From 34cf0628d14d0bc2a3d4cade3d3110b3b8d39495 Mon Sep 17 00:00:00 2001 From: James Agnew Date: Sun, 27 Oct 2019 17:44:22 -0400 Subject: [PATCH] Fix https://github.com/jamesagnew/hapi-fhir/issues/1549 - Account for latest HAPI FHIR API interfaces --- .../org/hl7/fhir/dstu2/model/BaseBinary.java | 2 +- .../org/hl7/fhir/dstu2/model/Enumeration.java | 6 + .../fhir/dstu2016may/model/BaseBinary.java | 2 +- .../org/hl7/fhir/dstu3/model/BaseBinary.java | 2 +- .../org/hl7/fhir/r4/model/BaseBinary.java | 2 +- .../java/org/hl7/fhir/r4/model/Binary.java | 2 +- .../org/hl7/fhir/r5/model/BaseBinary.java | 2 +- .../java/org/hl7/fhir/r5/model/Binary.java | 2 +- .../hl7/fhir/utilities/xhtml/XhtmlNode.java | 14 + .../tests/InstanceValidatorR4Test.java | 1202 ----------------- pom.xml | 2 +- 11 files changed, 28 insertions(+), 1210 deletions(-) delete mode 100644 org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/InstanceValidatorR4Test.java diff --git a/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/BaseBinary.java b/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/BaseBinary.java index 7f8725f33..80546d4c1 100644 --- a/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/BaseBinary.java +++ b/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/BaseBinary.java @@ -39,6 +39,6 @@ public abstract class BaseBinary extends Resource implements IBaseBinary { return this; } - abstract Base64BinaryType getContentElement(); + public abstract Base64BinaryType getContentElement(); } diff --git a/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/Enumeration.java b/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/Enumeration.java index 8d2173d2f..ecf12f071 100644 --- a/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/Enumeration.java +++ b/org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/Enumeration.java @@ -22,6 +22,7 @@ package org.hl7.fhir.dstu2.model; import ca.uhn.fhir.model.api.annotation.DatatypeDef; +import org.hl7.fhir.instance.model.api.IBaseEnumFactory; import org.hl7.fhir.instance.model.api.IBaseEnumeration; /* @@ -114,4 +115,9 @@ public class Enumeration> extends PrimitiveType implements public String fhirType() { return "code"; } + + @Override + public IBaseEnumFactory getEnumFactory() { + return myEnumFactory; + } } diff --git a/org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/model/BaseBinary.java b/org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/model/BaseBinary.java index ed9740497..40599f48e 100644 --- a/org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/model/BaseBinary.java +++ b/org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/model/BaseBinary.java @@ -41,6 +41,6 @@ public abstract class BaseBinary extends Resource implements IBaseBinary { return this; } - abstract Base64BinaryType getContentElement(); + public abstract Base64BinaryType getContentElement(); } diff --git a/org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/BaseBinary.java b/org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/BaseBinary.java index 148734046..add775865 100644 --- a/org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/BaseBinary.java +++ b/org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/BaseBinary.java @@ -41,6 +41,6 @@ public abstract class BaseBinary extends Resource implements IBaseBinary { return this; } - abstract Base64BinaryType getContentElement(); + public abstract Base64BinaryType getContentElement(); } diff --git a/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/BaseBinary.java b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/BaseBinary.java index d5adce27c..0dfe853ac 100644 --- a/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/BaseBinary.java +++ b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/BaseBinary.java @@ -41,6 +41,6 @@ public abstract class BaseBinary extends Resource implements IBaseBinary { return this; } - abstract Base64BinaryType getContentElement(); + public abstract Base64BinaryType getContentElement(); } diff --git a/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Binary.java b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Binary.java index a20ffb71b..1578da191 100644 --- a/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Binary.java +++ b/org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Binary.java @@ -400,7 +400,7 @@ public class Binary extends BaseBinary implements IBaseBinary { } @Override - Base64BinaryType getContentElement() { + public Base64BinaryType getContentElement() { return getDataElement(); } diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/BaseBinary.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/BaseBinary.java index 0079e203f..090641486 100644 --- a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/BaseBinary.java +++ b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/BaseBinary.java @@ -41,6 +41,6 @@ public abstract class BaseBinary extends Resource implements IBaseBinary { return this; } - abstract Base64BinaryType getContentElement(); + public abstract Base64BinaryType getContentElement(); } diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Binary.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Binary.java index d905c4ea0..175af0671 100644 --- a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Binary.java +++ b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Binary.java @@ -392,7 +392,7 @@ public class Binary extends BaseBinary implements IBaseBinary { } @Override - Base64BinaryType getContentElement() { + public Base64BinaryType getContentElement() { return getDataElement(); } diff --git a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java index a47df8aea..f517fc067 100644 --- a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java +++ b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java @@ -456,6 +456,20 @@ public class XhtmlNode implements IBaseXhtml { throw new UnsupportedOperationException(); } + /** + * NOT SUPPORTED - Throws {@link UnsupportedOperationException} + */ + public Object getUserData(String theName) { + throw new UnsupportedOperationException(); + } + + /** + * NOT SUPPORTED - Throws {@link UnsupportedOperationException} + */ + public void setUserData(String theName, Object theValue) { + throw new UnsupportedOperationException(); + } + public Location getLocation() { return location; diff --git a/org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/InstanceValidatorR4Test.java b/org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/InstanceValidatorR4Test.java deleted file mode 100644 index c442284b1..000000000 --- a/org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/InstanceValidatorR4Test.java +++ /dev/null @@ -1,1202 +0,0 @@ -package org.hl7.fhir.validation.tests; - -import static org.hamcrest.Matchers.containsString; -import static org.hamcrest.Matchers.empty; -import static org.hamcrest.Matchers.greaterThan; -import static org.hamcrest.Matchers.hasItem; -import static org.hamcrest.Matchers.hasSize; -import static org.hamcrest.Matchers.lessThan; -import static org.hamcrest.Matchers.not; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertThat; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; -import static org.mockito.ArgumentMatchers.anyBoolean; -import static org.mockito.ArgumentMatchers.anyString; -import static org.mockito.ArgumentMatchers.nullable; -import static org.mockito.Mockito.mock; -import static org.mockito.Mockito.when; - -import java.io.IOException; -import java.io.InputStream; -import java.io.StringReader; -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.apache.commons.io.input.ReaderInputStream; -import org.apache.commons.lang3.Validate; -import org.hl7.fhir.exceptions.FHIRException; -import org.hl7.fhir.exceptions.TerminologyServiceException; -import org.hl7.fhir.instance.model.api.IBaseResource; -import org.hl7.fhir.r4.conformance.ProfileUtilities; -import org.hl7.fhir.r4.context.IWorkerContext; -import org.hl7.fhir.r4.elementmodel.Manager; -import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport; -import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext; -import org.hl7.fhir.r4.hapi.ctx.IValidationSupport.CodeValidationResult; -import org.hl7.fhir.r4.model.Base; -import org.hl7.fhir.r4.model.Base64BinaryType; -import org.hl7.fhir.r4.model.BooleanType; -import org.hl7.fhir.r4.model.Bundle; -import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; -import org.hl7.fhir.r4.model.CodeSystem; -import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent; -import org.hl7.fhir.r4.model.CodeType; -import org.hl7.fhir.r4.model.CodeableConcept; -import org.hl7.fhir.r4.model.Consent; -import org.hl7.fhir.r4.model.ContactPoint; -import org.hl7.fhir.r4.model.DateTimeType; -import org.hl7.fhir.r4.model.Extension; -import org.hl7.fhir.r4.model.Media; -import org.hl7.fhir.r4.model.Narrative; -import org.hl7.fhir.r4.model.Observation; -import org.hl7.fhir.r4.model.Observation.ObservationStatus; -import org.hl7.fhir.r4.model.Patient; -import org.hl7.fhir.r4.model.Period; -import org.hl7.fhir.r4.model.Practitioner; -import org.hl7.fhir.r4.model.Procedure; -import org.hl7.fhir.r4.model.QuestionnaireResponse; -import org.hl7.fhir.r4.model.Reference; -import org.hl7.fhir.r4.model.RelatedPerson; -import org.hl7.fhir.r4.model.Resource; -import org.hl7.fhir.r4.model.StringType; -import org.hl7.fhir.r4.model.StructureDefinition; -import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind; -import org.hl7.fhir.r4.model.ValueSet; -import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent; -import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent; -import org.hl7.fhir.r4.terminologies.ValueSetExpander; -import org.hl7.fhir.r4.utils.FHIRPathEngine; -import org.hl7.fhir.r4.utils.IResourceValidator; -import org.hl7.fhir.r4.validation.InstanceValidator; -import org.hl7.fhir.utilities.validation.ValidationMessage; -import org.hl7.fhir.utilities.xhtml.XhtmlNode; -import org.junit.AfterClass; -import org.junit.Before; -import org.junit.BeforeClass; -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.junit.runner.RunWith; -import org.mockito.Mock; -import org.mockito.invocation.InvocationOnMock; -import org.mockito.junit.MockitoJUnitRunner; -import org.mockito.stubbing.Answer; - -import com.google.common.base.Charsets; - -import ca.uhn.fhir.context.FhirContext; -import ca.uhn.fhir.rest.api.Constants; -import ca.uhn.fhir.util.TestUtil; - -@RunWith(MockitoJUnitRunner.class) -public class InstanceValidatorR4Test { - - private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(InstanceValidatorR4Test.class); - private static DefaultProfileValidationSupport ourDefaultValidationSupport = new DefaultProfileValidationSupport(); - private static FhirContext ourCtx = FhirContext.forR4(); - @Rule - public TestRule watcher = new TestWatcher() { - @Override - protected void starting(Description description) { - ourLog.info("Starting test: " + description.getMethodName()); - } - }; - private InstanceValidator myInstanceVal; - - private Map mySupportedCodeSystemsForExpansion; - private ArrayList myValidConcepts; - private Set myValidSystems = new HashSet<>(); - private DefaultProfileValidationSupport myDefaultProfileValidationSupport = new DefaultProfileValidationSupport(); - - @BeforeClass - public static void beforeClass() { - ourDefaultValidationSupport.fetchAllStructureDefinitions(ourCtx); - } - - private IWorkerContext myWorkerContext; - @Mock - private FHIRPathEngine.IEvaluationContext myEvaluationContext; - private FhirContext myCtx = FhirContext.forR4(); - - private void addValidConcept(String theSystem, String theCode) { - myValidSystems.add(theSystem); - myValidConcepts.add(theSystem + "___" + theCode); - } - - /** - * An invalid local reference should not cause a ServiceException. - */ - @Test - public void testInvalidLocalReference() { - QuestionnaireResponse resource = new QuestionnaireResponse(); - resource.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED); - resource.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - resource.setSubject(new Reference("#invalid-ref")); - - List output = validateAndReturnResult(resource); - List nonInfo = logResultsAndReturnNonInformationalOnes(output); - assertThat(nonInfo, hasSize(2)); - } - - private List validateAndReturnResult(Resource theResource) { - ArrayList issues = new ArrayList<>(); - try { - myInstanceVal.validate(null, issues, theResource); - } catch (FHIRException e) { - ourLog.error("Failure during validation", e); - fail("Failure during validation" + e.toString()); - } - return issues; - } - - private List validateAndReturnResult(String theResource) { - ArrayList issues = new ArrayList<>(); - try { - ReaderInputStream stringInputStream = new ReaderInputStream(new StringReader(theResource), Charsets.UTF_8); - Manager.FhirFormat fhirFormat = Manager.FhirFormat.XML; - if (theResource.startsWith("{")) { - fhirFormat = Manager.FhirFormat.JSON; - } - myInstanceVal.validate(null, issues, stringInputStream, fhirFormat); - } catch (FHIRException e) { - ourLog.error("Failure during validation", e); - fail("Failure during validation" + e.toString()); - } - return issues; - } - - @SuppressWarnings("unchecked") - @Before - public void before() throws TerminologyServiceException { - myWorkerContext = mock(IWorkerContext.class); - myInstanceVal = new InstanceValidator(myWorkerContext, myEvaluationContext); - - mySupportedCodeSystemsForExpansion = new HashMap<>(); - - myValidConcepts = new ArrayList<>(); - - when(myWorkerContext.expandVS(nullable(ConceptSetComponent.class), anyBoolean())).thenAnswer(theInvocation -> { - ConceptSetComponent arg = (ConceptSetComponent) theInvocation.getArguments()[1]; - ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem()); - if (retVal == null) { - ValueSetExpander.ValueSetExpansionOutcome outcome = ourDefaultValidationSupport.expandValueSet(ourCtx, arg); - return outcome; - } - ourLog.debug("expandValueSet({}) : {}", new Object[]{theInvocation.getArguments()[0], retVal}); - - ValueSet valueset = new ValueSet(); - valueset.setExpansion(retVal); - return new ValueSetExpander.ValueSetExpansionOutcome(valueset); - }); - - when(myWorkerContext.supportsSystem(anyString())).thenAnswer(theInvocation -> { - String system = (String) theInvocation.getArguments()[0]; - boolean retVal = myValidSystems.contains(system); - ourLog.debug("isCodeSystemSupported({}) : {}", new Object[]{theInvocation.getArguments()[0], retVal}); - return retVal; - }); - - when(myWorkerContext.fetchResource(nullable(Class.class), nullable(String.class))).thenAnswer(new Answer() { - @Override - public IBaseResource answer(InvocationOnMock theInvocation) throws Throwable { - IBaseResource retVal; - String id = (String) theInvocation.getArguments()[1]; - Class type = (Class) theInvocation.getArguments()[0]; - retVal = ourDefaultValidationSupport.fetchResource(myCtx, type, id); - ourLog.debug("fetchResource({}, {}) : {}", theInvocation.getArguments()[1], id, retVal); - return retVal; - } - }); - - when(myWorkerContext.validateCode(null, nullable(String.class), nullable(String.class), nullable(String.class))).thenAnswer(new Answer() { - @Override - public CodeValidationResult answer(InvocationOnMock theInvocation) throws Throwable { - String system = (String) theInvocation.getArguments()[0]; - String code = (String) theInvocation.getArguments()[1]; - CodeValidationResult retVal; - if (myValidConcepts.contains(system + "___" + code)) { - retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code))); - } else { - retVal = ourDefaultValidationSupport.validateCode(myCtx, system, code, (String) theInvocation.getArguments()[2]); - } - ourLog.debug("validateCode({}, {}, {}) : {}", system, code, (String) theInvocation.getArguments()[2], retVal); - return retVal; - } - }); - when(myWorkerContext.fetchCodeSystem(nullable(String.class))).thenAnswer(new Answer() { - @Override - public CodeSystem answer(InvocationOnMock theInvocation) throws Throwable { - CodeSystem retVal = ourDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0], (String) theInvocation.getArguments()[1]); - ourLog.debug("fetchCodeSystem({}) : {}", new Object[]{(String) theInvocation.getArguments()[0], retVal}); - return retVal; - } - }); - when(myWorkerContext.fetchTypeDefinition(nullable(String.class))).thenAnswer(new Answer() { - @Override - public StructureDefinition answer(InvocationOnMock theInvocation) throws Throwable { - String url = (String) theInvocation.getArguments()[0]; - StructureDefinition retVal = ourDefaultValidationSupport.fetchStructureDefinition(myCtx, url); - ourLog.debug("fetchStructureDefinition({}) : {}", new Object[]{url, retVal}); - return retVal; - } - }); - when(myWorkerContext.allStructures()).thenAnswer(new Answer>() { - @Override - public List answer(InvocationOnMock theInvocation) throws Throwable { - List retVal = ourDefaultValidationSupport.fetchAllStructureDefinitions(myCtx); - ourLog.debug("fetchAllStructureDefinitions()", new Object[]{}); - return retVal; - } - }); - - } - - private Object defaultString(Integer theLocationLine) { - return theLocationLine != null ? theLocationLine.toString() : ""; - } - - private StructureDefinition loadStructureDefinition(String theResName) throws IOException, FHIRException { - StructureDefinition derived = ourCtx.newXmlParser().parseResource(StructureDefinition.class, IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream(theResName), Charsets.UTF_8)); - StructureDefinition base = myDefaultProfileValidationSupport.fetchStructureDefinition(ourCtx, derived.getBaseDefinition()); - Validate.notNull(base); - - IWorkerContext worker = new HapiWorkerContext(ourCtx, myDefaultProfileValidationSupport); - List issues = new ArrayList<>(); - ProfileUtilities profileUtilities = new ProfileUtilities(worker, issues, null); - profileUtilities.generateSnapshot(base, derived, "", "", ""); - - return derived; - } - - private List logResultsAndReturnAll(List theOutput) { - List retVal = new ArrayList<>(); - - int index = 0; - for (ValidationMessage next : theOutput) { - ourLog.info("Result {}: {} - {}:{} {} - {}", - index, next.getLevel(), defaultString(next.getLine()), defaultString(next.getCol()), next.getLocation(), next.getMessage()); - index++; - - retVal.add(next); - } - return retVal; - } - - @Test - public void testValidateCodeWithTailingSpace() { - Patient p = new Patient(); - p.getMaritalStatus() - .addCoding() - .setSystem("http://foo") - .setCode("AA "); - - List result = validateAndReturnResult(p); - List all = logResultsAndReturnErrorOnes(result); - assertEquals("The code 'AA ' is not valid (whitespace rules)", all.get(0).getMessage()); - - } - - /** - * See #938 - */ - @Test - public void testValidateEmptyElement() { - String input = "" + - " \n" + - " \n" + - "
AAA
\n" + - " " + - " " + - ""; - - List result = validateAndReturnResult(input); - List all = logResultsAndReturnNonInformationalOnes(result); - assertEquals("Primitive types must have a value that is not empty", all.get(0).getMessage()); - } - - /** - * See #942 - */ - @Test - public void testValidateDoesntEnforceBestPracticesByDefault() throws FHIRException { - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - input.setStatus(ObservationStatus.AMENDED); - input.getCode().addCoding().setSystem("http://loinc.org").setCode("1234").setDisplay("FOO"); - - InstanceValidator instanceModule; - InstanceValidator val; - List all; - List result; - - // With BPs disabled - val = new InstanceValidator(myWorkerContext, myEvaluationContext); - val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Hint); - result = new ArrayList<>(); - val.validate(null, result, input); - all = logResultsAndReturnNonInformationalOnes(result); - assertThat(all, empty()); - - // With BPs enabled - val = new InstanceValidator(myWorkerContext, myEvaluationContext); - val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Error); - result = new ArrayList<>(); - val.validate(null, result, input); - all = logResultsAndReturnNonInformationalOnes(result); - assertEquals("All observations should have a subject", all.get(0).getMessage()); - } - - - private List logResultsAndReturnNonInformationalOnes(List theErrors) { - List retVal = new ArrayList<>(); - - int index = 0; - for (ValidationMessage next : theErrors) { - ourLog.info("Result {}: {} - {} - {}", index, next.getLevel(), next.getLocation(), next.getMessage()); - index++; - - if (next.getLevel() != ValidationMessage.IssueSeverity.INFORMATION) { - retVal.add(next); - } - } - - return retVal; - } - - private List logResultsAndReturnErrorOnes(List theOutput) { - List retVal = new ArrayList<>(); - - int index = 0; - for (ValidationMessage next : theOutput) { - ourLog.info("Result {}: {} - {} - {}", index, next.getLevel(), next.getLocation(), next.getMessage(), next.getDisplay()); - index++; - - if (next.getLevel().ordinal() < ValidationMessage.IssueSeverity.WARNING.ordinal()) { - retVal.add(next); - } - } - - return retVal; - } - - @Test - public void testBase64Invalid() { - Base64BinaryType value = new Base64BinaryType(new byte[]{2, 3, 4, 4, 6, 7, 8, 9, 8, 7, 6, 4, 4, 3, 2, 1}); - Media med = new Media(); - med.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - med.getContent().setContentType(Constants.CT_OCTET_STREAM); - med.getContent().setDataElement(value); - med.getContent().setTitle("bbbb syst"); - med.setStatus(Media.MediaStatus.NOTDONE); - String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(med); - - encoded = encoded.replace(value.getValueAsString(), "%%%2@()()"); - - ourLog.info("Encoded: {}", encoded); - - List output = validateAndReturnResult(encoded); - List errors = logResultsAndReturnNonInformationalOnes(output); - assertEquals(1, errors.size()); - assertEquals("The value \"%%%2@()()\" is not a valid Base64 value", errors.get(0).getMessage()); - - } - - @Test - public void testValidateBundleWithNoFullUrl() throws IOException { - String encoded = IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/r4/r4-caredove-bundle.json")); - - List output = validateAndReturnResult(encoded); - List errors = logResultsAndReturnNonInformationalOnes(output); - assertEquals(48, errors.size()); - } - - @Test - public void testBase64Valid() { - Base64BinaryType value = new Base64BinaryType(new byte[]{2, 3, 4, 4, 6, 7, 8, 9, 8, 7, 6, 4, 4, 3, 2, 1}); - Media med = new Media(); - med.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - med.getContent().setContentType(Constants.CT_OCTET_STREAM); - med.getContent().setDataElement(value); - med.getContent().setTitle("bbbb syst"); - med.setStatus(Media.MediaStatus.NOTDONE); - String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(med); - - ourLog.info("Encoded: {}", encoded); - - List output = validateAndReturnResult(encoded); - List errors = logResultsAndReturnErrorOnes(output); - assertEquals(0, errors.size()); - - } - - /** - * See #873 - */ - @Test - public void testCompareTimesWithDifferentTimezones() { - Procedure procedure = new Procedure(); - procedure.setStatus(Procedure.ProcedureStatus.COMPLETED); - procedure.getSubject().setReference("Patient/1"); - procedure.getCode().setText("Some proc"); - - Period period = new Period(); - period.setStartElement(new DateTimeType("2000-01-01T00:00:01+04:00")); - period.setEndElement(new DateTimeType("2000-01-01T00:00:00+04:00")); - assertThat(period.getStart().getTime(), lessThan(period.getEnd().getTime())); - procedure.setPerformed(period); - - List result = validateAndReturnResult(procedure); - List issues = logResultsAndReturnErrorOnes(result); - assertThat(issues, empty()); - } - - /** - * See #431 - */ - @Test - public void testContactPointSystemUrlWorks() { - Patient p = new Patient(); - p.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - ContactPoint t = p.addTelecom(); - t.setSystem(ContactPoint.ContactPointSystem.URL); - t.setValue("http://infoway-inforoute.ca"); - - List results = validateAndReturnResult(p); - List outcome = logResultsAndReturnNonInformationalOnes(results); - assertThat(outcome, empty()); - - } - - /** - * See #872 - */ - @Test - public void testExtensionUrlWithHl7Url() throws IOException { - String input = IOUtils.toString(InstanceValidator.class.getResourceAsStream("/bug872-ext-with-hl7-url.json"), Charsets.UTF_8); - List output = validateAndReturnResult(input); - List nonInfo = logResultsAndReturnNonInformationalOnes(output); - assertThat(nonInfo, empty()); - } - - @Test - public void testIsNoTerminologyChecks() { - assertFalse(myInstanceVal.isNoTerminologyChecks()); - myInstanceVal.setNoTerminologyChecks(true); - assertTrue(myInstanceVal.isNoTerminologyChecks()); - } - - @Test - public void testLargeBase64() throws IOException { - when(myWorkerContext.validateCode(null, nullable(CodeableConcept.class), nullable(ValueSet.class))).thenReturn( - new IWorkerContext.ValidationResult(ValidationMessage.IssueSeverity.INFORMATION, "Code http://loinc.org/1-8 was not validated because the code system is not present") - ); - - String input = IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/r4/diagnosticreport-example-gingival-mass.json"), Constants.CHARSET_UTF8); - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnNonInformationalOnes(output); - assertEquals(1, errors.size()); - assertEquals("Code http://loinc.org/1-8 was not validated because the code system is not present", errors.get(0).getMessage()); - } - - @Test - @Ignore - public void testValidateBigRawJsonResource() throws Exception { - InputStream stream = InstanceValidatorR4Test.class.getResourceAsStream("/r4/conformance.json.gz"); - stream = new GZIPInputStream(stream); - String input = IOUtils.toString(stream); - - long start = System.currentTimeMillis(); - List output = null; - int passes = 1; - for (int i = 0; i < passes; i++) { - ourLog.info("Pass {}", i + 1); - output = validateAndReturnResult(input); - } - - long delay = System.currentTimeMillis() - start; - long per = delay / passes; - - logResultsAndReturnAll(output); - - ourLog.info("Took {} ms -- {}ms / pass", delay, per); - } - - @Test - @Ignore - public void testValidateBuiltInProfiles() throws Exception { - Bundle bundle; - String name = "profiles-resources"; - ourLog.info("Uploading " + name); - String vsContents; - vsContents = IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/org/hl7/fhir/r4/model/profile/" + name + ".xml"), "UTF-8"); - - TreeSet ids = new TreeSet<>(); - - bundle = ourCtx.newXmlParser().parseResource(Bundle.class, vsContents); - for (BundleEntryComponent i : bundle.getEntry()) { - 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)); - - List output = validateAndReturnResult(next); - List results = logResultsAndReturnAll(output); - - // This isn't a validator problem but a definition problem.. it should get fixed at some point and - // we can remove this. Tracker #17207 was filed about this - // https://gforge.hl7.org/gf/project/fhir/tracker/?action=TrackerItemEdit&tracker_item_id=17207 - if (next.getId().equalsIgnoreCase("http://hl7.org/fhir/OperationDefinition/StructureDefinition-snapshot")) { - assertEquals(1, results.size()); - assertEquals("A search type can only be specified for parameters of type string [searchType.exists() implies type = 'string']", results.get(0).getMessage()); - continue; - } - - - List errors = logResultsAndReturnNonInformationalOnes(results); - assertThat("Failed to validate " + i.getFullUrl() + " - " + errors, errors, empty()); - } - - ourLog.info("Validated the following:\n{}", ids); - } - - @Test - public void testValidateBundleWithNoType() throws Exception { - String vsContents = IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/r4/bundle-with-no-type.json"), "UTF-8"); - - List output = validateAndReturnResult(vsContents); - logResultsAndReturnNonInformationalOnes(output); - assertThat(output.toString(), containsString("Element 'Bundle.type': minimum required = 1")); - } - - @Test - @Ignore - public void testValidateBundleWithObservations() throws Exception { - String name = "profiles-resources"; - ourLog.info("Uploading " + name); - String inputString; - inputString = IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/brian_reinhold_bundle.json"), "UTF-8"); - Bundle bundle = ourCtx.newJsonParser().parseResource(Bundle.class, inputString); - - FHIRPathEngine fp = new FHIRPathEngine(myWorkerContext); - List 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()); - - List output = validateAndReturnResult(inputString); - List errors = logResultsAndReturnNonInformationalOnes(output); - assertThat(errors, empty()); - - } - - @Test - @Ignore - public void testValidateDocument() throws Exception { - String vsContents = IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/sample-document.xml"), "UTF-8"); - - List output = validateAndReturnResult(vsContents); - List result = logResultsAndReturnNonInformationalOnes(output); - assertTrue(result.isEmpty()); - } - - @Test - public void testValidateProfileWithExtension() throws IOException, FHIRException { - - // Prepopulate SDs - loadStructureDefinition("/r4/myconsent-profile.xml"); - loadStructureDefinition("/r4/myconsent-ext.xml"); - - Consent input = ourCtx.newJsonParser().parseResource(Consent.class, IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/r4/myconsent-resource.json"))); - - input.getPolicyFirstRep().setAuthority("http://foo"); - input.getScope() - .getCodingFirstRep() - .setSystem("http://terminology.hl7.org/CodeSystem/consentscope") - .setCode("adr"); - input.addCategory() - .getCodingFirstRep() - .setSystem("http://terminology.hl7.org/CodeSystem/consentcategorycodes") - .setCode("acd"); - - // Should pass - List output = validateAndReturnResult(input); - List all = logResultsAndReturnErrorOnes(output); - assertEquals(all.toString(), 0, all.size()); - - // Now with the wrong datatype - input.getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/PruebaExtension").get(0).setValue(new CodeType("AAA")); - - // Should fail - output = validateAndReturnResult(input); - all = logResultsAndReturnErrorOnes(output); - assertThat(all.toString(), containsString("definition allows for the types [string] but found type code")); - - } - - @Test - public void testValidateRawJsonResource() { - String input = "{" + - " \"resourceType\":\"Patient\"," + - " \"text\": {\n" + - " \"status\": \"generated\",\n" + - " \"div\": \"
\"\n" + - " },\n" + - " \"id\":\"123\"" + - "}"; - - List output = validateAndReturnResult(input); - assertEquals(output.toString(), 0, output.size()); - } - - @Test - public void testValidateRawJsonResourceBadAttributes() { - String input = - "{" + - "\"resourceType\":\"Patient\"," + - " \"text\": {\n" + - " \"status\": \"generated\",\n" + - " \"div\": \"
\"\n" + - " },\n" + - "\"id\":\"123\"," + - "\"foo\":\"123\"" + - "}"; - - List output = validateAndReturnResult(input); - assertEquals(output.toString(), 1, output.size()); - ourLog.info(output.get(0).getLocation()); - ourLog.info(output.get(0).getMessage()); - assertEquals("/Patient", output.get(0).getLocation()); - assertEquals("Unrecognised property '@foo'", output.get(0).getMessage()); - } - - @Test - public void testValidateRawJsonResourceWithUnknownExtension() { - - Patient patient = new Patient(); - patient.setId("1"); - patient.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - 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" - * } - * ] - * } - */ - - List output = validateAndReturnResult(encoded); - assertEquals(output.toString(), 1, output.size()); - - assertEquals("Unknown extension http://hl7.org/fhir/v3/ethnicity", output.get(0).getMessage()); - assertEquals(ValidationMessage.IssueSeverity.INFORMATION, output.get(0).getLevel()); - } - - @Test - public void testValidateRawJsonResourceWithUnknownExtensionNotAllowed() { - - Patient patient = new Patient(); - patient.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - 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); - List output = validateAndReturnResult(encoded); - assertEquals(output.toString(), 1, output.size()); - - assertEquals("The extension http://hl7.org/fhir/v3/ethnicity is unknown, and not allowed here", output.get(0).getMessage()); - assertEquals(ValidationMessage.IssueSeverity.ERROR, output.get(0).getLevel()); - } - - @Test - public void testValidateRawXmlResource() { - String input = "" + - "" + - " \n" + - " \n" + - "
AAA
\n" + - " " + - ""; - - List output = validateAndReturnResult(input); - assertEquals(output.toString(), 0, output.size()); - } - - @Test - public void testValidateRawXmlResourceBadAttributes() { - String input = - "" + - "" + - " \n" + - " \n" + - "
AAA
\n" + - " " + - "" + - ""; - - List output = validateAndReturnResult(input); - assertEquals(output.toString(), 1, output.size()); - ourLog.info(output.get(0).getLocation()); - ourLog.info(output.get(0).getMessage()); - assertEquals("/f:Patient", output.get(0).getLocation()); - assertEquals("Undefined element 'foo'", output.get(0).getMessage()); - } - - @Test - public void testValidateRawXmlResourceWithEmptyPrimitive() { - String input = "" + - " \n" + - " \n" + - "
AAA
\n" + - " " + - "" + - ""; - - List output = validateAndReturnResult(input); - List messages = logResultsAndReturnNonInformationalOnes(output); - assertEquals(output.toString(), 3, messages.size()); - assertThat(messages.get(0).getMessage(), containsString("Element must have some content")); - assertThat(messages.get(1).getMessage(), containsString("Primitive types must have a value or must have child extensions")); - assertThat(messages.get(2).getMessage(), containsString("All FHIR elements must have a @value or children [hasValue() or (children().count() > id.count())]")); - } - - @Test - public void testValidateRawXmlResourceWithPrimitiveContainingOnlyAnExtension() { - String input = "\n" + - " \n" + - " \n" + - " \n" + - "
AAA
\n" + - " " + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " \n" + - " "; - - - myInstanceVal.setAnyExtensionsAllowed(true); - List output = validateAndReturnResult(input); - List res = logResultsAndReturnNonInformationalOnes(output); - assertEquals(output.toString(), 0, res.size()); - } - - @Test - public void testValidateRawXmlWithMissingRootNamespace() { - //@formatter:off - String input = "" - + "" - + " " - + " " - + "
Some narrative
" - + " " - + " " - + " " - + " " - + " " - + " " - + " " - + " " - + ""; - //@formatter:on - - List output = validateAndReturnResult(input); - assertEquals(output.toString(), 1, output.size()); - assertEquals("This cannot be parsed as a FHIR object (no namespace)", output.get(0).getMessage()); - ourLog.info(output.get(0).getLocation()); - } - - /** - * A reference with only an identifier should be valid - */ - @Test - public void testValidateReferenceWithDisplayValid() throws Exception { - Patient p = new Patient(); - p.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - p.getManagingOrganization().setDisplay("HELLO"); - - List output = validateAndReturnResult(p); - List nonInfo = logResultsAndReturnNonInformationalOnes(output); - assertThat(nonInfo, empty()); - } - - /** - * A reference with only an identifier should be valid - */ - @Test - public void testValidateReferenceWithIdentifierValid() throws Exception { - Patient p = new Patient(); - p.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - p.getManagingOrganization().getIdentifier().setSystem("http://acme.org"); - p.getManagingOrganization().getIdentifier().setValue("foo"); - - List output = validateAndReturnResult(p); - List nonInfo = logResultsAndReturnNonInformationalOnes(output); - assertThat(nonInfo, 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.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - rp.getPatient().setReference("Patient/1"); - rp.addRelationship().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/v2-0131").setCode("C"); - - List results = validateAndReturnResult(rp); - List outcome = logResultsAndReturnNonInformationalOnes(results); - assertThat(outcome, empty()); - - /* - * Now a bad code - */ - rp = new RelatedPerson(); - rp.getPatient().setReference("Patient/1"); - rp.addRelationship().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/v2-0131").setCode("GAGAGAGA"); - - results = validateAndReturnResult(rp); - outcome = logResultsAndReturnNonInformationalOnes(results); - assertThat(outcome, not(empty())); - - } - - @Test - public void testValidateResourceContainingLoincCode() { - addValidConcept("http://loinc.org", "1234467"); - - Observation input = new Observation(); - // input.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/devicemetricobservation"); - - input.addIdentifier().setSystem("http://acme").setValue("12344"); - input.getEncounter().setReference("http://foo.com/Encounter/9"); - input.setStatus(ObservationStatus.FINAL); - input.getCode().addCoding().setSystem("http://loinc.org").setCode("12344"); - - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnAll(output); - - assertThat(errors.toString(), containsString("warning")); - assertThat(errors.toString(), containsString("Unknown code: http://loinc.org / 12344")); - } - - @Test - public void testValidateResourceContainingProfileDeclaration() { - addValidConcept("http://loinc.org", "12344"); - - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - input.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/devicemetricobservation"); - - input.addIdentifier().setSystem("http://acme").setValue("12344"); - input.getEncounter().setReference("http://foo.com/Encounter/9"); - input.setStatus(ObservationStatus.FINAL); - input.getCode().addCoding().setSystem("http://loinc.org").setCode("12344"); - - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnNonInformationalOnes(output); - - assertThat(errors.toString(), containsString("Element 'Observation.subject': minimum required = 1, but only found 0")); - assertThat(errors.toString(), containsString("Element 'Observation.encounter': 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", "12344"); - - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - input.getMeta().addProfile("http://foo/structuredefinition/myprofile"); - - input.getCode().addCoding().setSystem("http://loinc.org").setCode("12344"); - input.setStatus(ObservationStatus.FINAL); - - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnNonInformationalOnes(output); - assertEquals(errors.toString(), 1, errors.size()); - assertEquals("StructureDefinition reference \"http://foo/structuredefinition/myprofile\" could not be resolved", errors.get(0).getMessage()); - } - - @Test - public void testValidateResourceFailingInvariant() { - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - // Has a value, but not a status (which is required) - input.getCode().addCoding().setSystem("http://loinc.org").setCode("12344"); - input.setValue(new StringType("AAA")); - - List output = validateAndReturnResult(input); - assertThat(output.size(), greaterThan(0)); - assertEquals("Profile http://hl7.org/fhir/StructureDefinition/Observation, Element 'Observation.status': minimum required = 1, but only found 0", output.get(0).getMessage()); - - } - - @Test - public void testValidateResourceWithDefaultValueset() { - Observation input = new Observation(); - - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - input.setStatus(ObservationStatus.FINAL); - input.getCode().setText("No code here!"); - - ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input)); - - List output = validateAndReturnResult(input); - assertEquals(output.size(), 0); - } - - @Test - public void testValidateResourceWithDefaultValuesetBadCode() { - String input = - "\n" + - " \n" + - " \n" + - "
AAA
\n" + - " " + - " \n" + - " \n" + - " \n" + - " \n" + - ""; - List output = validateAndReturnResult(input); - List issues = logResultsAndReturnNonInformationalOnes(output); - assertEquals( - "The value provided ('notvalidcode') is not in the value set http://hl7.org/fhir/ValueSet/observation-status|4.0.0 (http://hl7.org/fhir/ValueSet/observation-status, and a code is required from this value set) (error message = Unknown code[notvalidcode] in system[null])", - issues.get(0).getMessage()); - } - - @Test - public void testValidateResourceWithExampleBindingCodeValidationFailing() { - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - input.setStatus(ObservationStatus.FINAL); - input.getCode().addCoding().setSystem("http://loinc.org").setCode("12344"); - - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnNonInformationalOnes(output); - assertEquals(errors.toString(), 0, errors.size()); - - } - - @Test - public void testValidateResourceWithExampleBindingCodeValidationFailingNonLoinc() { - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - addValidConcept("http://acme.org", "12344"); - - input.setStatus(ObservationStatus.FINAL); - input.getCode().addCoding().setSystem("http://acme.org").setCode("9988877"); - - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnAll(output); - assertThat(errors.toString(), errors.size(), greaterThan(0)); - assertEquals("Unknown code: http://acme.org / 9988877", errors.get(0).getMessage()); - - } - - @Test - public void testValidateResourceWithExampleBindingCodeValidationPassingLoinc() { - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - addValidConcept("http://loinc.org", "12344"); - - input.setStatus(ObservationStatus.FINAL); - input.getCode().addCoding().setSystem("http://loinc.org").setCode("12344"); - - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnNonInformationalOnes(output); - assertEquals(errors.toString(), 0, errors.size()); - } - - @Test - public void testValidateResourceWithExampleBindingCodeValidationPassingLoincWithExpansion() { - Observation input = new Observation(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - ValueSetExpansionComponent expansionComponent = new ValueSetExpansionComponent(); - expansionComponent.addContains().setSystem("http://loinc.org").setCode("12344").setDisplay("Some display code"); - - mySupportedCodeSystemsForExpansion.put("http://loinc.org", expansionComponent); - addValidConcept("http://loinc.org", "12344"); - - input.setStatus(ObservationStatus.FINAL); - input.getCode().addCoding().setSystem("http://loinc.org").setCode("1234"); - - List output = validateAndReturnResult(input); - List 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(); - input.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - - addValidConcept("http://acme.org", "12344"); - - input.setStatus(ObservationStatus.FINAL); - input.getCode().addCoding().setSystem("http://acme.org").setCode("12344"); - - List output = validateAndReturnResult(input); - List errors = logResultsAndReturnAll(output); - assertEquals(errors.toString(), 0, errors.size()); - } - - @Test - public void testValidateResourceWithValuesetExpansionBad() { - - Patient p = new Patient(); - p.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - p.addIdentifier().setSystem("http://example.com/").setValue("12344").getType().addCoding().setSystem("http://example.com/foo/bar").setCode("bar"); - - List output = validateAndReturnResult(p); - List all = logResultsAndReturnAll(output); - assertEquals(1, all.size()); - assertEquals("Patient.identifier.type", all.get(0).getLocation()); - assertEquals( - "Code http://example.com/foo/bar/bar was not validated because the code system is not present", - all.get(0).getMessage()); - assertEquals(ValidationMessage.IssueSeverity.WARNING, all.get(0).getLevel()); - - } - - @Test - public void testMultiplePerformer() { - Observation o = new Observation(); - Practitioner p1 = new Practitioner(); - Practitioner p2 = new Practitioner(); - - o.addPerformer(new Reference(p1)); - o.addPerformer(new Reference(p2)); - - List output = validateAndReturnResult(o); - List valMessages = logResultsAndReturnAll(output); - List messages = new ArrayList<>(); - for (String msg : messages) { - messages.add(msg); - } - assertThat(messages, not(hasItem("All observations should have a performer"))); - } - - @Test - public void testValidateResourceWithValuesetExpansionGood() { - Patient patient = new Patient(); - patient.getText().setDiv(new XhtmlNode().setValue("
AA
")).setStatus(Narrative.NarrativeStatus.GENERATED); - patient - .addIdentifier() - .setSystem("http://system") - .setValue("12345") - .getType() - .addCoding() - .setSystem("http://terminology.hl7.org/CodeSystem/v2-0203") - .setCode("MR"); - - List output = validateAndReturnResult(patient); - List all = logResultsAndReturnAll(output); - assertEquals(0, all.size()); - } - - @Test - @Ignore - public void testValidateStructureDefinition() throws IOException { - String input = IOUtils.toString(InstanceValidatorR4Test.class.getResourceAsStream("/sdc-questionnaire.profile.xml")); - - List output = validateAndReturnResult(input); - logResultsAndReturnAll(output); - - assertEquals(output.toString(), 3, output.size()); - ourLog.info(output.get(0).getLocation()); - ourLog.info(output.get(0).getMessage()); - } - - @AfterClass - public static void afterClassClearContext() { - ourDefaultValidationSupport.flush(); - ourDefaultValidationSupport = null; - TestUtil.clearAllStaticFieldsForUnitTest(); - } - - -} diff --git a/pom.xml b/pom.xml index 16b1852e4..593c5b8db 100644 --- a/pom.xml +++ b/pom.xml @@ -16,7 +16,7 @@ 4.0.26-SNAPSHOT - 4.0.0 + 4.1.0-SNAPSHOT org.hl7.fhir.core