Validate JAXBElement in JPA/JAX-RS Web Service

You could handle this by creating a custom MessageBodyReader. The example below is based on a Customer model:

import java.io.IOException;
import java.io.InputStream;
import java.lang.annotation.Annotation;
import java.lang.reflect.Type;
import java.net.URL;

import javax.ws.rs.Consumes;
import javax.ws.rs.WebApplicationException;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.MultivaluedMap;
import javax.ws.rs.ext.ContextResolver;
import javax.ws.rs.ext.MessageBodyReader;
import javax.ws.rs.ext.Provider;
import javax.ws.rs.ext.Providers;
import javax.xml.XMLConstants;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import javax.xml.validation.Schema;
import javax.xml.validation.SchemaFactory;

@Provider
@Consumes("application/xml")
public class ValidatingReader implements MessageBodyReader<Customer> {

    @Context
    protected Providers providers;

    private Schema schema;

    public ValidatingReader() {
        try {
            SchemaFactory sf = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
            URL schemaURL = null;
            schema = sf.newSchema(schemaURL);
        } catch(Exception e) {
            throw new RuntimeException(e);
        }
    }

    public boolean isReadable(Class<?> arg0, Type arg1, Annotation[] arg2, MediaType arg3) {
        return arg0 == Customer.class;
    }

    public Customer readFrom(Class<Customer> arg0, Type arg1, Annotation[] arg2, MediaType arg3, MultivaluedMap<String, String> arg4, InputStream arg5)
            throws IOException, WebApplicationException {
        try {
            JAXBContext jaxbContext = null;
            ContextResolver<JAXBContext> resolver = providers.getContextResolver(JAXBContext.class, arg3);
            if(null != resolver) {
                jaxbContext = resolver.getContext(arg0);
            }
            if(null == jaxbContext) {
                jaxbContext = JAXBContext.newInstance(arg0);
            }
            Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
            unmarshaller.setSchema(schema);
            return (Customer) unmarshaller.unmarshal(arg5);
        } catch(JAXBException e) {
            throw new RuntimeException(e);
        }
    }

}