Improving validation documentation
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jamesagnew
parent
685bd9345b
commit
59da230702
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@ -29,12 +29,43 @@ import ca.uhn.fhir.parser.StrictErrorHandler;
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import ca.uhn.fhir.rest.client.IGenericClient;
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import ca.uhn.fhir.rest.server.RestfulServer;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.IValidatorModule;
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import ca.uhn.fhir.validation.SchemaBaseValidator;
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import ca.uhn.fhir.validation.SingleValidationMessage;
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import ca.uhn.fhir.validation.ValidationResult;
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import ca.uhn.fhir.validation.schematron.SchematronBaseValidator;
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@SuppressWarnings("serial")
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public class ValidatorExamples {
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public void validationIntro() {
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// START SNIPPET: validationIntro
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FhirContext ctx = FhirContext.forDstu2();
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// Ask the context for a validator
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FhirValidator validator = ctx.newValidator();
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// Create some modules and register them
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IValidatorModule module1 = new SchemaBaseValidator(ctx);
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validator.registerValidatorModule(module1);
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IValidatorModule module2 = new SchematronBaseValidator(ctx);
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validator.registerValidatorModule(module2);
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// Pass a resource in to be validated. The resource can
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// be an IBaseResource instance, or can be a raw String
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// containing a serialized resource as text.
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Patient resource = new Patient();
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ValidationResult result = validator.validateWithResult(resource);
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String resourceText = "<Patient.....>";
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ValidationResult result2 = validator.validateWithResult(resourceText);
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// The result object now contains the validation results
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for (SingleValidationMessage next : result.getMessages()) {
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System.out.println(next.getLocationString() + " " + next.getMessage());
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}
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// END SNIPPET: validationIntro
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}
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// START SNIPPET: serverValidation
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public class MyRestfulServer extends RestfulServer {
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@ -96,6 +127,15 @@ public class ValidatorExamples {
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// Request a validator and apply it
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FhirValidator val = ctx.newValidator();
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// Create the Schema/Schematron modules and register them. Note that
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// you might want to consider keeping these modules around as long-term
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// objects: they parse and then store schemas, which can be an expensive
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// operation.
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IValidatorModule module1 = new SchemaBaseValidator(ctx);
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IValidatorModule module2 = new SchematronBaseValidator(ctx);
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val.registerValidatorModule(module1);
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val.registerValidatorModule(module2);
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ValidationResult result = val.validateWithResult(p);
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if (result.isSuccessful()) {
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@ -26,12 +26,28 @@ import ca.uhn.fhir.model.api.Bundle;
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*/
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/**
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* Registers
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* An individual validation module, which applies validation rules against
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* resources and adds failure/informational messages as it goes.
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*
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* See <a href="http://jamesagnew.github.io/hapi-fhir/doc_validation.html">Validation</a>
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* for a list of available modules. You may also create your own.
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*/
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public interface IValidatorModule {
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/**
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* Validate the actual resource.
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*
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* The {@link IValidationContext} can be used to access the resource being validated,
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* and is populated with the results.
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*/
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void validateResource(IValidationContext<IBaseResource> theCtx);
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/**
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* This method applies only to DSTU1 Atom Bundles. All other validation will pass through
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* {@link #validateResource(IValidationContext)} inclusing DSTU2+ Bundle resources. If you
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* will not be validating DSTU1 Bundles, you may implement this method as
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* a NO-OP.
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*/
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void validateBundle(IValidationContext<Bundle> theContext);
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}
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@ -75,7 +75,7 @@ public class SchemaBaseValidator implements IValidatorModule {
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private Map<String, Schema> myKeyToSchema = new HashMap<String, Schema>();
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private FhirContext myCtx;
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SchemaBaseValidator(FhirContext theContext) {
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public SchemaBaseValidator(FhirContext theContext) {
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myCtx = theContext;
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}
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@ -11,8 +11,10 @@ import static org.mockito.Mockito.when;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.dstu21.hapi.validation.DefaultProfileValidationSupport;
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@ -51,9 +53,11 @@ public class FhirInstanceValidatorTest {
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private FhirValidator myVal;
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private ArrayList<String> myValidConcepts;
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private Set<String> myValidSystems = new HashSet<String>();
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private Map<String, ValueSetExpansionComponent> mySupportedCodeSystemsForExpansion;
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private void addValidConcept(String theSystem, String theCode) {
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myValidSystems.add(theSystem);
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myValidConcepts.add(theSystem + "___" + theCode);
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}
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@ -87,8 +91,8 @@ public class FhirInstanceValidatorTest {
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when(myMockSupport.isCodeSystemSupported(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<Boolean>() {
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@Override
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public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
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boolean retVal = mySupportedCodeSystemsForExpansion.containsKey(theInvocation.getArguments()[0]);
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ourLog.info("isCodeSystemSupported({}) : {}", new Object[] { theInvocation.getArguments()[0], retVal });
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boolean retVal = myValidSystems.contains(theInvocation.getArguments()[1]);
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ourLog.info("isCodeSystemSupported({}) : {}", new Object[] { theInvocation.getArguments()[1], retVal });
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return retVal;
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}
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});
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@ -289,6 +293,27 @@ public class FhirInstanceValidatorTest {
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assertThat(errors.toString(), containsString(""));
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}
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@Test
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public void testValidateResourceContainingLoincCode() {
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addValidConcept("http://loinc.org", "1234567");
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Observation input = new Observation();
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// input.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/devicemetricobservation");
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input.addIdentifier().setSystem("http://acme").setValue("12345");
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input.getEncounter().setReference("http://foo.com/Encounter/9");
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input.setStatus(ObservationStatus.FINAL);
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input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
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myInstanceVal.setValidationSupport(myMockSupport);
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ValidationResult output = myVal.validateWithResult(input);
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List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
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assertThat(errors.toString(), containsString("information"));
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assertThat(errors.toString(), containsString("Unknown code: http://loinc.org / 12345"));
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assertEquals(1, errors.size());
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}
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@Test
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public void testValidateResourceWithDefaultValueset() {
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Observation input = new Observation();
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@ -273,7 +273,9 @@
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</p>
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<p>
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See the <a href="./doc_validation.html">Validation Page</a> for information on
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available IValidationModule validation modules. Any of the <b>Resource Validators</b>
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available
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<a href="./apidocs/ca/uhn/fhir/validation/IValidatorModule.html">IValidatorModule</a>
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validation modules. Any of the <b>Resource Validators</b>
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listed on that page can be enabled in these interceptors (note that the <b>Parser Validators</b>
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can not).
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</p>
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@ -14,6 +14,12 @@
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sections below.
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</p>
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<ul>
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<li>
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<b>Resource Validation</b>
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is validation of the raw or parsed resource against
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the official FHIR validation rules (e.g. Schema/Schematron/Profile/StructureDefinition/ValueSet)
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as well as against custom profiles which have been developed.
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</li>
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<li>
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<b>Parser Validation</b>
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is validation at runtime during the parsing
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@ -25,85 +31,40 @@
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that no data is being lost during parsing, but is less comprehensive than resource validation
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against raw text data.
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</li>
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<li>
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<b>Resource Validation</b>
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is validation of the raw or parsed resource against
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the official FHIR validation rules (e.g. Schema/Schematron/Profile/StructureDefinition/ValueSet).
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</li>
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</ul>
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</section>
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<section name="Parser Validation">
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<p>
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Parser validation is controlled by calling
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<code>setParserErrorHandler(IParserErrorHandler)</code>
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on
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either the FhirContext or on individual parser instances. This method
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takes an
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<code>IParserErrorHandler</code>
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, which is a callback that
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will be invoked any time a parse issue is detected.
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</p>
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<p>
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There are two implementations of
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<code>IParserErrorHandler</code>
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worth
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mentioning. You can also supply your own implementation if you want.
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</p>
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<ul>
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<li>
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<a href="./apidocs/ca/uhn/fhir/parser/LenientErrorHandler.html">LenientErrorHandler</a>
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logs any errors but does not abort parsing. By default this handler is used, and it
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logs errors at "warning" level. It can also be configured to silently
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ignore issues.
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</li>
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<li>
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<a href="./apidocs/ca/uhn/fhir/parser/StrictErrorHandler.html">StrictErrorHandler</a>
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throws a
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<code>DataFormatException</code>
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if any errors are detected.
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</li>
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</ul>
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<p>
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The following example shows how to configure a parser to use strict validation.
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</p>
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<macro name="snippet">
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<param name="id" value="parserValidation" />
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<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
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</macro>
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<p>
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You can also configure the error handler at the FhirContext level, which is useful
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for clients.
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</p>
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<macro name="snippet">
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<param name="id" value="clientValidation" />
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<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
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</macro>
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<p>
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FhirContext level validators can also be useful on servers.
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</p>
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<macro name="snippet">
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<param name="id" value="serverValidation" />
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<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
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</macro>
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</section>
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<!-- RESOURCE VALIDATION -->
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<section name="Resource Validation (Schema/Schematron)">
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<section name="Resource Validation">
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<p>
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HAPI provides a built-in and configurable mechanism for validating resources.
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This mechanism is called the
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<i>Resource Validator</i>
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.
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<i>Resource Validator.</i>
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</p>
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<p>
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The resource validator is an extendible and modular system, and you
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can configure it in a number of ways in order to get the specific
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type of validation you want to achieve.
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</p>
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<p>
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The validator can be manually invoked at any time by creating a
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validator and configuring it with one or more
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<a href="./apidocs/ca/uhn/fhir/validation/IValidatorModule.html">IValidatorModule</a>
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instances.
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</p>
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<macro name="snippet">
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<param name="id" value="validationIntro" />
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<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
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</macro>
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</section>
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<section name="Resource Validation Module: Schema/Schematron">
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<p>
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FHIR resource definitions are distributed with a set of XML schema files (XSD)
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@ -262,6 +223,66 @@
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</section>
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<section name="Parser Validation">
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<p>
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Parser validation is controlled by calling
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<code>setParserErrorHandler(IParserErrorHandler)</code>
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on
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either the FhirContext or on individual parser instances. This method
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takes an
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<code>IParserErrorHandler</code>
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, which is a callback that
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will be invoked any time a parse issue is detected.
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</p>
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<p>
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There are two implementations of
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<code>IParserErrorHandler</code>
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worth
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mentioning. You can also supply your own implementation if you want.
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</p>
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<ul>
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<li>
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<a href="./apidocs/ca/uhn/fhir/parser/LenientErrorHandler.html">LenientErrorHandler</a>
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logs any errors but does not abort parsing. By default this handler is used, and it
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logs errors at "warning" level. It can also be configured to silently
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ignore issues.
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</li>
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<li>
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<a href="./apidocs/ca/uhn/fhir/parser/StrictErrorHandler.html">StrictErrorHandler</a>
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throws a
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<code>DataFormatException</code>
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if any errors are detected.
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</li>
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</ul>
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<p>
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The following example shows how to configure a parser to use strict validation.
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</p>
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<macro name="snippet">
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<param name="id" value="parserValidation" />
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<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
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</macro>
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<p>
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You can also configure the error handler at the FhirContext level, which is useful
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for clients.
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</p>
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<macro name="snippet">
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<param name="id" value="clientValidation" />
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<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
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</macro>
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<p>
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FhirContext level validators can also be useful on servers.
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</p>
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<macro name="snippet">
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<param name="id" value="serverValidation" />
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<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
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</macro>
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</section>
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</body>
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</document>
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