config.json

{
    "input": "examples/input",
    "output": "examples/output",
    "output-type": "xml",
    
    "fixing": {
	"dont-fix": false,
	"fix-flux-objectives": {
	    "flux-coefficients": [],
	    "flux-objectives": []
	}
    },
    
    "polishing": {
	"polish-even-if-model-invalid": false
    },
    
    "annotation": {
	"bigg": {
	    "annotate-with-bigg": true,
	    "include-any-uri": true,
	    "document-title-pattern": "[biggId] - [organism]",
	    "notes": {
		"no-model-notes": true,
		"model-notes-file": null,
		"document-notes-file": null
	    },
	    "db-config": {
		"db-name": "bigg",
		"host": "localhost",
		"password": "postgres",
		"user": "postgres",
		"port": 1310
	    }
	},
	"annotatedb": {
	    "annotate-with-adb": true,
	    "db-config": {
		"db-name": "adb",
		"host": "localhost",
		"password": "postgres",
		"user": "postgres",
		"port": 1013
	    }
	}
    },
    
    "sbo-terms": {
	"add-generic-terms": false
    },
    
    "sbml-validation": false
}