Jun 20, 2025
76fc1ce
Make MongoDB backup credentials optional
oesteban Jun 20, 2025
a339386
Update README.md
oesteban Jun 20, 2025
6bd3ba7
Merge branch 'master' into codex/create-crontab-script-for-daily-data…
oesteban Jun 20, 2025
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11 changes: 11 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
28 changes: 23 additions & 5 deletions scripts/backup_mongodb.sh
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Expand Up @@ -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"
Expand All @@ -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
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