This repository contains Python scripts to query ClassyFire API and to update the ChemOnt classification in MassBank record files. In addition, a sunburst plot can be created.

Retry and timeout behaviour

All requests to the ClassyFire API (utils.request_with_retry, used by structure_query, get_results and request_by_inchikey.py) go through a shared requests.Session and are retried with exponential backoff plus jitter:

• Retried: HTTP 429, 500, 502, 503, 504, connection errors and timeouts (a numeric Retry-After header is honoured).
• Not retried: all other 4xx responses (the request fails immediately).
• Every retry is logged as a warning; a final failure is logged as an error with method, URL, status code, number of attempts and a short excerpt of the response, and raises utils.ClassyFireRequestError (a subclass of requests.exceptions.RequestException).
• In request.py a chunk that cannot be submitted does not abort the run. It is reported as a GitHub Actions warning and its SMILES are written to results/retry_later.tsv. The affected records keep having no ChemOnt classification and are therefore queried again in the next run.

Configuration via environment variables:

Variable	Default	Description
CLASSYFIRE_URL	http://classyfire.wishartlab.com	Base URL of the ClassyFire API
CLASSYFIRE_MAX_ATTEMPTS	5	Maximum number of attempts per request
CLASSYFIRE_BACKOFF_INITIAL	1.0	Initial backoff in seconds (doubled after each attempt, plus up to this value as jitter)
CLASSYFIRE_BACKOFF_MAX	60.0	Upper bound for a single backoff in seconds
CLASSYFIRE_CONNECT_TIMEOUT	5	Connect timeout in seconds
CLASSYFIRE_READ_TIMEOUT	30	Read timeout in seconds

HTTP is kept as default because the public ClassyFire API is only documented and used (e.g. by pyclassyfire) via HTTP and HTTPS support could not be verified. Set CLASSYFIRE_URL=https://classyfire.wishartlab.com to use HTTPS.

Run the unit tests with python -m unittest discover -s tests.