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Looking at the stack, that is not using the JsonDeserializer, it's using GlueSchemaRegistryDeserializationFacade, which assumes the data has the version of the schema to use, which has to be inserted there by using GlueSchemaRegistrySerializationFacade to generate the data, which it doesn't sound is your case.
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What class is that JsonDeserialiser?, also what's the stacktrace, it sounds that is intended for AVRO
stack trace : Exception in thread "main" com.amazonaws.services.schemaregistry.exception.GlueSchemaRegistryIncompatibleDataException: Invalid schema registry header version byte in data at com.amazonaws.services.schemaregistry.deserializers.GlueSchemaRegistryDeserializerDataParser.validateData(GlueSchemaRegistryDeserializerDataParser.java:178) at com.amazonaws.services.schemaregistry.deserializers.GlueSchemaRegistryDeserializerDataParser.getSchemaVersionId(GlueSchemaRegistryDeserializerDataParser.java:73) at com.amazonaws.services.schemaregistry.deserializers.GlueSchemaRegistryDeserializationFacade.getAwsDeserializerSchema(GlueSchemaRegistryDeserializationFacade.java:200) at com.amazonaws.services.schemaregistry.deserializers.GlueSchemaRegistryDeserializationFacade.deserialize(GlueSchemaRegistryDeserializationFacade.java:167) at com.amazonaws.services.schemaregistry.examples.kds.GlueSchemaRegistryExample.main(GlueSchemaRegistryExample.java:80)
class is : public class JsonDeserializer implements GlueSchemaRegistryDataFormatDeserializer