ca.uhn.hapi.fhir.docs.ValidatorExamples Maven / Gradle / Ivy
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* Licensed under the Apache License, Version 2.0 (the "License");
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* Unless required by applicable law or agreed to in writing, software
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package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.LookupCodeRequest;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.SchemaBaseValidator;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
import jakarta.annotation.Nonnull;
import jakarta.servlet.ServletException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.filefilter.WildcardFileFilter;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.NpmPackageValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.PrePopulatedValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.ContactPoint;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.ValueSet;
import java.io.File;
import java.io.FileReader;
import java.util.List;
@SuppressWarnings({"serial", "unused"})
public class ValidatorExamples {
public void validationIntro() {
// START SNIPPET: validationIntro
FhirContext ctx = FhirContext.forR4();
// Ask the context for a validator
FhirValidator validator = ctx.newValidator();
// Create a validation module and register it
IValidatorModule module = new FhirInstanceValidator(ctx);
validator.registerValidatorModule(module);
// Pass a resource instance as input to be validated
Patient resource = new Patient();
resource.addName().setFamily("Simpson").addGiven("Homer");
ValidationResult result = validator.validateWithResult(resource);
// The input can also be a raw string (this mechanism can
// potentially catch syntax issues that would have been missed
// otherwise, since the HAPI FHIR Parser is forgiving about
// its input.
String resourceText = "";
ValidationResult result2 = validator.validateWithResult(resourceText);
// The result object now contains the validation results
for (SingleValidationMessage next : result.getMessages()) {
System.out.println(next.getLocationString() + " " + next.getMessage());
}
// END SNIPPET: validationIntro
}
// START SNIPPET: serverValidation
public class MyRestfulServer extends RestfulServer {
@Override
protected void initialize() throws ServletException {
// ...Configure resource providers, etc...
// Create a context, set the error handler and instruct
// the server to use it
FhirContext ctx = FhirContext.forR4();
ctx.setParserErrorHandler(new StrictErrorHandler());
setFhirContext(ctx);
}
}
// END SNIPPET: serverValidation
@SuppressWarnings("unused")
public void enableValidation() {
// START SNIPPET: clientValidation
FhirContext ctx = FhirContext.forR4();
ctx.setParserErrorHandler(new StrictErrorHandler());
// This client will have strict parser validation enabled
IGenericClient client = ctx.newRestfulGenericClient("http://hapi.fhir.org/baseR4");
// END SNIPPET: clientValidation
}
public void parserValidation() {
// START SNIPPET: parserValidation
FhirContext ctx = FhirContext.forR4();
// Create a parser and configure it to use the strict error handler
IParser parser = ctx.newXmlParser();
parser.setParserErrorHandler(new StrictErrorHandler());
// This example resource is invalid, as Patient.active can not repeat
String input = " messages = result.getMessages();
for (SingleValidationMessage next : messages) {
System.out.println("Message:");
System.out.println(" * Location: " + next.getLocationString());
System.out.println(" * Severity: " + next.getSeverity());
System.out.println(" * Message : " + next.getMessage());
}
// You can also convert the results into an OperationOutcome resource
OperationOutcome oo = (OperationOutcome) result.toOperationOutcome();
String results = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo);
System.out.println(results);
// END SNIPPET: basicValidation
}
public static void main(String[] args) throws Exception {
instanceValidator();
}
private static void instanceValidator() throws Exception {
// START SNIPPET: instanceValidator
FhirContext ctx = FhirContext.forR4();
// Create a validation support chain
ValidationSupportChain validationSupportChain = new ValidationSupportChain(
new DefaultProfileValidationSupport(ctx),
new InMemoryTerminologyServerValidationSupport(ctx),
new CommonCodeSystemsTerminologyService(ctx));
// Create a FhirInstanceValidator and register it to a validator
FhirValidator validator = ctx.newValidator();
FhirInstanceValidator instanceValidator = new FhirInstanceValidator(validationSupportChain);
validator.registerValidatorModule(instanceValidator);
/*
* If you want, you can configure settings on the validator to adjust
* its behaviour during validation
*/
instanceValidator.setAnyExtensionsAllowed(true);
/*
* Let's create a resource to validate. This Observation has some fields
* populated, but it is missing Observation.status, which is mandatory.
*/
Observation obs = new Observation();
obs.getCode().addCoding().setSystem("http://loinc.org").setCode("12345-6");
obs.setValue(new StringType("This is a value"));
// Validate
ValidationResult result = validator.validateWithResult(obs);
/*
* Note: You can also explicitly declare a profile to validate against
* using the block below.
*/
// ValidationResult result = validator.validateWithResult(obs, new
// ValidationOptions().addProfile("http://myprofile.com"));
// Do we have any errors or fatal errors?
System.out.println(result.isSuccessful()); // false
// Show the issues
for (SingleValidationMessage next : result.getMessages()) {
System.out.println(
" Next issue " + next.getSeverity() + " - " + next.getLocationString() + " - " + next.getMessage());
}
// Prints:
// Next issue ERROR - /f:Observation - Element '/f:Observation.status': minimum required = 1, but only found 0
// Next issue WARNING - /f:Observation/f:code - Unable to validate code "12345-6" in code system
// "http://loinc.org"
// You can also convert the result into an operation outcome if you
// need to return one from a server
OperationOutcome oo = (OperationOutcome) result.toOperationOutcome();
// END SNIPPET: instanceValidator
}
private static void instanceValidatorCustom() throws Exception {
// START SNIPPET: instanceValidatorCustom
FhirContext ctx = FhirContext.forR4();
// Create a FhirInstanceValidator and register it to a validator
FhirValidator validator = ctx.newValidator();
FhirInstanceValidator instanceValidator = new FhirInstanceValidator(ctx);
validator.registerValidatorModule(instanceValidator);
IValidationSupport valSupport = new IValidationSupport() {
@Override
public List fetchAllConformanceResources() {
// TODO: implement (or return null if your implementation does not support this function)
return null;
}
@Override
public ValueSet fetchValueSet(String theSystem) {
// TODO: implement (or return null if your implementation does not support this function)
return null;
}
@Override
public T fetchResource(Class theClass, String theUri) {
// TODO: implement (or return null if your implementation does not support this function)
return null;
}
@Override
public StructureDefinition fetchStructureDefinition(String theUrl) {
// TODO: implement (or return null if your implementation does not support this function)
return null;
}
@Override
public boolean isCodeSystemSupported(
ValidationSupportContext theValidationSupportContext, String theSystem) {
// TODO: implement (or return null if your implementation does not support this function)
return false;
}
@Override
public CodeValidationResult validateCode(
@Nonnull ValidationSupportContext theValidationSupportContext,
@Nonnull ConceptValidationOptions theOptions,
String theCodeSystem,
String theCode,
String theDisplay,
String theValueSetUrl) {
// TODO: implement (or return null if your implementation does not support this function)
return null;
}
@Override
public LookupCodeResult lookupCode(
ValidationSupportContext theValidationSupportContext,
@Nonnull LookupCodeRequest validationSupportParameterObject) {
// TODO: implement (or return null if your implementation does not support this function)
return null;
}
@Override
public FhirContext getFhirContext() {
return ctx;
}
};
/*
* ValidationSupportChain strings multiple instances of IValidationSupport together. The
* code below is useful because it means that when the validator wants to load a
* StructureDefinition or a ValueSet, it will first use DefaultProfileValidationSupport,
* which loads the default HL7 versions. Any StructureDefinitions which are not found in
* the built-in set are delegated to your custom implementation.
*/
ValidationSupportChain support =
new ValidationSupportChain(new DefaultProfileValidationSupport(ctx), valSupport);
instanceValidator.setValidationSupport(support);
// END SNIPPET: instanceValidatorCustom
}
public void validateSupplyProfiles() {
StructureDefinition someStructureDefnition = null;
ValueSet someValueSet = null;
String input = null;
// START SNIPPET: validateSupplyProfiles
FhirContext ctx = FhirContext.forR4();
// Create a chain that will hold our modules
ValidationSupportChain supportChain = new ValidationSupportChain();
// DefaultProfileValidationSupport supplies base FHIR definitions. This is generally required
// even if you are using custom profiles, since those profiles will derive from the base
// definitions.
DefaultProfileValidationSupport defaultSupport = new DefaultProfileValidationSupport(ctx);
supportChain.addValidationSupport(defaultSupport);
// This module supplies several code systems that are commonly used in validation
supportChain.addValidationSupport(new CommonCodeSystemsTerminologyService(ctx));
// This module implements terminology services for in-memory code validation
supportChain.addValidationSupport(new InMemoryTerminologyServerValidationSupport(ctx));
// Create a PrePopulatedValidationSupport which can be used to load custom definitions.
// In this example we're loading two things, but in a real scenario we might
// load many StructureDefinitions, ValueSets, CodeSystems, etc.
PrePopulatedValidationSupport prePopulatedSupport = new PrePopulatedValidationSupport(ctx);
prePopulatedSupport.addStructureDefinition(someStructureDefnition);
prePopulatedSupport.addValueSet(someValueSet);
// Add the custom definitions to the chain
supportChain.addValidationSupport(prePopulatedSupport);
// Wrap the chain in a cache to improve performance
CachingValidationSupport cache = new CachingValidationSupport(supportChain);
// Create a validator using the FhirInstanceValidator module. We can use this
// validator to perform validation
FhirInstanceValidator validatorModule = new FhirInstanceValidator(cache);
FhirValidator validator = ctx.newValidator().registerValidatorModule(validatorModule);
ValidationResult result = validator.validateWithResult(input);
// END SNIPPET: validateSupplyProfiles
}
public void validateUsingRemoteTermServer() {
StructureDefinition someStructureDefnition = null;
ValueSet someValueSet = null;
String input = null;
// START SNIPPET: validateUsingRemoteTermSvr
FhirContext ctx = FhirContext.forR4();
// Create a chain that will hold our modules
ValidationSupportChain supportChain = new ValidationSupportChain();
// DefaultProfileValidationSupport supplies base FHIR definitions. This is generally required
// even if you are using custom profiles, since those profiles will derive from the base
// definitions.
DefaultProfileValidationSupport defaultSupport = new DefaultProfileValidationSupport(ctx);
supportChain.addValidationSupport(defaultSupport);
// Create a module that uses a remote terminology service
RemoteTerminologyServiceValidationSupport remoteTermSvc = new RemoteTerminologyServiceValidationSupport(ctx);
remoteTermSvc.setBaseUrl("http://hapi.fhir.org/baseR4");
supportChain.addValidationSupport(remoteTermSvc);
// Wrap the chain in a cache to improve performance
CachingValidationSupport cache = new CachingValidationSupport(supportChain);
// Create a validator using the FhirInstanceValidator module. We can use this
// validator to perform validation
FhirInstanceValidator validatorModule = new FhirInstanceValidator(cache);
FhirValidator validator = ctx.newValidator().registerValidatorModule(validatorModule);
ValidationResult result = validator.validateWithResult(input);
// END SNIPPET: validateUsingRemoteTermSvr
}
@SuppressWarnings("unused")
private static void validateFiles() throws Exception {
// START SNIPPET: validateFiles
FhirContext ctx = FhirContext.forR4();
// Create a validator and configure it
FhirValidator validator = ctx.newValidator();
validator.setValidateAgainstStandardSchema(true);
validator.setValidateAgainstStandardSchematron(true);
// Get a list of files in a given directory
String[] fileList = new File("/home/some/dir").list(new WildcardFileFilter("*.txt"));
for (String nextFile : fileList) {
// For each file, load the contents into a string
String nextFileContents = IOUtils.toString(new FileReader(nextFile));
// Parse that string (this example assumes JSON encoding)
IBaseResource resource = ctx.newJsonParser().parseResource(nextFileContents);
// Apply the validation. This will throw an exception on the first
// validation failure
ValidationResult result = validator.validateWithResult(resource);
if (result.isSuccessful() == false) {
throw new Exception(Msg.code(640) + "We failed!");
}
}
// END SNIPPET: validateFiles
}
@SuppressWarnings("unused")
private static void npm() throws Exception {
// START SNIPPET: npm
// Create an NPM Package Support module and load one package in from
// the classpath
FhirContext ctx = FhirContext.forR4();
NpmPackageValidationSupport npmPackageSupport = new NpmPackageValidationSupport(ctx);
npmPackageSupport.loadPackageFromClasspath("classpath:package/UK.Core.r4-1.1.0.tgz");
// Create a support chain including the NPM Package Support
ValidationSupportChain validationSupportChain = new ValidationSupportChain(
npmPackageSupport,
new DefaultProfileValidationSupport(ctx),
new CommonCodeSystemsTerminologyService(ctx),
new InMemoryTerminologyServerValidationSupport(ctx),
new SnapshotGeneratingValidationSupport(ctx));
CachingValidationSupport validationSupport = new CachingValidationSupport(validationSupportChain);
// Create a validator. Note that for good performance you can create as many validator objects
// as you like, but you should reuse the same validation support object in all of the,.
FhirValidator validator = ctx.newValidator();
FhirInstanceValidator instanceValidator = new FhirInstanceValidator(validationSupport);
validator.registerValidatorModule(instanceValidator);
// Create a test patient to validate
Patient patient = new Patient();
patient.getMeta().addProfile("https://fhir.nhs.uk/R4/StructureDefinition/UKCore-Patient");
// System but not value set for NHS identifier (this should generate an error)
patient.addIdentifier().setSystem("https://fhir.nhs.uk/Id/nhs-number");
// Perform the validation
ValidationResult outcome = validator.validateWithResult(patient);
// END SNIPPET: npm
}
}
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