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2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.10 (#2545) 

* 2540 - Upgraded the fhir_core_version from 5.3.0 to 5.3.9.

* 2540 - Updated the Unit Test messages due to the upgraded dependencies.

* 2540 - Fixed some additional Unit Test message checks.

* 2540 - Updated the POM to refer to fhir_core_version 5.3.10-SNAPSHOT so a FULL Pipeline Build can run to verify that everything is fixed now.

* 2540 - Added some DEBUG Sysout logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...

* 2540 - Added some more logging to try and determine why the Pipeline Builds fail for a specific Unit Test when it passes locally...

* 2540 - Updated a Unit Test to account for a newly returned search param.

* 2540 - Updated a Unit Test to account for a newly returned search param and removed some debug output.
This commit is contained in:
Kevin Dougan SmileCDR 2021-04-29 15:00:37 -04:00 committed by GitHub
parent 239d2496ea
commit 646faa10e1
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10 changed files with 31 additions and 28 deletions
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24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
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@ -437,25 +437,25 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("non-existing-code").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Valid code with no system
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem(null).setCode("CODE3").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Valid code with wrong system
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem("http://foo").setCode("CODE3").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Code that exists but isn't in the valueset
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Invalid code in built-in VS/CS
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
@ -813,7 +813,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
} catch (PreconditionFailedException e) {
outcome = (OperationOutcome) e.getOperationOutcome();
ourLog.info("Outcome: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("None of the codes provided are in the value set http://example.com/valueset (http://example.com/valueset), and a code from this value set is required) (codes = http://example.com/foo-foo#some-code)", outcome.getIssueFirstRep().getDiagnostics());
assertEquals("None of the codings provided are in the value set http://example.com/valueset (http://example.com/valueset), and a coding from this value set is required) (codes = http://example.com/foo-foo#some-code)", outcome.getIssueFirstRep().getDiagnostics());
assertEquals(OperationOutcome.IssueSeverity.ERROR, outcome.getIssueFirstRep().getSeverity());
}
}
@ -872,25 +872,25 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem("http://loinc.org").setCode("non-existing-code").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://loinc.org#non-existing-code)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Valid code with no system
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem(null).setCode("CODE3").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = null#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Valid code with wrong system
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem("http://foo").setCode("CODE3").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://foo#CODE3)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Code that exists but isn't in the valueset
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
obs.getCode().getCodingFirstRep().setSystem("http://terminology.hl7.org/CodeSystem/observation-category").setCode("vital-signs").setDisplay("Display 3");
oo = validateAndReturnOutcome(obs);
assertEquals("None of the codes provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a code from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
assertEquals("None of the codings provided are in the value set http://example.com/fhir/ValueSet/observation-vitalsignresult (http://example.com/fhir/ValueSet/observation-vitalsignresult), and a coding from this value set is required) (codes = http://terminology.hl7.org/CodeSystem/observation-category#vital-signs)", oo.getIssueFirstRep().getDiagnostics(), encode(oo));
// Invalid code in built-in VS/CS
obs.getText().setStatus(Narrative.NarrativeStatus.GENERATED);
@ -1028,7 +1028,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
ourLog.info(myFhirCtx.newJsonParser().encodeResourceToString(allergy));
OperationOutcome oo = validateAndReturnOutcome(allergy);
assertThat(encode(oo), containsString("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/allergyintolerance-clinical"));
assertThat(encode(oo), containsString("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/allergyintolerance-clinical"));
}
@SuppressWarnings("unchecked")
@ -1138,7 +1138,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
// It would be ok for this to produce 0 issues, or just an information message too
assertEquals(1, OperationOutcomeUtil.getIssueCount(myFhirCtx, oo));
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 and the validator cannot judge what is suitable) (codes = http://foo#bar)", OperationOutcomeUtil.getFirstIssueDetails(myFhirCtx, oo));
assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), 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 = http://foo#bar)", OperationOutcomeUtil.getFirstIssueDetails(myFhirCtx, oo));
}
@ -1630,7 +1630,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
} catch (PreconditionFailedException e) {
OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
assertThat(oo.getIssueFirstRep().getDiagnostics(), containsString("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/condition-clinical"));
assertThat(oo.getIssueFirstRep().getDiagnostics(), containsString("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/condition-clinical"));
}
}

13
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r5/ResourceProviderR5ConceptMapTest.java
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@ -26,7 +26,6 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
@Test
public void testTranslateWithConceptMapUrlAndVersion() {
//- conceptMap1 v1
ConceptMap conceptMap1 = new ConceptMap();
conceptMap1.setUrl(CM_URL).setVersion("v1").setSource(new UriType(VS_URL)).setTarget(new UriType(VS_URL_2));
@ -63,7 +62,6 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
ourLog.info("ConceptMap: 2 \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap2));
Parameters inParams = new Parameters();
inParams.addParameter().setName("url").setValue(new UriType(CM_URL));
inParams.addParameter().setName("conceptMapVersion").setValue(new StringType("v2"));
@ -73,7 +71,6 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
ourLog.info("Request Parameters:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inParams));
Parameters respParams = myClient
.operation()
.onType(ConceptMap.class)
@ -82,8 +79,7 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
.execute();
ourLog.info("Response Parameters\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(respParams));
ParametersParameterComponent param = getParameterByName(respParams, "result");
assertTrue(((BooleanType) param.getValue()).booleanValue());
@ -92,7 +88,8 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
param = getParametersByName(respParams, "match").get(0);
assertEquals(2, param.getPart().size());
assertEquals(3, param.getPart().size());
ParametersParameterComponent part = getPartByName(param, "concept");
Coding coding = (Coding) part.getValue();
@ -104,7 +101,9 @@ public class ResourceProviderR5ConceptMapTest extends BaseResourceProviderR5Test
part = getPartByName(param, "source");
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
part = getPartByName(param, "equivalence");
assertEquals("relatedto", part.getValue().toString());
}
@Test

4
hapi-fhir-validation/pom.xml
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@ -63,6 +63,10 @@
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>

4
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java
View File

@ -596,7 +596,7 @@ public class FhirInstanceValidatorDstu3Test {
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> issues = logResultsAndReturnNonInformationalOnes(output);
assertThat(issues.toString(), containsString("None of the codes provided are in the value set http://phr.kanta.fi/ValueSet/fiphr-vs-medicationcontext"));
assertThat(issues.toString(), containsString("None of the codings provided are in the value set http://phr.kanta.fi/ValueSet/fiphr-vs-medicationcontext"));
}
@Test
@ -1278,7 +1278,7 @@ public class FhirInstanceValidatorDstu3Test {
assertEquals(1, all.size());
assertEquals("Patient.identifier[0].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 and the validator cannot judge what is suitable) (codes = http://example.com/foo/bar#bar)",
"None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), 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 = http://example.com/foo/bar#bar)",
all.get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());

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

@ -118,7 +118,7 @@ public class QuestionnaireValidatorDstu3Test {
ValidationResult errors = myVal.validateWithResult(q);
ourLog.info(errors.toString());
assertThat(errors.isSuccessful(), Matchers.is(true));
assertThat(errors.getMessages().get(0).getMessage(), containsString("and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = null#text-box)"));
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)"));
}
}

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/ResourceValidatorDstu3Test.java
View File

@ -165,7 +165,7 @@ public class ResourceValidatorDstu3Test {
ValidationResult output = val.validateWithResult(p);
List<SingleValidationMessage> all = logResultsAndReturnNonInformationalOnes(output);
assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status), and a code should come from this value set unless it has no suitable code and the validator cannot judge what is suitable) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status), 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 = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, output.getMessages().get(0).getSeverity());
}

4
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -628,7 +628,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnAll(output);
assertEquals(1, errors.size());
assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/report-codes (http://hl7.org/fhir/ValueSet/report-codes), and a code is recommended to come from this value set) (codes = http://loinc.org#1-8)", errors.get(0).getMessage());
assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/report-codes (http://hl7.org/fhir/ValueSet/report-codes), and a coding is recommended to come from this value set) (codes = http://loinc.org#1-8)", errors.get(0).getMessage());
}
@Test
@ -1333,7 +1333,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
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 codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type"));
assertThat(all.get(0).getMessage(), containsString("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type"));
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
}

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/FhirInstanceValidatorR5Test.java
View File

@ -945,7 +945,7 @@ public class FhirInstanceValidatorR5Test {
assertEquals(1, all.size());
assertEquals("Patient.identifier[0].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 and the validator cannot judge what is suitable) (codes = http://example.com/foo/bar#bar)",
"None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type), 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 = http://example.com/foo/bar#bar)",
all.get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());

2
osgi/hapi-fhir-karaf-integration-tests/src/test/java/ca/uhn/fhir/tests/integration/karaf/dstu3/ResourceValidatorDstu3FeatureTest.java
View File

@ -142,7 +142,7 @@ public class ResourceValidatorDstu3FeatureTest {
ValidationResult output = val.validateWithResult(p);
List<SingleValidationMessage> all = logResultsAndReturnNonInformationalOnes(output);
assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status, and a code should come from this value set unless it has no suitable code) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
assertEquals("None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/marital-status (http://hl7.org/fhir/ValueSet/marital-status, and a coding should come from this value set unless it has no suitable code) (codes = http://hl7.org/fhir/v3/MaritalStatus#FOO)", output.getMessages().get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, output.getMessages().get(0).getSeverity());
}

2
pom.xml
View File

@ -743,7 +743,7 @@
<properties>
<fhir_core_version>5.3.0</fhir_core_version>
<fhir_core_version>5.3.10</fhir_core_version>
<ucum_version>1.0.3</ucum_version>
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>