package ca.uhn.fhir.validation;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import java.util.zip.GZIPInputStream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.hapi.validation.HapiWorkerContext;
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.IValidationSupport.CodeValidationResult;
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.dstu3.model.Base;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.ContactPoint;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.RelatedPerson;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestRule;
import org.junit.rules.TestWatcher;
import org.junit.runner.Description;
import org.mockito.invocation.InvocationOnMock;
import org.mockito.stubbing.Answer;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.util.TestUtil;
public class FhirInstanceValidatorDstu3Test {
private static DefaultProfileValidationSupport myDefaultValidationSupport = new DefaultProfileValidationSupport();
private static FhirContext ourCtx = FhirContext.forDstu3();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorDstu3Test.class);
private FhirInstanceValidator myInstanceVal;
private IValidationSupport myMockSupport;
private Map<String, ValueSetExpansionComponent> mySupportedCodeSystemsForExpansion;
private FhirValidator myVal;
private ArrayList<String> myValidConcepts;
private Set<String> myValidSystems = new HashSet<String>();
@Rule
public TestRule watcher = new TestWatcher() {
protected void starting(Description description) {
ourLog.info("Starting test: " + description.getMethodName());
}
};
private void addValidConcept(String theSystem, String theCode) {
myValidSystems.add(theSystem);
myValidConcepts.add(theSystem + "___" + theCode);
}
/**
* See #531
*/
@Test
public void testContactPointSystemUrlWorks() {
Patient p = new Patient();
ContactPoint t = p.addTelecom();
t.setSystem(org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem.URL);
t.setValue("http://infoway-inforoute.ca");
ValidationResult results = myVal.validateWithResult(p);
List<SingleValidationMessage> outcome = logResultsAndReturnNonInformationalOnes(results);
assertThat(outcome, empty());
}
/**
* See #370
*/
@Test
public void testValidateRelatedPerson() {
/*
* Try with a code that is in http://hl7.org/fhir/ValueSet/relatedperson-relationshiptype
* and therefore should validate
*/
RelatedPerson rp = new RelatedPerson();
rp.getPatient().setReference("Patient/1");
rp.getRelationship().addCoding().setSystem("http://hl7.org/fhir/v2/0131").setCode("c");
ValidationResult results = myVal.validateWithResult(rp);
List<SingleValidationMessage> outcome = logResultsAndReturnNonInformationalOnes(results);
assertThat(outcome, empty());
/*
* Code system is case insensitive, so try with capital C
*/
rp = new RelatedPerson();
rp.getPatient().setReference("Patient/1");
rp.getRelationship().addCoding().setSystem("http://hl7.org/fhir/v2/0131").setCode("C");
results = myVal.validateWithResult(rp);
outcome = logResultsAndReturnNonInformationalOnes(results);
assertThat(outcome, empty());
/*
* Now a bad code
*/
rp = new RelatedPerson();
rp.getPatient().setReference("Patient/1");
rp.getRelationship().addCoding().setSystem("http://hl7.org/fhir/v2/0131").setCode("GAGAGAGA");
results = myVal.validateWithResult(rp);
outcome = logResultsAndReturnNonInformationalOnes(results);
assertThat(outcome, not(empty()));
}
@Test
// @Ignore
public void testValidateBuiltInProfiles() throws Exception {
org.hl7.fhir.dstu3.model.Bundle bundle;
String name = "profiles-resources";
ourLog.info("Uploading " + name);
String vsContents;
vsContents = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/org/hl7/fhir/instance/model/dstu3/profile/" + name + ".xml"), "UTF-8");
TreeSet<String> ids = new TreeSet<String>();
bundle = ourCtx.newXmlParser().parseResource(org.hl7.fhir.dstu3.model.Bundle.class, vsContents);
for (BundleEntryComponent i : bundle.getEntry()) {
org.hl7.fhir.dstu3.model.Resource next = i.getResource();
ids.add(next.getId());
if (next instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) next;
if (sd.getKind() == StructureDefinitionKind.LOGICAL) {
ourLog.info("Skipping logical type: {}", next.getId());
continue;
}
}
ourLog.info("Validating {}", next.getId());
ourLog.trace(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(next));
ValidationResult output = myVal.validateWithResult(next);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat("Failed to validate " + i.getFullUrl() + " - " + errors, errors, empty());
}
ourLog.info("Validated the following:\n{}", ids);
}
/**
* FHIRPathEngine was throwing Error...
*/
@Test
public void testValidateCrucibleCarePlan() throws Exception {
org.hl7.fhir.dstu3.model.Bundle bundle;
String name = "profiles-resources";
ourLog.info("Uploading " + name);
String vsContents;
vsContents = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/crucible-condition.xml"), "UTF-8");
ValidationResult output = myVal.validateWithResult(vsContents);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
}
@Test
@Ignore
public void testValidateBundleWithObservations() throws Exception {
String name = "profiles-resources";
ourLog.info("Uploading " + name);
String inputString;
inputString = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/brian_reinhold_bundle.json"), "UTF-8");
Bundle bundle = ourCtx.newJsonParser().parseResource(Bundle.class, inputString);
FHIRPathEngine fp = new FHIRPathEngine(new HapiWorkerContext(ourCtx, myDefaultValidationSupport));
List<Base> fpOutput;
BooleanType bool;
fpOutput = fp.evaluate(bundle.getEntry().get(0).getResource(), "component.where(code = %resource.code).empty()");
assertEquals(1, fpOutput.size());
bool = (BooleanType) fpOutput.get(0);
assertTrue(bool.getValue());
//
// fpOutput = fp.evaluate(bundle, "component.where(code = %resource.code).empty()");
// assertEquals(1, fpOutput.size());
// bool = (BooleanType) fpOutput.get(0);
// assertTrue(bool.getValue());
ValidationResult output = myVal.validateWithResult(inputString);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat(errors, empty());
}
@Test
public void testValidateDocument() throws Exception {
String vsContents = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/sample-document.xml"), "UTF-8");
ValidationResult output = myVal.validateWithResult(vsContents);
logResultsAndReturnNonInformationalOnes(output);
assertTrue(output.isSuccessful());
}
@SuppressWarnings("unchecked")
@Before
public void before() {
myVal = ourCtx.newValidator();
myVal.setValidateAgainstStandardSchema(false);
myVal.setValidateAgainstStandardSchematron(false);
myMockSupport = mock(IValidationSupport.class);
ValidationSupportChain validationSupport = new ValidationSupportChain(myMockSupport, myDefaultValidationSupport);
myInstanceVal = new FhirInstanceValidator(validationSupport);
myVal.registerValidatorModule(myInstanceVal);
mySupportedCodeSystemsForExpansion = new HashMap<String, ValueSet.ValueSetExpansionComponent>();
myValidConcepts = new ArrayList<String>();
when(myMockSupport.expandValueSet(any(FhirContext.class), any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
@Override
public ValueSetExpansionComponent answer(InvocationOnMock theInvocation) throws Throwable {
ConceptSetComponent arg = (ConceptSetComponent) theInvocation.getArguments()[0];
ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem());
if (retVal == null) {
retVal = myDefaultValidationSupport.expandValueSet(any(FhirContext.class), arg);
}
ourLog.debug("expandValueSet({}) : {}", new Object[] { theInvocation.getArguments()[0], retVal });
return retVal;
}
});
when(myMockSupport.isCodeSystemSupported(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<Boolean>() {
@Override
public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
boolean retVal = myValidSystems.contains(theInvocation.getArguments()[1]);
ourLog.debug("isCodeSystemSupported({}) : {}", new Object[] { theInvocation.getArguments()[1], retVal });
return retVal;
}
});
when(myMockSupport.fetchResource(any(FhirContext.class), any(Class.class), any(String.class))).thenAnswer(new Answer<IBaseResource>() {
@Override
public IBaseResource answer(InvocationOnMock theInvocation) throws Throwable {
IBaseResource retVal;
String id = (String) theInvocation.getArguments()[2];
if ("Questionnaire/q_jon".equals(id)) {
retVal = ourCtx.newJsonParser().parseResource(IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/q_jon.json")));
} else {
retVal = myDefaultValidationSupport.fetchResource((FhirContext) theInvocation.getArguments()[0], (Class<IBaseResource>) theInvocation.getArguments()[1], id);
}
ourLog.debug("fetchResource({}, {}) : {}", new Object[] { theInvocation.getArguments()[1], id, retVal });
return retVal;
}
});
when(myMockSupport.validateCode(any(FhirContext.class), any(String.class), any(String.class), any(String.class))).thenAnswer(new Answer<CodeValidationResult>() {
@Override
public CodeValidationResult answer(InvocationOnMock theInvocation) throws Throwable {
FhirContext ctx = (FhirContext) theInvocation.getArguments()[0];
String system = (String) theInvocation.getArguments()[1];
String code = (String) theInvocation.getArguments()[2];
CodeValidationResult retVal;
if (myValidConcepts.contains(system + "___" + code)) {
retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
} else {
retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
}
ourLog.debug("validateCode({}, {}, {}) : {}", new Object[] { system, code, (String) theInvocation.getArguments()[2], retVal });
return retVal;
}
});
when(myMockSupport.fetchCodeSystem(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<CodeSystem>() {
@Override
public CodeSystem answer(InvocationOnMock theInvocation) throws Throwable {
CodeSystem retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0], (String) theInvocation.getArguments()[1]);
ourLog.debug("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[1], retVal });
return retVal;
}
});
when(myMockSupport.fetchStructureDefinition(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<StructureDefinition>() {
@Override
public StructureDefinition answer(InvocationOnMock theInvocation) throws Throwable {
StructureDefinition retVal = myDefaultValidationSupport.fetchStructureDefinition((FhirContext) theInvocation.getArguments()[0], (String) theInvocation.getArguments()[1]);
ourLog.debug("fetchStructureDefinition({}) : {}", new Object[] { (String) theInvocation.getArguments()[1], retVal });
return retVal;
}
});
when(myMockSupport.fetchAllStructureDefinitions(any(FhirContext.class))).thenAnswer(new Answer<List<StructureDefinition>>() {
@Override
public List<StructureDefinition> answer(InvocationOnMock theInvocation) throws Throwable {
List<StructureDefinition> retVal = myDefaultValidationSupport.fetchAllStructureDefinitions((FhirContext) theInvocation.getArguments()[0]);
ourLog.debug("fetchAllStructureDefinitions()", new Object[] {});
return retVal;
}
});
}
private Object defaultString(Integer theLocationLine) {
return theLocationLine != null ? theLocationLine.toString() : "";
}
private List<SingleValidationMessage> logResultsAndReturnAll(ValidationResult theOutput) {
List<SingleValidationMessage> retVal = new ArrayList<SingleValidationMessage>();
int index = 0;
for (SingleValidationMessage next : theOutput.getMessages()) {
ourLog.info("Result {}: {} - {}:{} {} - {}",
new Object[] { index, next.getSeverity(), defaultString(next.getLocationLine()), defaultString(next.getLocationCol()), next.getLocationString(), next.getMessage() });
index++;
retVal.add(next);
}
return retVal;
}
private List<SingleValidationMessage> logResultsAndReturnNonInformationalOnes(ValidationResult theOutput) {
List<SingleValidationMessage> retVal = new ArrayList<SingleValidationMessage>();
int index = 0;
for (SingleValidationMessage next : theOutput.getMessages()) {
ourLog.info("Result {}: {} - {} - {}", new Object[] { index, next.getSeverity(), next.getLocationString(), next.getMessage() });
index++;
if (next.getSeverity() != ResultSeverityEnum.INFORMATION) {
retVal.add(next);
}
}
return retVal;
}
@Test
public void testValidateBigRawJsonResource() throws Exception {
InputStream stream = FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/conformance.json.gz");
stream = new GZIPInputStream(stream);
String input = IOUtils.toString(stream);
long start = System.currentTimeMillis();
ValidationResult output = null;
int passes = 1;
for (int i = 0; i < passes; i++) {
ourLog.info("Pass {}", i + 1);
output = myVal.validateWithResult(input);
}
long delay = System.currentTimeMillis() - start;
long per = delay / passes;
logResultsAndReturnAll(output);
ourLog.info("Took {} ms -- {}ms / pass", delay, per);
}
@Test
public void testValidateQuestionnaireResponse() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/qr_jon.xml"));
ValidationResult output = myVal.validateWithResult(input);
logResultsAndReturnAll(output);
assertThat(output.getMessages().toString(), containsString("Items not of type group should not have items - Item with linkId 5.1 of type BOOLEAN has 1 item(s)"));
}
@Test
public void testValidateRawJsonResource() {
//@formatter:off
String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"" + "}";
//@formatter:on
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.toString(), 0, output.getMessages().size());
}
@Test
public void testValidateRawJsonResourceWithUnknownExtension() {
Patient patient = new Patient();
patient.setId("1");
Extension ext = patient.addExtension();
ext.setUrl("http://hl7.org/fhir/v3/ethnicity");
ext.setValue(new CodeType("Hispanic or Latino"));
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
ourLog.info(encoded);
/*
* {
* "resourceType": "Patient",
* "id": "1",
* "extension": [
* {
* "url": "http://hl7.org/fhir/v3/ethnicity",
* "valueCode": "Hispanic or Latino"
* }
* ]
* }
*/
ValidationResult output = myVal.validateWithResult(encoded);
assertEquals(output.toString(), 1, output.getMessages().size());
assertEquals("Unknown extension http://hl7.org/fhir/v3/ethnicity", output.getMessages().get(0).getMessage());
assertEquals(ResultSeverityEnum.INFORMATION, output.getMessages().get(0).getSeverity());
}
@Test
public void testValidateRawJsonResourceWithUnknownExtensionNotAllowed() {
Patient patient = new Patient();
patient.setId("1");
Extension ext = patient.addExtension();
ext.setUrl("http://hl7.org/fhir/v3/ethnicity");
ext.setValue(new CodeType("Hispanic or Latino"));
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
ourLog.info(encoded);
/*
* {
* "resourceType": "Patient",
* "id": "1",
* "extension": [
* {
* "url": "http://hl7.org/fhir/v3/ethnicity",
* "valueCode": "Hispanic or Latino"
* }
* ]
* }
*/
myInstanceVal.setAnyExtensionsAllowed(false);
ValidationResult output = myVal.validateWithResult(encoded);
assertEquals(output.toString(), 1, output.getMessages().size());
assertEquals("The extension http://hl7.org/fhir/v3/ethnicity is unknown, and not allowed here", output.getMessages().get(0).getMessage());
assertEquals(ResultSeverityEnum.ERROR, output.getMessages().get(0).getSeverity());
}
@Test
public void testValidateRawXmlWithMissingRootNamespace() {
//@formatter:off
String input = ""
+ "<Patient>"
+ " <text>"
+ " <status value=\"generated\"/>"
+ " <div xmlns=\"http://www.w3.org/1999/xhtml\">Some narrative</div>"
+ " </text>"
+ " <name>"
+ " <use value=\"official\"/>"
+ " <family value=\"Doe\"/>"
+ " <given value=\"John\"/>"
+ " </name>"
+ " <gender value=\"male\"/>"
+ " <birthDate value=\"1974-12-25\"/>"
+ "</Patient>";
//@formatter:on
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.toString(), 1, output.getMessages().size());
assertEquals("This cannot be parsed as a FHIR object (no namespace)", output.getMessages().get(0).getMessage());
ourLog.info(output.getMessages().get(0).getLocationString());
}
@Test
public void testValidateRawJsonResourceBadAttributes() {
//@formatter:off
String input =
"{" +
"\"resourceType\":\"Patient\"," +
"\"id\":\"123\"," +
"\"foo\":\"123\"" +
"}";
//@formatter:on
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.toString(), 1, output.getMessages().size());
ourLog.info(output.getMessages().get(0).getLocationString());
ourLog.info(output.getMessages().get(0).getMessage());
assertEquals("/Patient", output.getMessages().get(0).getLocationString());
assertEquals("Unrecognised property '@foo'", output.getMessages().get(0).getMessage());
}
@Test
public void testValidateRawJsonResourceFromExamples() throws Exception {
// @formatter:off
String input = IOUtils.toString(FhirInstanceValidator.class.getResourceAsStream("/testscript-search.json"));
// @formatter:on
ValidationResult output = myVal.validateWithResult(input);
logResultsAndReturnNonInformationalOnes(output);
// assertEquals(output.toString(), 1, output.getMessages().size());
// ourLog.info(output.getMessages().get(0).getLocationString());
// ourLog.info(output.getMessages().get(0).getMessage());
// assertEquals("/foo", output.getMessages().get(0).getLocationString());
// assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
}
@Test
public void testValidateRawXmlResource() {
// @formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "</Patient>";
// @formatter:on
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.toString(), 0, output.getMessages().size());
}
@Test
public void testValidateRawXmlResourceWithEmptyPrimitive() {
// @formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\"><name><given/></name></Patient>";
// @formatter:on
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.toString(), 2, output.getMessages().size());
assertThat(output.getMessages().get(0).getMessage(), containsString("Element must have some content"));
assertThat(output.getMessages().get(1).getMessage(), containsString("primitive types must have a value or must have child extensions"));
}
@Test
public void testValidateRawXmlResourceWithPrimitiveContainingOnlyAnExtension() {
// @formatter:off
String input = "<ActivityDefinition xmlns=\"http://hl7.org/fhir\">\n" +
" <id value=\"referralToMentalHealthCare\"/>\n" +
" <status value=\"draft\"/>\n" +
" <description value=\"refer to primary care mental-health integrated care program for evaluation and treatment of mental health conditions now\"/>\n" +
" <code>\n" +
" <coding>\n" +
" <!-- Error: Connection to http://localhost:960 refused -->\n" +
" <!--<system value=\"http://snomed.info/sct\"/>-->\n" +
" <code value=\"306206005\"/>\n" +
" </coding>\n" +
" </code>\n" +
" <!-- Specifying this this way results in a null reference exception in the validator -->\n" +
" <timingTiming>\n" +
" <event>\n" +
" <extension url=\"http://fhir.org/cql-expression\">\n" +
" <valueString value=\"Now()\"/>\n" +
" </extension>\n" +
" </event>\n" +
" </timingTiming>\n" +
" </ActivityDefinition>";
// @formatter:on
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> res = logResultsAndReturnNonInformationalOnes(output);
assertEquals(output.toString(), 0, res.size());
}
@Test
public void testValidateRawXmlResourceBadAttributes() {
//@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "<foo value=\"222\"/>"
+ "</Patient>";
//@formatter:on
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.toString(), 1, output.getMessages().size());
ourLog.info(output.getMessages().get(0).getLocationString());
ourLog.info(output.getMessages().get(0).getMessage());
assertEquals("/f:Patient", output.getMessages().get(0).getLocationString());
assertEquals("Undefined element 'foo\"", output.getMessages().get(0).getMessage());
}
@Test
public void testValidateResourceContainingLoincCode() {
addValidConcept("http://loinc.org", "1234567");
Observation input = new Observation();
// input.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/devicemetricobservation");
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getContext().setReference("http://foo.com/Encounter/9");
input.setStatus(ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertThat(errors.toString(), containsString("warning"));
assertThat(errors.toString(), containsString("Unknown code: http://loinc.org / 12345"));
}
@Test
public void testValidateResourceContainingProfileDeclaration() {
addValidConcept("http://loinc.org", "12345");
Observation input = new Observation();
input.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/devicemetricobservation");
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getContext().setReference("http://foo.com/Encounter/9");
input.setStatus(ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertThat(errors.toString(), containsString("Element 'Observation.subject': minimum required = 1, but only found 0"));
assertThat(errors.toString(), containsString("Element 'Observation.context: max allowed = 0, but found 1"));
assertThat(errors.toString(), containsString("Element 'Observation.device': minimum required = 1, but only found 0"));
assertThat(errors.toString(), containsString(""));
}
@Test
public void testValidateResourceContainingProfileDeclarationDoesntResolve() {
addValidConcept("http://loinc.org", "12345");
Observation input = new Observation();
input.getMeta().addProfile("http://foo/myprofile");
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
input.setStatus(ObservationStatus.FINAL);
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(errors.toString(), 1, errors.size());
assertEquals("StructureDefinition reference \"http://foo/myprofile\" could not be resolved", errors.get(0).getMessage());
}
@Test
public void testValidateResourceFailingInvariant() {
Observation input = new Observation();
// Has a value, but not a status (which is required)
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
input.setValue(new StringType("AAA"));
ValidationResult output = myVal.validateWithResult(input);
assertThat(output.getMessages().size(), greaterThan(0));
assertEquals("Profile http://hl7.org/fhir/StructureDefinition/Observation, Element 'Observation.status': minimum required = 1, but only found 0", output.getMessages().get(0).getMessage());
}
@Test
public void testValidateResourceWithDefaultValueset() {
Observation input = new Observation();
input.setStatus(ObservationStatus.FINAL);
input.getCode().setText("No code here!");
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input));
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.getMessages().size(), 0);
}
@Test
public void testValidateResourceWithDefaultValuesetBadCode() {
//@formatter:off
String input =
"<Observation xmlns=\"http://hl7.org/fhir\">\n" +
" <status value=\"notvalidcode\"/>\n" +
" <code>\n" +
" <text value=\"No code here!\"/>\n" +
" </code>\n" +
"</Observation>";
//@formatter:on
ValidationResult output = myVal.validateWithResult(input);
logResultsAndReturnAll(output);
assertEquals(
"The value provided ('notvalidcode') is not in the value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set) (error message = Unknown code[notvalidcode] in system[null])",
output.getMessages().get(0).getMessage());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
Observation input = new Observation();
myInstanceVal.setValidationSupport(myMockSupport);
input.setStatus(ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(errors.toString(), 0, errors.size());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationPassingLoinc() {
Observation input = new Observation();
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://loinc.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(errors.toString(), 0, errors.size());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationPassingLoincWithExpansion() {
Observation input = new Observation();
ValueSetExpansionComponent expansionComponent = new ValueSetExpansionComponent();
expansionComponent.addContains().setSystem("http://loinc.org").setCode("12345").setDisplay("Some display code");
mySupportedCodeSystemsForExpansion.put("http://loinc.org", expansionComponent);
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://loinc.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("1234");
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(1, errors.size());
assertEquals("Unknown code: http://loinc.org / 1234", errors.get(0).getMessage());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationPassingNonLoinc() {
Observation input = new Observation();
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://acme.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://acme.org").setCode("12345");
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertEquals(errors.toString(), 0, errors.size());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationFailingNonLoinc() {
Observation input = new Observation();
myInstanceVal.setValidationSupport(myMockSupport);
addValidConcept("http://acme.org", "12345");
input.setStatus(ObservationStatus.FINAL);
input.getCode().addCoding().setSystem("http://acme.org").setCode("9988877");
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertThat(errors.toString(), errors.size(), greaterThan(0));
assertEquals("Unknown code: http://acme.org / 9988877", errors.get(0).getMessage());
}
@Test
public void testValidateResourceWithValuesetExpansionBad() {
Patient patient = new Patient();
patient.addIdentifier().setSystem("http://example.com/").setValue("12345").getType().addCoding().setSystem("http://example.com/foo/bar").setCode("bar");
ValidationResult output = myVal.validateWithResult(patient);
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
assertEquals(1, all.size());
assertEquals("Patient.identifier.type", all.get(0).getLocationString());
assertEquals(
"None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code) (codes = http://example.com/foo/bar#bar)",
all.get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
}
@Test
public void testValidateResourceWithValuesetExpansionGood() {
Patient patient = new Patient();
patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR");
ValidationResult output = myVal.validateWithResult(patient);
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
assertEquals(0, all.size());
}
@Test
@Ignore
public void testValidateStructureDefinition() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/sdc-questionnaire.profile.xml"));
ValidationResult output = myVal.validateWithResult(input);
logResultsAndReturnAll(output);
assertEquals(output.toString(), 3, output.getMessages().size());
ourLog.info(output.getMessages().get(0).getLocationString());
ourLog.info(output.getMessages().get(0).getMessage());
}
@AfterClass
public static void afterClassClearContext() {
myDefaultValidationSupport.flush();
myDefaultValidationSupport = null;
TestUtil.clearAllStaticFieldsForUnitTest();
}
}