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Updated tests for missed dstu2 code coverage.

This commit is contained in:
ianmarshall 2020-09-30 18:10:57 -04:00
parent dc3443665c
commit 90f1981817
3 changed files with 159 additions and 14 deletions
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26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu2.java
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@ -47,18 +47,18 @@ public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
@Autowired
private IValidationSupport myValidationSupport;
private void addAllChildren(String theSystemString, org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
private void addAllChildren(String theSystemString, ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
if (isNotBlank(theCode.getCode())) {
theListToPopulate.add(new FhirVersionIndependentConcept(theSystemString, theCode.getCode()));
}
for (org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent nextChild : theCode.getConcept()) {
for (ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept nextChild : theCode.getConcept()) {
addAllChildren(theSystemString, nextChild, theListToPopulate);
}
}
private boolean addTreeIfItContainsCode(String theSystemString, org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent theNext, String theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
private boolean addTreeIfItContainsCode(String theSystemString, ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept theNext, String theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
boolean foundCodeInChild = false;
for (org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent nextChild : theNext.getConcept()) {
for (ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept nextChild : theNext.getConcept()) {
foundCodeInChild |= addTreeIfItContainsCode(theSystemString, nextChild, theCode, theListToPopulate);
}
@ -95,9 +95,9 @@ public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
throw new UnsupportedOperationException();
}
private void findCodesAbove(org.hl7.fhir.dstu2.model.ValueSet theSystem, String theSystemString, String theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
List<org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent> conceptList = theSystem.getCodeSystem().getConcept();
for (org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent next : conceptList) {
private void findCodesAbove(ca.uhn.fhir.model.dstu2.resource.ValueSet theSystem, String theSystemString, String theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
List<ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept> conceptList = theSystem.getCodeSystem().getConcept();
for (ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept next : conceptList) {
addTreeIfItContainsCode(theSystemString, next, theCode, theListToPopulate);
}
}
@ -105,20 +105,20 @@ public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
@Override
public List<FhirVersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<FhirVersionIndependentConcept> retVal = new ArrayList<>();
org.hl7.fhir.dstu2.model.ValueSet system = (org.hl7.fhir.dstu2.model.ValueSet) myValidationSupport.fetchCodeSystem(theSystem);
ca.uhn.fhir.model.dstu2.resource.ValueSet system = (ca.uhn.fhir.model.dstu2.resource.ValueSet) myValidationSupport.fetchCodeSystem(theSystem);
if (system != null) {
findCodesAbove(system, theSystem, theCode, retVal);
}
return retVal;
}
private void findCodesBelow(org.hl7.fhir.dstu2.model.ValueSet theSystem, String theSystemString, String theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
List<org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent> conceptList = theSystem.getCodeSystem().getConcept();
private void findCodesBelow(ca.uhn.fhir.model.dstu2.resource.ValueSet theSystem, String theSystemString, String theCode, List<FhirVersionIndependentConcept> theListToPopulate) {
List<ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept> conceptList = theSystem.getCodeSystem().getConcept();
findCodesBelow(theSystemString, theCode, theListToPopulate, conceptList);
}
private void findCodesBelow(String theSystemString, String theCode, List<FhirVersionIndependentConcept> theListToPopulate, List<org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent> conceptList) {
for (org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent next : conceptList) {
private void findCodesBelow(String theSystemString, String theCode, List<FhirVersionIndependentConcept> theListToPopulate, List<ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept> conceptList) {
for (ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept next : conceptList) {
if (theCode.equals(next.getCode())) {
addAllChildren(theSystemString, next, theListToPopulate);
} else {
@ -130,7 +130,7 @@ public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
@Override
public List<FhirVersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<FhirVersionIndependentConcept> retVal = new ArrayList<>();
org.hl7.fhir.dstu2.model.ValueSet system = (org.hl7.fhir.dstu2.model.ValueSet) myValidationSupport.fetchCodeSystem(theSystem);
ca.uhn.fhir.model.dstu2.resource.ValueSet system = (ca.uhn.fhir.model.dstu2.resource.ValueSet) myValidationSupport.fetchCodeSystem(theSystem);
if (system != null) {
findCodesBelow(system, theSystem, theCode, retVal);
}

89
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu2Test.java
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@ -1,13 +1,34 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.dstu2.BaseJpaDstu2Test;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.FhirVersionIndependentConcept;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.r4.model.Coding;
import org.junit.jupiter.api.Test;
import org.mockito.Answers;
import org.mockito.Mock;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import java.util.Set;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class TerminologySvcImplDstu2Test {
public class TerminologySvcImplDstu2Test extends BaseJpaDstu2Test {
@Autowired
protected ITermReadSvc myTermReadSvc;
@Mock(answer = Answers.RETURNS_DEEP_STUBS)
protected ServletRequestDetails mySrd;
@Test
public void testToCanonicalCoding() {
@ -17,4 +38,70 @@ public class TerminologySvcImplDstu2Test {
assertEquals("dstuCode", convertedCoding.getCode());
assertEquals("dstuSystem", convertedCoding.getSystem());
}
@Test
public void testFindCodesBelowBuiltInCodeSystem() {
List<FhirVersionIndependentConcept> concepts;
Set<String> codes;
ValueSet upload = new ValueSet();
upload.setId(new IdDt("testVs"));
upload.setUrl("http://myVs");
ValueSet.CodeSystem codeSystem = new ValueSet.CodeSystem().setSystem("http://myCs");
codeSystem.addConcept(new ValueSet.CodeSystemConcept().setCode("codeA").addConcept(new ValueSet.CodeSystemConcept().setCode("codeAB")));
upload.setCodeSystem(codeSystem);
myValueSetDao.update(upload, mySrd);
concepts = myTermReadSvc.findCodesBelow("http://myVs", "codeA");
codes = toCodes(concepts);
assertThat(codes, containsInAnyOrder("codeA", "codeAB"));
concepts = myTermReadSvc.findCodesBelow("http://myVs", "codeAB");
codes = toCodes(concepts);
assertThat(codes, containsInAnyOrder("codeAB"));
// Unknown code
concepts = myTermReadSvc.findCodesBelow("http://myVs", "FOO");
codes = toCodes(concepts);
assertThat(codes, empty());
// Unknown system
concepts = myTermReadSvc.findCodesBelow("http://myVs2222", "codeA");
codes = toCodes(concepts);
assertThat(codes, empty());
}
@Test
public void testFindCodesAboveBuiltInCodeSystem() {
List<FhirVersionIndependentConcept> concepts;
Set<String> codes;
ValueSet upload = new ValueSet();
upload.setId(new IdDt("testVs"));
upload.setUrl("http://myVs");
ValueSet.CodeSystem codeSystem = new ValueSet.CodeSystem().setSystem("http://myCs");
codeSystem.addConcept(new ValueSet.CodeSystemConcept().setCode("codeA").addConcept(new ValueSet.CodeSystemConcept().setCode("codeAB")));
upload.setCodeSystem(codeSystem);
myValueSetDao.update(upload, mySrd);
concepts = myTermReadSvc.findCodesAbove("http://myVs", "codeA");
codes = toCodes(concepts);
assertThat(codes, containsInAnyOrder("codeA"));
concepts = myTermReadSvc.findCodesAbove("http://myVs", "codeAB");
codes = toCodes(concepts);
assertThat(codes, containsInAnyOrder("codeA", "codeAB"));
// Unknown code
concepts = myTermReadSvc.findCodesAbove("http://myVs", "FOO");
codes = toCodes(concepts);
assertThat(codes, empty());
// Unknown system
concepts = myTermReadSvc.findCodesBelow("http://myVs2222", "codeA");
codes = toCodes(concepts);
assertThat(codes, empty());
}
}

58
hapi-fhir-validation/src/test/java/org/hl7/fhir/common/hapi/validation/support/InMemoryTerminologyServerValidationSupportTest.java
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@ -5,11 +5,15 @@ import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.util.HashMap;
import java.util.Map;
import static org.junit.jupiter.api.Assertions.*;
class InMemoryTerminologyServerValidationSupportTest {
@ -54,5 +58,59 @@ class InMemoryTerminologyServerValidationSupportTest {
}
@Test
public void testValidateCodeDstu2() {
FhirContext ctxDstu2 = FhirContext.forDstu2Hl7Org();
PrePopulatedValidationSupportDstu2 dstu2PrePopulated = new PrePopulatedValidationSupportDstu2(ctxDstu2);
mySvc = new InMemoryTerminologyServerValidationSupport(ctxDstu2);
myDefaultSupport = new DefaultProfileValidationSupport(ctxDstu2);
myChain = new ValidationSupportChain(mySvc, dstu2PrePopulated, myDefaultSupport);
org.hl7.fhir.dstu2.model.ValueSet vs = new org.hl7.fhir.dstu2.model.ValueSet();
vs.setUrl("http://vs");
vs
.getCompose()
.addInclude()
.setSystem("http://cs")
.addConcept(new org.hl7.fhir.dstu2.model.ValueSet.ConceptReferenceComponent(new org.hl7.fhir.dstu2.model.CodeType("code1")))
.addConcept(new org.hl7.fhir.dstu2.model.ValueSet.ConceptReferenceComponent(new org.hl7.fhir.dstu2.model.CodeType("code2")));
vs.getCodeSystem()
.addConcept(new org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent(new org.hl7.fhir.dstu2.model.CodeType("code1")))
.addConcept(new org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionComponent(new org.hl7.fhir.dstu2.model.CodeType("code2")));
dstu2PrePopulated.addValueSet(vs, "http://vs", "http://cs");
ValidationSupportContext valCtx = new ValidationSupportContext(myChain);
ConceptValidationOptions options = new ConceptValidationOptions();
IValidationSupport.CodeValidationResult outcome = mySvc.validateCode(valCtx, options, "http://cs", "code1", null, "http://vs");
assertTrue(outcome.isOk());
}
private static class PrePopulatedValidationSupportDstu2 extends PrePopulatedValidationSupport {
private final Map<String, IBaseResource> myDstu2ValueSets;
PrePopulatedValidationSupportDstu2(FhirContext theFhirContext) {
super(theFhirContext);
myDstu2ValueSets = new HashMap<>();
}
public void addValueSet(org.hl7.fhir.dstu2.model.ValueSet theValueSet, String valueSetUrl, String codeSystemUrl) {
myDstu2ValueSets.put(valueSetUrl, theValueSet);
myDstu2ValueSets.put(codeSystemUrl, theValueSet);
}
@Override
public IBaseResource fetchValueSet(String theUri) {
return myDstu2ValueSets.get(theUri);
}
@Override
public IBaseResource fetchCodeSystem(String theSystem) {
return myDstu2ValueSets.get(theSystem);
}
}
}