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More bug-hunting. DSTU3 was missing a null check.

This commit is contained in:
Diederik Muylwyk 2019-09-10 11:56:07 -04:00
parent 67d24eedff
commit 57d4cc23ee
8 changed files with 226 additions and 34 deletions
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9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
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@ -93,12 +93,12 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
boolean allSystemsAreSuppportedByTerminologyService = true;
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
@ -125,12 +125,12 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
boolean allSystemsAreSuppportedByTerminologyService = true;
for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
if (!myTerminologySvc.supportsSystem(next.getSystem())) {
if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
allSystemsAreSuppportedByTerminologyService = false;
}
}
@ -160,6 +160,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
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@ -156,6 +156,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
}
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
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@ -162,6 +162,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
}
ValueSet source = new ValueSet();
source.setUrl(theUri);
source.getCompose().addInclude().addValueSet(theUri);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
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@ -210,6 +210,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
// TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may time-out.
ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
if (vs == null) {
super.throwInvalidValueSet(theValueSet);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
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@ -122,6 +122,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
// TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may time-out.
ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
if (vs == null) {
super.throwInvalidValueSet(theValueSet);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
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@ -131,6 +131,7 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
// TODO: DM 2019-09-10 - This is problematic because an incorrect URL that matches ValueSet.id will not be found in the terminology tables but will yield a ValueSet here. Depending on the ValueSet, the expansion may time-out.
ValueSet valueSetR5 = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
if (valueSetR5 == null) {
super.throwInvalidValueSet(theValueSet);

236
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -1,14 +1,16 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoR4TerminologyTest;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
@ -25,11 +27,14 @@ import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.codesystems.HttpVerb;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
@ -43,18 +48,86 @@ import static org.junit.Assert.*;
public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3ValueSetTest.class);
private IIdType myExtensionalCsId;
private IIdType myExtensionalVsId;
private IIdType myLocalValueSetId;
private Long myExtensionalCsIdOnResourceTable;
private Long myExtensionalVsIdOnResourceTable;
private ValueSet myLocalVs;
@Before
@Transactional
public void before02() throws IOException {
CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
myCodeSystemDao.create(cs, mySrd);
// @Before
// @Transactional
// public void before02() throws IOException {
// CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
// myCodeSystemDao.create(cs, mySrd);
//
// ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
// myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
// }
ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
private void loadAndPersistCodeSystemAndValueSet(HttpVerb theVerb) throws IOException {
loadAndPersistCodeSystem(theVerb);
loadAndPersistValueSet(theVerb);
}
private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
codeSystem.setId("CodeSystem/cs");
persistCodeSystem(codeSystem, theVerb);
}
private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
switch (theVerb) {
case POST:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
case PUT:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalCsId = myCodeSystemDao.update(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
default:
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
}
myExtensionalCsIdOnResourceTable = myCodeSystemDao.readEntity(myExtensionalCsId, null).getId();
}
private void loadAndPersistValueSet(HttpVerb theVerb) throws IOException {
ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
valueSet.setId("ValueSet/vs");
persistValueSet(valueSet, theVerb);
}
private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
switch (theVerb) {
case POST:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
case PUT:
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
myExtensionalVsId = myValueSetDao.update(theValueSet, mySrd).getId().toUnqualifiedVersionless();
}
});
break;
default:
throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
}
myExtensionalVsIdOnResourceTable = myValueSetDao.readEntity(myExtensionalVsId, null).getId();
}
private CodeSystem createExternalCs() {
@ -169,7 +242,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandValueSetPropertySearchWithRegexExcludeUsingOr() {
public void testExpandValueSetPropertySearchWithRegexExcludeUsingOr() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
createLoincSystemWithSomeCodes();
List<String> codes;
@ -207,7 +282,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandValueSetPropertySearchWithRegexExcludeNoFilter() {
public void testExpandValueSetPropertySearchWithRegexExcludeNoFilter() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
createLoincSystemWithSomeCodes();
List<String> codes;
@ -233,7 +310,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandById() {
public void testExpandById() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
//@formatter:off
Parameters respParam = ourClient
.operation()
@ -263,7 +342,41 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
}
@Test
public void testExpandByIdWithFilter() {
public void testExpandByIdWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onInstance(myExtensionalVsId)
.named("expand")
.withNoParameters(Parameters.class)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, Matchers.containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
assertThat(resp, Matchers.containsString("<expansion>"));
assertThat(resp, Matchers.containsString("<contains>"));
assertThat(resp, Matchers.containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, Matchers.containsString("<code value=\"8450-9\"/>"));
assertThat(resp, Matchers.containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
assertThat(resp, Matchers.containsString("</contains>"));
assertThat(resp, Matchers.containsString("<contains>"));
assertThat(resp, Matchers.containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, Matchers.containsString("<code value=\"11378-7\"/>"));
assertThat(resp, Matchers.containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
assertThat(resp, Matchers.containsString("</contains>"));
assertThat(resp, Matchers.containsString("</expansion>"));
}
@Test
public void testExpandByIdWithFilter() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
//@formatter:off
Parameters respParam = ourClient
@ -290,7 +403,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
* https://groups.google.com/d/msgid/hapi-fhir/CAN2Cfy8kW%2BAOkgC6VjPsU3gRCpExCNZBmJdi-k5R_TWeyWH4tA%40mail.gmail.com?utm_medium=email&utm_source=footer
*/
@Test
public void testExpandByIdentifier() {
public void testExpandByIdentifier() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -308,7 +423,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
}
@Test
public void testExpandByUrl() {
public void testExpandByUrl() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -325,8 +442,70 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
}
@Test
public void testExpandByUrlWithBogusUrl() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
try {
ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
.execute();
} catch (ResourceNotFoundException e) {
assertEquals(404, e.getStatusCode());
assertEquals("HTTP 404 Not Found: Unknown ValueSet: http%3A%2F%2Fwww.healthintersections.com.au%2Ffhir%2FValueSet%2Fbogus", e.getMessage());
}
}
@Test
public void testExpandByUrlWithPreExpansion() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, Matchers.stringContainsInOrder(
"<code value=\"11378-7\"/>",
"<display value=\"Systolic blood pressure at First encounter\"/>"));
}
@Test
public void testExpandByUrlWithPreExpansionAndBogusUrl() throws Exception {
myDaoConfig.setPreExpandValueSetsExperimental(true);
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
try {
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
.execute();
} catch (ResourceNotFoundException e) {
assertEquals(404, e.getStatusCode());
assertEquals("HTTP 404 Not Found: Unknown ValueSet: http%3A%2F%2Fwww.healthintersections.com.au%2Ffhir%2FValueSet%2Fbogus", e.getMessage());
}
}
@Test
public void testExpandByValueSet() throws IOException {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
//@formatter:off
@ -397,6 +576,8 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandInvalidParams() throws IOException {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
try {
ourClient
.operation()
@ -576,7 +757,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
}
@Test
public void testValidateCodeOperationByCodeAndSystemInstance() {
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
//@formatter:off
Parameters respParam = ourClient
.operation()
@ -595,6 +778,8 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testValidateCodeOperationByCodeAndSystemInstanceOnInstance() throws IOException {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
createLocalCsAndVs();
createLocalVsWithIncludeConcept();
@ -617,7 +802,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
}
@Test
public void testValidateCodeOperationByCodeAndSystemType() {
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
//@formatter:off
Parameters respParam = ourClient
.operation()
@ -638,7 +825,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
* Technically this is the wrong param name
*/
@Test
public void testValiedateCodeAgainstBuiltInSystem() {
public void testValiedateCodeAgainstBuiltInSystem() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -666,7 +855,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
* Technically this is the right param name
*/
@Test
public void testValiedateCodeAgainstBuiltInSystemByUrl() {
public void testValiedateCodeAgainstBuiltInSystemByUrl() throws Exception {
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
@ -690,6 +881,11 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
assertEquals("Burn", ((StringType) respParam.getParameter().get(2).getValue()).getValue());
}
@After
public void afterResetPreExpansionDefault() {
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -52,16 +52,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
private Long myExtensionalVsIdOnResourceTable;
private ValueSet myLocalVs;
// @Before
// @Transactional
// public void before02() throws IOException {
// CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
// myCodeSystemDao.create(cs, mySrd);
//
// ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
// myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
// }
private void loadAndPersistCodeSystemAndValueSet(HttpVerb theVerb) throws IOException {
loadAndPersistCodeSystem(theVerb);
loadAndPersistValueSet(theVerb);