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Fix more tests

This commit is contained in:
dotasek.dev 2024-02-28 14:54:20 -05:00
parent 01f4604350
commit 5f152a7e78
6 changed files with 53 additions and 35 deletions
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3
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/VersionSpecificWorkerContextWrapper.java
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@ -775,7 +775,8 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
.setDiagnostics(message)
.setDetails(new CodeableConcept().setText(message));
return new ValidationResult(ValidationMessage.IssueSeverity.ERROR, null, Collections.singletonList(issue));
return new ValidationResult(
ValidationMessage.IssueSeverity.ERROR, null, Collections.singletonList(issue));
}
ValidationResult retVal = validateCode(theOptions, next, theVs);
if (retVal.isOk()) {

34
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java
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@ -71,6 +71,7 @@ import org.mockito.stubbing.Answer;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@ -351,9 +352,9 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
ValidationResult result = val.validateWithResult(p);
assertFalse(result.isSuccessful());
List<SingleValidationMessage> all = logResultsAndReturnAll(result);
assertEquals(1, all.size());
assertEquals(2, all.size());
assertEquals(ResultSeverityEnum.ERROR, all.get(0).getSeverity());
assertEquals("Unknown code 'urn:iso:std:iso:3166#QQ' for 'urn:iso:std:iso:3166#QQ'", all.get(0).getMessage());
assertEquals("Unknown code (for 'urn:iso:std:iso:3166#QQ')", all.get(0).getMessage());
}
}
@ -516,6 +517,7 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
@Test
public void testGoal() {
addValidConcept("http://foo", "some other goal");
Goal goal = new Goal();
goal.setSubject(new Reference("Patient/123"));
goal.setDescription(new CodeableConcept().addCoding(new Coding("http://foo", "some other goal", "")));
@ -778,9 +780,7 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
ValidationResult results = myVal.validateWithResult(is);
List<SingleValidationMessage> outcome = logResultsAndReturnNonInformationalOnes(results);
assertEquals(1, outcome.size());
assertEquals("Unknown code 'http://dicom.nema.org/resources/ontology/DCM#BAR' for 'http://dicom.nema.org/resources/ontology/DCM#BAR'", outcome.get(0).getMessage());
// assertEquals("The Coding provided is not in the value set http://hl7.org/fhir/ValueSet/dicom-cid29, and a code should come from this value set unless it has no suitable code. (error message = Unknown code[BAR] in system[http://dicom.nema.org/resources/ontology/DCM])", outcome.get(1).getMessage());
assertThat(outcome.get(0).getMessage(), containsString("The Coding provided (http://dicom.nema.org/resources/ontology/DCM#BAR) was not found in the value set 'Acquisition Modality Codes' (http://hl7.org/fhir/ValueSet/dicom-cid29|20121129)") );
}
/**
@ -1048,7 +1048,7 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> res = logResultsAndReturnNonInformationalOnes(output);
assertEquals(1, res.size(), output.toString());
assertEquals("A code with no system has no defined meaning, and it cannot be validated. A system should be provided", output.getMessages().get(0).getMessage());
assertEquals("Coding has no system. A code with no system has no defined meaning, and it cannot be validated. A system should be provided", output.getMessages().get(0).getMessage());
}
/**
@ -1137,7 +1137,7 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertEquals(ResultSeverityEnum.ERROR, errors.get(0).getSeverity());
assertEquals("Unknown code for 'http://loinc.org#12345'", errors.get(0).getMessage());
assertEquals("Unknown code (for 'http://loinc.org#12345')", errors.get(0).getMessage());
}
@Test
@ -1233,6 +1233,8 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
@Test
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
addValidConcept("http://loinc.org", "12345");
Observation input = createObservationWithDefaultSubjectPerfomerEffective();
myInstanceVal.setValidationSupport(myValidationSupport);
@ -1259,7 +1261,7 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertThat(errors.toString(), errors.size(), greaterThan(0));
assertEquals("Unknown code for 'http://acme.org#9988877'", errors.get(0).getMessage());
assertEquals("Unknown code (for 'http://acme.org#9988877')", errors.get(0).getMessage());
}
@ -1295,7 +1297,7 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(1, errors.size());
assertEquals("Unknown code for 'http://loinc.org#1234'", errors.get(0).getMessage());
assertEquals("Unknown code (for 'http://loinc.org#1234')", errors.get(0).getMessage());
}
@Test
@ -1321,12 +1323,14 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
ValidationResult output = myVal.validateWithResult(patient);
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
assertEquals(1, all.size());
assertEquals(2, all.size());
assertThat(all.get(0).getMessage(), containsString("Unknown code (for 'http://example.com/foo/bar#bar')"));
assertEquals(ResultSeverityEnum.ERROR, all.get(0).getSeverity());
assertEquals("Patient.identifier[0].type", all.get(0).getLocationString());
assertThat(
all.get(0).getMessage(),
all.get(1).getMessage(),
containsString("None of the codings provided are in the value set 'Identifier Type Codes'"));
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
assertEquals(ResultSeverityEnum.WARNING, all.get(1).getSeverity());
}
@ -1359,6 +1363,9 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
IValidationPolicyAdvisor policyAdvisor = mock(IValidationPolicyAdvisor.class);
IValidatorResourceFetcher fetcher = mock(IValidatorResourceFetcher.class);
when(policyAdvisor.policyForElement(any(), any(),any(),any(),any())).thenReturn(EnumSet.allOf(IValidationPolicyAdvisor.ElementValidationAction.class));
when(policyAdvisor.policyForCodedContent(any(),any(),any(),any(),any(),any(),any(),any(),any())).thenReturn(EnumSet.allOf(IValidationPolicyAdvisor.CodedContentValidationAction.class));
when(policyAdvisor.policyForReference(any(), any(), any(), any())).thenReturn(ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS);
when(policyAdvisor.policyForReference(any(), any(), any(), any())).thenReturn(ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS);
@ -1373,8 +1380,9 @@ public class FhirInstanceValidatorDstu3Test extends BaseValidationTestWithInline
@Test
public void testValueWithWhitespace() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/dstu3-rick-test.json"), Charsets.UTF_8);
addValidConcept("http://loinc.org", "34133-1");
String input = IOUtils.toString(FhirInstanceValidatorDstu3Test.class.getResourceAsStream("/dstu3-rick-test.json"), Charsets.UTF_8);
ValidationResult results = myVal.validateWithResult(input);
List<SingleValidationMessage> outcome = logResultsAndReturnNonInformationalOnes(results);
assertEquals(2, outcome.size());

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireResponseValidatorDstu3Test.java
View File

@ -278,7 +278,7 @@ public class QuestionnaireResponseValidatorDstu3Test {
errors = myVal.validateWithResult(qa);
errors = stripBindingHasNoSourceMessage(errors);
ourLog.info(errors.toString());
assertThat(errors.toString(), containsString("Unknown code: http://codesystems.com/system / code1 for 'http://codesystems.com/system#code1'"));
assertThat(errors.toString(), containsString("Unknown code: http://codesystems.com/system / code1 (for 'http://codesystems.com/system#code1')"));
assertThat(errors.toString(), containsString("QuestionnaireResponse.item[0].answer[0]"));
// Unhandled system

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/QuestionnaireValidatorDstu3Test.java
View File

@ -119,7 +119,7 @@ public class QuestionnaireValidatorDstu3Test extends BaseValidationTestWithInlin
ValidationResult errors = myVal.validateWithResult(q);
ourLog.info(errors.toString());
assertThat(errors.isSuccessful(), Matchers.is(true));
assertThat(errors.getMessages().get(0).getMessage(), containsString("and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = null#text-box)"));
assertThat(errors.getMessages().get(1).getMessage(), containsString("and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = null#text-box)"));
}
}

45
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
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@ -377,7 +377,7 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
ValidationResult result = val.validateWithResult(input);
List<SingleValidationMessage> all = logResultsAndReturnErrorOnes(result);
assertFalse(result.isSuccessful(), all.toString());
assertThat(result.getMessages().get(0).getMessage(), startsWith("Unknown code 'https://hapifhir.io/fhir/CodeSystem/hapi-fhir-storage-response-code#foo'"));
assertThat(result.getMessages().get(0).getMessage(), startsWith("Unknown code (for 'https://hapifhir.io/fhir/CodeSystem/hapi-fhir-storage-response-code#foo')"));
}
@ -396,7 +396,7 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
ValidationResult result = val.validateWithResult(p);
List<SingleValidationMessage> all = logResultsAndReturnErrorOnes(result);
assertFalse(result.isSuccessful());
assertEquals("The code 'AA ' is not valid (whitespace rules)", all.get(0).getMessage());
assertEquals("The code 'AA ' is not valid (whitespace rules)", all.get(1).getMessage());
}
@ -518,6 +518,8 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
*/
@Test
public void testValidateDoesntEnforceBestPracticesByDefault() {
addValidConcept("http://loinc.org", "1234");
Observation input = new Observation();
input.addPerformer(new Reference("Practitioner/124"));
input.setEffective(new DateTimeType("2023-01-01T11:22:33Z"));
@ -708,10 +710,11 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
public void testLargeBase64() throws IOException {
String input = IOUtils.toString(FhirInstanceValidatorR4Test.class.getResourceAsStream("/r4/diagnosticreport-example-gingival-mass.json"), Constants.CHARSET_UTF8);
ValidationResult output = myFhirValidator.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertEquals(2, errors.size());
assertThat(errors.get(0).getMessage(), containsString("None of the codings provided are in the value set 'LOINC Diagnostic Report Codes'"));
assertEquals("Base64 encoded values SHOULD not contain any whitespace (per RFC 4648). Note that non-validating readers are encouraged to accept whitespace anyway", errors.get(1).getMessage());
List<SingleValidationMessage> messages = logResultsAndReturnAll(output);
assertEquals(3, messages.size());
assertThat(messages.get(0).getMessage(), containsString("Unknown code (for 'http://loinc.org#1-8')"));
assertThat(messages.get(1).getMessage(), containsString("None of the codings provided are in the value set 'LOINC Diagnostic Report Codes'"));
assertEquals("Base64 encoded values SHOULD not contain any whitespace (per RFC 4648). Note that non-validating readers are encouraged to accept whitespace anyway", messages.get(2).getMessage());
}
@Test
@ -1112,7 +1115,7 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
ValidationResult output = myFhirValidator.validateWithResult(input);
List<SingleValidationMessage> res = logResultsAndReturnNonInformationalOnes(output);
assertEquals(1, res.size(), output.toString());
assertEquals("A code with no system has no defined meaning, and it cannot be validated. A system should be provided", output.getMessages().get(0).getMessage());
assertEquals("Coding has no system. A code with no system has no defined meaning, and it cannot be validated. A system should be provided", output.getMessages().get(0).getMessage());
}
/**
@ -1203,7 +1206,7 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertEquals(ResultSeverityEnum.ERROR, errors.get(0).getSeverity());
assertEquals("Unknown code for 'http://loinc.org#12345'", errors.get(0).getMessage());
assertEquals("Unknown code (for 'http://loinc.org#12345')", errors.get(0).getMessage());
}
@Test
@ -1330,6 +1333,7 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
@Test
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
addValidConcept("http://loinc.org", "12345");
Observation input = createObservationWithDefaultSubjectPerfomerEffective();
input.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
@ -1400,7 +1404,7 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
ValidationResult output = myFhirValidator.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertThat(errors.toString(), errors.size(), greaterThan(0));
assertEquals("Unknown code for 'http://acme.org#9988877'", errors.get(0).getMessage());
assertEquals("Unknown code (for 'http://acme.org#9988877')", errors.get(0).getMessage());
}
@ -1439,7 +1443,7 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
ValidationResult output = myFhirValidator.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(1, errors.size());
assertEquals("Unknown code for 'http://loinc.org#1234'", errors.get(0).getMessage());
assertEquals("Unknown code (for 'http://loinc.org#1234')", errors.get(0).getMessage());
}
@Test
@ -1467,10 +1471,13 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
ValidationResult output = myFhirValidator.validateWithResult(p);
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
assertEquals(1, all.size());
assertEquals("Patient.identifier[0].type", all.get(0).getLocationString());
assertThat(all.get(0).getMessage(), containsString("None of the codings provided are in the value set 'IdentifierType'"));
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
assertEquals(2, all.size());
assertThat(all.get(0).getMessage(), containsString("Unknown code (for 'http://example.com/foo/bar#bar')"));
assertEquals(ResultSeverityEnum.ERROR, all.get(0).getSeverity());
assertThat(all.get(1).getMessage(), containsString("None of the codings provided are in the value set 'IdentifierType'"));
assertEquals(ResultSeverityEnum.WARNING, all.get(1).getSeverity());
}
@ -1731,6 +1738,8 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
@Test
void testValidateCommonCodes_Currency_ErrorMessageIsPreserved() {
addValidConcept("http://loinc.org", "1234");
buildValidationSupportWithLogicalAndSupport(false);
Observation input = createObservationWithDefaultSubjectPerfomerEffective();
@ -1752,10 +1761,10 @@ public class FhirInstanceValidatorR4Test extends BaseValidationTestWithInlineMoc
OperationOutcome oo = (OperationOutcome) result.toOperationOutcome();
ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals("Unknown code 'urn:iso:std:iso:4217#blah' (for 'urn:iso:std:iso:4217#blah')", result.getMessages().get(0).getMessage());
assertEquals(ResultSeverityEnum.ERROR, result.getMessages().get(0).getSeverity());
assertEquals(22, result.getMessages().get(0).getLocationLine());
assertEquals(4, result.getMessages().get(0).getLocationCol());
assertEquals("Unknown code 'urn:iso:std:iso:4217#blah' (for 'urn:iso:std:iso:4217#blah')", result.getMessages().get(1).getMessage());
assertEquals(ResultSeverityEnum.ERROR, result.getMessages().get(1).getSeverity());
assertEquals(22, result.getMessages().get(1).getLocationLine());
assertEquals(4, result.getMessages().get(1).getLocationCol());
assertEquals("Observation.value.ofType(Quantity)", result.getMessages().get(0).getLocationString());
assertEquals("Terminology_PassThrough_TX_Message", result.getMessages().get(0).getMessageId());

2
pom.xml
View File

@ -910,7 +910,7 @@
</licenses>
<properties>
<fhir_core_version>6.2.16-SNAPSHOT</fhir_core_version>
<fhir_core_version>6.3.1-SNAPSHOT</fhir_core_version>
<spotless_version>2.41.1</spotless_version>
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>