augur.validate
Validate files related to augur consumption or export.
- exception augur.validate.ValidateError
Bases:
Exception
- class augur.validate.ValidationErrors
Bases:
ValidationWarnings
- show()
- augur.validate.auspice_config_v2(config_json, **kwargs)
- augur.validate.export_v1(meta_json, tree_json, **kwargs)
- augur.validate.export_v2(main_json, **kwargs)
- augur.validate.fatal(message)
- augur.validate.get_unique_keys(list_of_dicts)
Returns a set of unique keys from a list of dicts
>>> list_of_dicts = [{"key1": "val1", "key2": "val2"}, {"key1": "val1", "key3": "val3"}] >>> sorted(get_unique_keys(list_of_dicts)) ['key1', 'key2', 'key3']
- augur.validate.load_json(path)
- augur.validate.load_json_schema(path)
Load a JSON schema from the augur included set of schemas (located in augur/data)
- augur.validate.measurements(measurements_json, **kwargs)
- augur.validate.measurements_collection_config(collection_config_json, **kwargs)
- augur.validate.register_parser(parent_subparsers)
- augur.validate.run(args)
- augur.validate.validate(jsonToValidate, schema, filename)
- augur.validate.validate_collection_config_fields(collection, index=None)
Validates a single collection’s config field keys provided in fields, groupings, and filters are valid fields that exist in measurements’ fields.
Prints any validation errors to stderr.
- Parameters
collection (dict) – A single collection to validate. Assumes that the collection has already passed the schema validation.
index (int, optional) – the index of the collection within a list of collections in a measurements JSON. Used to print more detailed error messages.
- Returns
True if collection’s config is valid
- Return type
bool
- augur.validate.validate_collection_display_defaults(collection, index=None)
Validates a single collection’s display defaults. If a default group-by field is provided, the field must be included in groupings.
Prints validation errors to stderr.
- Parameters
collection (dict) – A single collection to validate. Assumest htat the collection has already passed the schema validation.
index (int, optional) – The index of the collection within a list of collections in a measurements JSON. Used to print more detailed error messages.
- Returns
True if collection’s display defaults are valid
- Return type
bool
- augur.validate.validate_json(jsonToValidate, schema, filename)
- augur.validate.validate_measurements_config(measurements)
Validate measurements’ config values meet expectations described in the measurements JSON schema descriptions that cannot be verified via validate_json: 1. Individual collections have valid config values 2. All collections have unique keys 3. If a default collection is provided, it matches one of the collections
Prints any validation errors to stderr.
- Parameters
measurements (dict) – Loaded measurements JSON to validate. Assumes the measurements JSON has already passed the schema validation.
- Returns
True if measurements’ config is valid
- Return type
bool