cpo-qc-collector

Collect QC data from Carbapenemase-Producing Organism (CPO) genomic analyses, for loading into the BCCDC-PHL/cpo-qc-site.

Installation

Usage

Start the tool as follows:

cpo-qc-collector --config config.json

See the Configuration section of this document for details on preparing a configuration file.

More detailed logs can be produced by controlling the log level using the --log-level flag:

cpo-qc-collector --config config.json --log-level debug

Configuration

This tool takes a single config file, in JSON format, with the following structure:

{
    "analysis_by_run_dir": "/path/to/analysis_by_run",
    "excluded_runs_list": "/path/to/excluded_runs.csv",
    "known_species_list": "/path/to/known_species.csv",
    "scan_interval_seconds": 3600,
    "output_dir": "/path/to/output/data"
}

Logging

This tool outputs structured logs in JSON Lines format:

Every log line should include the fields:

• timestamp
• level
• module
• function_name
• line_num
• message

...and the contents of the message key will be a JSON object that includes at event_type. The remaining keys inside the message will vary by event type.

{"timestamp": "2022-09-22T11:32:52.287", "level": "INFO", "module", "core", "function_name": "scan", "line_num", 56, "message": {"event_type": "scan_start"}}