Validation documentation
This commit is contained in:
jamesagnew
parent
f3e44eea3b
commit
773608f860
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@ -30,6 +30,11 @@
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<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
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<version>1.2-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
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<version>1.2-SNAPSHOT</version>
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</dependency>
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<dependency>
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<groupId>javax.servlet</groupId>
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<artifactId>javax.servlet-api</artifactId>
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@ -8,17 +8,22 @@ import javax.servlet.ServletException;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.filefilter.WildcardFileFilter;
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import org.hl7.fhir.instance.model.ValueSet;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.dstu2.resource.Observation;
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import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.model.dstu2.valueset.ContactPointSystemEnum;
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import ca.uhn.fhir.model.primitive.StringDt;
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import ca.uhn.fhir.parser.IParser;
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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.FhirInstanceValidator;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.IValidationSupport;
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import ca.uhn.fhir.validation.SingleValidationMessage;
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import ca.uhn.fhir.validation.ValidationResult;
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@ -114,10 +119,88 @@ public class ValidatorExamples {
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}
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public static void main(String[] args) throws Exception {
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validateFiles();
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instanceValidator();
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}
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private static void instanceValidator() throws Exception {
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// START SNIPPET: instanceValidator
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FhirContext ctx = FhirContext.forDstu2();
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// Create a FhirInstanceValidator and register it to a validator
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FhirValidator validator = ctx.newValidator();
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FhirInstanceValidator instanceValidator = new FhirInstanceValidator();
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validator.registerValidatorModule(instanceValidator);
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/*
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* Let's create a resource to validate. This Observation has some fields
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* populated, but it is missing Observation.status, which is mandatory.
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*/
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Observation obs = new Observation();
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obs.getCode().addCoding().setSystem("http://loinc.org").setCode("12345-6");
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obs.setValue(new StringDt("This is a value"));
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// Validate
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ValidationResult result = validator.validateWithResult(obs);
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// Do we have any errors or fatal errors?
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System.out.println(result.isSuccessful()); // false
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// Show the issues
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for (SingleValidationMessage next : result.getMessages()) {
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System.out.println(" Next issue " + next.getSeverity() + " - " + next.getLocationString() + " - " + next.getMessage());
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}
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// Prints:
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// Next issue ERROR - /f:Observation - Element '/f:Observation.status': minimum required = 1, but only found 0
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// Next issue WARNING - /f:Observation/f:code - Unable to validate code "12345-6" in code system "http://loinc.org"
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// You can also convert the result into an operation outcome if you
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// need to return one from a server
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OperationOutcome oo = (OperationOutcome) result.toOperationOutcome();
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// END SNIPPET: instanceValidator
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}
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private static void instanceValidatorCustom() throws Exception {
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// START SNIPPET: instanceValidatorCustom
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FhirContext ctx = FhirContext.forDstu2();
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// Create a FhirInstanceValidator and register it to a validator
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FhirValidator validator = ctx.newValidator();
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FhirInstanceValidator instanceValidator = new FhirInstanceValidator();
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validator.registerValidatorModule(instanceValidator);
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IValidationSupport valSupport = new IValidationSupport() {
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@Override
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public org.hl7.fhir.instance.utils.IWorkerContext.ValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
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// TODO: Implement
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return null;
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}
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@Override
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public boolean isCodeSystemSupported(String theSystem) {
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// TODO: Implement
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return false;
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}
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@Override
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public <T extends IBaseResource> T fetchResource(FhirContext theContext, Class<T> theClass, String theUri) {
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// TODO: Implement
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return null;
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}
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@Override
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public ValueSet fetchCodeSystem(String theSystem) {
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// TODO: Implement
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return null;
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}
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};
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instanceValidator.setValidationSupport(valSupport);
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// END SNIPPET: instanceValidatorCustom
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}
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@SuppressWarnings("unused")
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private static void validateFiles() throws Exception {
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// START SNIPPET: validateFiles
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FhirContext ctx = FhirContext.forDstu2();
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@ -54,14 +54,13 @@ public class FhirValidator {
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private static volatile Boolean ourPhlocPresentOnClasspath;
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private final FhirContext myContext;
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private volatile List<IValidatorModule> myValidators = new ArrayList<IValidatorModule>();
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private List<IValidatorModule> myValidators = new ArrayList<IValidatorModule>();
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/**
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* Constructor (this should not be called directly, but rather {@link FhirContext#newValidator()} should be called to obtain an instance of {@link FhirValidator})
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*/
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public FhirValidator(FhirContext theFhirContext) {
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myContext = theFhirContext;
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setValidateAgainstStandardSchema(true);
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if (ourPhlocPresentOnClasspath == null) {
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try {
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@ -72,10 +71,6 @@ public class FhirValidator {
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ourPhlocPresentOnClasspath = false;
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}
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}
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if (ourPhlocPresentOnClasspath) {
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setValidateAgainstStandardSchematron(true);
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}
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}
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private void addOrRemoveValidator(boolean theValidateAgainstStandardSchema, Class<? extends IValidatorModule> type, IValidatorModule theInstance) {
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@ -183,7 +178,9 @@ public class FhirValidator {
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@Deprecated
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public void validate(Bundle theBundle) {
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Validate.notNull(theBundle, "theBundle must not be null");
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applyDefaultValidators();
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IValidationContext<Bundle> ctx = ValidationContext.forBundle(myContext, theBundle);
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for (IValidatorModule next : myValidators) {
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@ -197,6 +194,15 @@ public class FhirValidator {
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}
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private void applyDefaultValidators() {
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if (myValidators.isEmpty()) {
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setValidateAgainstStandardSchema(true);
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if (ourPhlocPresentOnClasspath) {
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setValidateAgainstStandardSchematron(true);
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}
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}
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}
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/**
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* Validates a resource instance, throwing a {@link ValidationFailureException} if the validation fails
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*
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*/
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@Deprecated
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public void validate(IResource theResource) throws ValidationFailureException {
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applyDefaultValidators();
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ValidationResult validationResult = validateWithResult(theResource);
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if (!validationResult.isSuccessful()) {
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throw new ValidationFailureException(myContext, validationResult.toOperationOutcome());
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@ -224,7 +233,9 @@ public class FhirValidator {
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*/
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public ValidationResult validateWithResult(Bundle theBundle) {
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Validate.notNull(theBundle, "theBundle must not be null");
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applyDefaultValidators();
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IValidationContext<Bundle> ctx = ValidationContext.forBundle(myContext, theBundle);
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for (IValidatorModule next : myValidators) {
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@ -244,7 +255,9 @@ public class FhirValidator {
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*/
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public ValidationResult validateWithResult(IBaseResource theResource) {
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Validate.notNull(theResource, "theResource must not be null");
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applyDefaultValidators();
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IValidationContext<IBaseResource> ctx = ValidationContext.forResource(myContext, theResource);
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for (IValidatorModule next : myValidators) {
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@ -264,7 +277,9 @@ public class FhirValidator {
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*/
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public ValidationResult validateWithResult(String theResource) {
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Validate.notNull(theResource, "theResource must not be null");
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applyDefaultValidators();
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IValidationContext<IBaseResource> ctx = ValidationContext.forText(myContext, theResource);
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for (IValidatorModule next : myValidators) {
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@ -59,7 +59,10 @@ public class ValidationResult {
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}
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/**
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* Was the validation successful
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* Was the validation successful (in other words, do we have no issues that are at
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* severity {@link ResultSeverityEnum#ERROR} or {@link ResultSeverityEnum#FATAL}. A validation
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* is still considered successful if it only has issues at level {@link ResultSeverityEnum#WARNING} or
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* lower.
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*
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* @return true if the validation was successful
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*/
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@ -93,10 +93,17 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
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/**
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* Returns the "best practice" warning level (default is
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* {@link BestPracticeWarningLevel#Hint})
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* {@link BestPracticeWarningLevel#Hint}).
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* <p>
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* The FHIR Instance Validator has
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* a number of checks for best practices in terms of FHIR usage. If this setting
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* is set to {@link BestPracticeWarningLevel#Error}, any resource data which does not
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* meet these best practices will be reported at the ERROR level. If this setting
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* is set to {@link BestPracticeWarningLevel#Ignore}, best practice guielines will
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* be ignored.
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* </p>
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*
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* @see #setBestPracticeWarningLevel(BestPracticeWarningLevel) for more
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* information on this value
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* @see {@link #setBestPracticeWarningLevel(BestPracticeWarningLevel)}
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*/
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public BestPracticeWarningLevel getBestPracticeWarningLevel() {
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return myBestPracticeWarningLevel;
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@ -115,10 +122,14 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
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/**
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* Sets the "best practice warning level". When validating, any deviations
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* from best practices will be reported at this level.
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* {@link BestPracticeWarningLevel#Ignore} means that best practice deviations
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* will not be reported, {@link BestPracticeWarningLevel#Warning} means that
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* best practice deviations will be reported as warnings, etc. Default is
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* {@link BestPracticeWarningLevel#Hint}
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* <p>
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* The FHIR Instance Validator has
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* a number of checks for best practices in terms of FHIR usage. If this setting
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* is set to {@link BestPracticeWarningLevel#Error}, any resource data which does not
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* meet these best practices will be reported at the ERROR level. If this setting
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* is set to {@link BestPracticeWarningLevel#Ignore}, best practice guielines will
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* be ignored.
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* </p>
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*
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* @param theBestPracticeWarningLevel
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* The level, must not be <code>null</code>
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@ -163,7 +163,7 @@
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Use the HAPI FHIR client in an application to fetch from or store
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resources to an external server.
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<br />
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<a href="./doc_rest_client.html">Learn Mode</a>
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<a href="/hapi-fhir/doc_rest_client.html">Learn Mode</a>
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</div></div></foreignObject>
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<text x="73" y="45" fill="#4D4D4D" text-anchor="middle"
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font-size="12px" font-family="Helvetica">[Not supported by viewer]</text>
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@ -266,7 +266,7 @@
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Use the HAPI FHIR server in an application to allow external
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applications to access or modify your application's data.
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<br />
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<a href="./doc_rest_server.html">Learn More</a>
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<a href="/hapi-fhir/doc_rest_server.html">Learn More</a>
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<br />
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</div></div></foreignObject>
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<text x="73" y="53" fill="#4D4D4D" text-anchor="middle"
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@ -382,7 +382,7 @@
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Use the HAPI JPA/Database Server to deploy a fully functional FHIR
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server you can develop applications against.
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<br />
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<a href="./doc_jpa.html">Learn More</a>
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<a href="/hapi-fhir/doc_jpa.html">Learn More</a>
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</div></div></foreignObject>
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<text x="73" y="59" fill="#4D4D4D" text-anchor="middle"
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font-size="12px" font-family="Helvetica">[Not supported by viewer]</text>
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@ -572,7 +572,7 @@
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Use the HAPI FHIR parser and encoder to convert between FHIR and
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your application's data model.
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<br />
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<a href="./doc_fhirobjects.html">Learn More</a>
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<a href="/hapi-fhir/doc_fhirobjects.html">Learn More</a>
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</div></div></foreignObject>
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<text x="73" y="45" fill="#4D4D4D" text-anchor="middle"
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font-size="12px" font-family="Helvetica">[Not supported by viewer]</text>
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@ -591,4 +591,4 @@
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<path d="M 565 399 C 565 407 595 407 595 399" fill="none" stroke="#666666"
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stroke-miterlimit="10" pointer-events="none" />
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</g>
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</svg>
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</svg>
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Before Width: | Height: | Size: 32 KiB After Width: | Height: | Size: 32 KiB |
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@ -120,6 +120,8 @@
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<item name="Core API" href="./apidocs/index.html" />
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<item name="Model API (DSTU1)" href="./apidocs-dstu/index.html" />
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<item name="Model API (DSTU2)" href="./apidocs-dstu2/index.html" />
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<item name="Model API (RI DSTU2)" href="./apidocs-hl7org-dstu2/index.html" />
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<item name="JPA Server API" href="./apidocs-jpaserver/index.html" />
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</menu>
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<menu name="JXR" inherit="top">
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<item name="Core" href="./xref-base/index.html" />
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@ -1,6 +1,5 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
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<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
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<properties>
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<title>Validation</title>
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@ -9,70 +8,82 @@
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<body>
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<section name="Validation">
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<p>
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HAPI supportes two types of validation, both of which are described in the
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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>Parser Validation</b> is validation at runtime during the parsing
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<b>Parser Validation</b>
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is validation at runtime during the parsing
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of a resource. It can be used to catch input data that is impossible to
|
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fit into the HAPI data model. For example, it can be used to throw exceptions
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fit into the HAPI data model. For
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example, it can be used to throw exceptions
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or display error messages if a resource being parsed contains tags for which
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there are no appropriate fields in a HAPI data structure.
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</li>
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<li>
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<b>Resource Validation</b> is validation of the parsed (or constructed) resource against
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<b>Resource Validation</b>
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is validation of the parsed (or constructed) resource against
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the official FHIR validation rules (e.g. Schema/Schematron).
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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 <code>setParserErrorHandler(IParserErrorHandler)</code> on
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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 <code>IParserErrorHandler</code>, which is a callback that
|
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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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<p>
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There are two implementations of <code>IParserErrorHandler</code> worth
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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 ignore issues.
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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 <code>DataFormatException</code> if any errors are detected.
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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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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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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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||||
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||||
<p>
|
||||
FhirContext level validators can also be useful on servers.
|
||||
FhirContext level validators can also be useful on servers.
|
||||
</p>
|
||||
<macro name="snippet">
|
||||
<param name="id" value="serverValidation" />
|
||||
|
|
@ -87,7 +98,9 @@
|
|||
|
||||
<p>
|
||||
HAPI provides a built-in and configurable mechanism for validating resources.
|
||||
This mechanism is called the <i>Resource Validator</i>.
|
||||
This mechanism is called the
|
||||
<i>Resource Validator</i>
|
||||
.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
|
|
@ -102,38 +115,42 @@
|
|||
</p>
|
||||
|
||||
<subsection name="Preparation">
|
||||
|
||||
|
||||
<p>
|
||||
In order to use HAPI's Schematron support, a libaray called
|
||||
In order to use HAPI's Schematron support, a libaray called
|
||||
<a href="https://code.google.com/p/phloc-schematron/">Phloc-Schematron</a>
|
||||
is used, so this library must be added to your classpath (or Maven POM file, Gradle
|
||||
file, etc.)
|
||||
Note that this library is specified as an optional dependency by HAPI FHIR
|
||||
Note that this library is specified as an optional dependency
|
||||
by HAPI FHIR
|
||||
so you need to explicitly include it if you want to use this
|
||||
functionality.
|
||||
functionality.
|
||||
</p>
|
||||
<p>
|
||||
See <a href="./download.html">Downloads</a> for more information on how
|
||||
See
|
||||
<a href="./download.html">Downloads</a>
|
||||
for more information on how
|
||||
to add it.
|
||||
</p>
|
||||
</subsection>
|
||||
|
||||
|
||||
<subsection name="Validating a Resource">
|
||||
|
||||
|
||||
<p>
|
||||
To validate a resource instance, a new validator instance is requested
|
||||
from the FHIR Context. This validator is then applied against
|
||||
a specific resource instance, as shown in the example below.
|
||||
a specific resource
|
||||
instance, as shown in the example below.
|
||||
</p>
|
||||
<macro name="snippet">
|
||||
<param name="id" value="basicValidation" />
|
||||
<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
|
||||
</macro>
|
||||
|
||||
|
||||
</subsection>
|
||||
|
||||
<subsection name="Validating a Set of Files">
|
||||
|
||||
|
||||
<p>
|
||||
The following example shows how to load a set of resources from files
|
||||
on disk and validate each one.
|
||||
|
|
@ -142,51 +159,100 @@
|
|||
<param name="id" value="validateFiles" />
|
||||
<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
|
||||
</macro>
|
||||
|
||||
|
||||
</subsection>
|
||||
|
||||
<a name="structure_definition_validation"/>
|
||||
<a name="structure_definition_validation" />
|
||||
</section>
|
||||
|
||||
<section name="Resource Validation (StructureDefinition / ValueSet)">
|
||||
|
||||
|
||||
<section name="Resource Validation (Profile/StructureDefinition)">
|
||||
|
||||
<p>
|
||||
As of HAPI FHIR 1.2, HAPI supports validation against StructureDefinition
|
||||
resources. This functionality uses the HL7 "InstanceValidator", which is able
|
||||
to check a resource for conformance to a given profile (StructureDefinition),
|
||||
including validating codes for conformance to their given ValueSets.
|
||||
to
|
||||
check a resource for conformance to a given profile
|
||||
(StructureDefinitions and ValueSets),
|
||||
including validating fields, extensions, and codes for conformance to their given ValueSets.
|
||||
</p>
|
||||
<p>
|
||||
StructureDefinition validation can be used to validate a resource against the
|
||||
official structure definitions (produced by HL7) as well as against custom
|
||||
definitions provided either by HL7 or by the user.
|
||||
</p>
|
||||
|
||||
|
||||
<subsection name="Preparation">
|
||||
|
||||
|
||||
<p>
|
||||
To use this functionality, you must add the following two dependencies
|
||||
to your classpath (or Maven POM file, Gradle file, etc.):
|
||||
to your classpath (or Maven POM file, Gradle file, etc.):
|
||||
</p>
|
||||
<ul>
|
||||
<li>
|
||||
<b>hapi-fhir-structures-hl7org-dstu2</b>: This file contains the "reference implementation"
|
||||
structures and tooling. You need to include it even if you are not using the RI model
|
||||
<b>hapi-fhir-structures-hl7org-dstu2</b>
|
||||
: This file contains the "reference implementation"
|
||||
structures and tooling. You need to include it even if you are not using the RI model
|
||||
(the StructureDefinition validation will work against HAPI structures as well)
|
||||
</li>
|
||||
<li>
|
||||
<b>hapi-fhir-validation-resources-dstu2</b>: This file contains the official FHIR
|
||||
<b>hapi-fhir-validation-resources-dstu2</b>
|
||||
: This file contains the official FHIR
|
||||
StructureDefinition files, and the ValueSets needed to support them.
|
||||
</li>
|
||||
</ul>
|
||||
<p>
|
||||
See the <a href="./download.html">download page</a> for more information.
|
||||
See the
|
||||
<a href="./download.html">download page</a>
|
||||
for more information.
|
||||
</p>
|
||||
|
||||
</subsection>
|
||||
|
||||
<subsection name="Running the Validator">
|
||||
|
||||
<p>
|
||||
To execute the validator, you simply create an instance of
|
||||
<a href="./apidocs-hl7org-dstu2/ca/uhn/fhir/validation/FhirInstanceValidator.html">FhirInstanceValidator</a>
|
||||
and register it to new validator, as shown in the example below.
|
||||
</p>
|
||||
|
||||
<p>
|
||||
Note that the example below uses the official FHIR StructureDefintions and ValueSets
|
||||
to validate the resource. It will not work unless you include the
|
||||
<code>hapi-fhir-validation-resources-[version].jar</code> to your classpath.
|
||||
</p>
|
||||
|
||||
<macro name="snippet">
|
||||
<param name="id" value="instanceValidator" />
|
||||
<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
|
||||
</macro>
|
||||
|
||||
</subsection>
|
||||
|
||||
<subsection name="Supplying your own StructureDefinitions">
|
||||
|
||||
<p>
|
||||
The FhirInstanceValidator relies on the
|
||||
<a href="./apidocs-hl7org-dstu2/ca/uhn/fhir/validation/IValidationSupport.html">IValidationSupport</a>
|
||||
interface to load StructureDefinitions, and validate codes.
|
||||
</p>
|
||||
<p>
|
||||
By default, the
|
||||
<a href="./apidocs-hl7org-dstu2/ca/uhn/fhir/validation/DefaultProfileValidationSupport.html">DefaultProfileValidationSupport</a>
|
||||
implementation is used. This implementation loads the FHIR profiles from the
|
||||
validator resources JAR. If you want to use your own profiles, you may wish to
|
||||
supply your own implementation.
|
||||
</p>
|
||||
|
||||
<macro name="snippet">
|
||||
<param name="id" value="instanceValidatorCustom" />
|
||||
<param name="file" value="examples/src/main/java/example/ValidatorExamples.java" />
|
||||
</macro>
|
||||
|
||||
</subsection>
|
||||
|
||||
</section>
|
||||
|
||||
|
||||
</body>
|
||||
|
||||
</document>
|
||||
|
|
|
|||
Loading…
Reference in New Issue