augur.validate module¶
Validate a set of JSON files intended for visualization in auspice.
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exception
augur.validate.
ValidateError
¶ Bases:
Exception
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augur.validate.
checkSchemaIsValid
(schema, name)¶
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augur.validate.
collectAAMutationGenesNextfluSchema
(root)¶ Returns a set of all genes specified in the tree in the “aa_muts” objects
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augur.validate.
collectMutationGenes
(root)¶ Returns a set of all genes specified in the tree in the “aa_muts” objects
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augur.validate.
collectTreeAttrs
(root, nextflu=False)¶ Collect all keys specified on node->attr (or node->traits) throughout the tree If the values of these keys are strings, then also collect the values
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augur.validate.
loadJSONsToValidate
(paths)¶ paths: array of paths to JSONs. JSON type (and therefore schema type) is inferred from the pathname, paralleling Auspice tree & meta JSONs are “nexflu-schema”, unified JSON is the new schema
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augur.validate.
loadSchemas
(types, nextflu_schema)¶ For types (such as “tree”, “meta”), load and internally-verify the schema.
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augur.validate.
register_arguments
(parser)¶
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augur.validate.
run
(args)¶ Validate auspice-compatable JSONs against a schema
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augur.validate.
verifyMainJSONIsInternallyConsistent
(main)¶ Check all possible sources of conflict within the main (unified) JSON This function is only used for schema v2.0
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augur.validate.
verifyMetaAndOrTreeJSONsAreInternallyConsistent
(meta, tree)¶ Check all possible sources of conflict internally & between the metadata & tree JSONs This is only that which cannot be checked by the schemas This function is only used for nexflu-like schemas