CLI Usage

Thresh ships a real CLI as thresh (and as clinisync for backwards compatibility) — installable globally, runnable via npx, or available as node bin/clinisync.js from a clone.

$ thresh
Thresh — privacy-first spreadsheet ETL.

Usage:
  thresh <command> [args] [options]

Commands:
  clean      Clean a workbook and write outputs to a directory.
  preview    Dry-run: produce a JSON report without writing files.
  serve      Run the HTTP server.
  version    Print the installed version.
  help [cmd] Show this help, or detailed help for a single command.

thresh clean <file>

Run the ETL pipeline on a workbook and write per-sheet CSVs plus a manifest to a directory.

thresh clean ./case-mix.xlsx -o ./out

Options:

Option	Default	Behavior
-o, --output <dir>	./out	Output directory; created if missing.
--rules <path>	bundled defaults	JSON rule set — see Field cleaning for the schema.
--quiet	off	Suppress the human-readable summary; emit a single line of JSON to stdout instead. Pipe-friendly.

In default (non-quiet) mode the CLI prints what it wrote to stderr and a summary block at the end:

  wrote converted-case_mix-sheet1.csv  (2 rows)
  wrote converted-case_mix-sheet2.csv  (2 rows)
  wrote manifest-case_mix.json

Summary:
  sheets             2
  rows processed     4
  duplicates removed 0
  invalid DOB        0
  missing NHI        0
  redacted cells     0
  output dir         out

In --quiet mode the only stdout line is JSON, ready for jq:

$ thresh clean ./case-mix.xlsx -o ./out --quiet | jq .sheetsProcessed
2

thresh preview <file>

Identical pipeline to clean, but writes nothing — emits a JSON dry-run report to stdout. Useful for verifying that a custom rule set does what you expect before running it for real.

thresh preview ./case-mix.xlsx --rules ./my-rules.json --limit 50

Options:

Option	Default	Behavior
--rules <path>	bundled defaults	Same as clean.
--limit <n>	25	Max rows to include in each sheet's preview block. The full file would be too big for a JSON response on a real workbook.

The output is the same structured JSON the POST /preview HTTP endpoint emits, with each sheet carrying a previewRows 2-D array plus stats.

thresh serve

Start the HTTP server. Honors all the runtime env vars from .env.example (CLINISYNC_API_KEY, CLINISYNC_CSV_TTL_HOURS, CLINISYNC_RULES_PATH, REDIS_URL, CLAMAV_TCP_HOST).

thresh serve --port 8080

--port overrides the PORT environment variable.

thresh version / thresh help

Print the version (read from VERSION) or the top-level / per-command help respectively. thresh help clean shows the full clean help block; same for preview and serve.

Exit codes

Code	Meaning
0	Success.
1	Recoverable error (missing input file, invalid rule set, ETL failure). The error message goes to stderr.
2	Unknown subcommand. Run thresh help for valid options.