brkraw-backup

CLI plugin that adds brkraw backup for scanning and archiving Bruker ParaVision datasets.

Getting started

Install the plugin:

pip install -U git+ssh://git@github.com/BrkRaw/brkraw-backup.git

Initialize paths in ~/.brkraw/config.yaml:

brkraw backup init /path/to/raw_dir /path/to/archive_dir

Scan and view status:

brkraw backup scan
brkraw backup info

Notes:

• Archives are stored under backup.archive as zip files.
• A JSON registry is written under the archive directory (default: .brkraw-backup-registry.json).
• If backup.rawdata / backup.archive are configured, most commands can omit positional paths.
• Progress bars show only on TTY; disable with --no-progress.
• Detailed ISSUES: sub-lines show only when log level is DEBUG.

Commands

brkraw backup init

Register raw/archive directories in brkraw config.

brkraw backup init /raw /archive
brkraw backup init /raw /archive --force

Writes:

• backup.rawdata: /raw
• backup.archive: /archive

brkraw backup scan

Scan rawdata + archive and update the registry.

brkraw backup scan
brkraw backup scan /raw /archive

brkraw backup info

Show the last recorded status from the JSON registry (no filesystem scan).

brkraw backup info
brkraw backup info /archive
brkraw backup info --status OK,ARCHIVED
brkraw backup info --status TODO
brkraw backup info --integ FAIL,WARN
brkraw backup info --exclude-status UNKNOWN

brkraw backup review

Scan and show only non-OK datasets.

brkraw backup review

brkraw backup run

Create/update archives for datasets that are missing a backup or mismatched.

brkraw backup run
brkraw backup run --only A,B,C
brkraw backup run --dry-run
brkraw backup run --rebuild
brkraw backup run --delete-raw --yes

Update behavior:

• Default: append missing files into existing zip (no full rebuild).
• --rebuild: recreate the zip from scratch.

brkraw backup migrate

Import legacy .brk-backup_cache into the new JSON registry.

brkraw backup migrate /raw /archive
brkraw backup migrate /raw /archive --old-cache /archive/.brk-backup_cache
brkraw backup migrate /raw /archive --no-scan

brkraw backup about

Show plugin + environment info (useful for debugging installs).

brkraw backup about

Deep integrity scan (optional)

Deep integrity scanning compares:

• raw file list vs zip file list
• raw total bytes vs zip uncompressed bytes (ZipInfo.file_size sum)

This is optional because it can be slow on large datasets / network storage.

Options (available on scan and run):

• --integrity off|new|all (default: off)
  • off: skip deep checks
  • new: check only datasets that need a check (based on last_backup vs integrity.checked_at)
  • all: check all raw+archive pairs (subject to limit)
• --integrity-limit N (default: 0)
  • 0: no limit
  • N: check at most N datasets per command invocation

The status table includes an INTEG column:

• -: not checked
• OK: file list + byte totals match
• WARN: file list OK but byte totals differ
• FAIL: missing files found in archive
• SKIP: archive is not a zip (cannot compare file lists / bytes)