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Correctly handle encoding contained resources where some have user 

assigned IDs and some do not
This commit is contained in:
James Agnew 2018-04-17 18:26:06 -04:00
parent c450d51440
commit 162069776a
5 changed files with 161 additions and 25 deletions
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53
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -193,6 +193,19 @@ public abstract class BaseParser implements IParser {
{
List<IBaseReference> allElements = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
for (IBaseReference next : allElements) {
IBaseResource resource = next.getResource();
if (resource == null && next.getReferenceElement().isLocal()) {
if (existingIdToContainedResource != null) {
IBaseResource potentialTarget = existingIdToContainedResource.remove(next.getReferenceElement().getValue());
if (potentialTarget != null) {
theContained.addContained(next.getReferenceElement(), potentialTarget);
containResourcesForEncoding(theContained, potentialTarget, theTarget);
}
}
}
}
for (IBaseReference next : allElements) {
IBaseResource resource = next.getResource();
if (resource != null) {
@ -210,15 +223,8 @@ public abstract class BaseParser implements IParser {
}
containResourcesForEncoding(theContained, resource, theTarget);
} else if (next.getReferenceElement().isLocal()) {
if (existingIdToContainedResource != null) {
IBaseResource potentialTarget = existingIdToContainedResource.remove(next.getReferenceElement().getValue());
if (potentialTarget != null) {
theContained.addContained(next.getReferenceElement(), potentialTarget);
containResourcesForEncoding(theContained, potentialTarget, theTarget);
}
}
}
}
}
@ -1170,8 +1176,9 @@ public abstract class BaseParser implements IParser {
static class ContainedResources {
private long myNextContainedId = 1;
private List<IBaseResource> myResources = new ArrayList<IBaseResource>();
private IdentityHashMap<IBaseResource, IIdType> myResourceToId = new IdentityHashMap<IBaseResource, IIdType>();
private List<IBaseResource> myResources = new ArrayList<>();
private IdentityHashMap<IBaseResource, IIdType> myResourceToId = new IdentityHashMap<>();
private Set<String> myExistingLocalIds = new HashSet<>();
public void addContained(IBaseResource theResource) {
if (myResourceToId.containsKey(theResource)) {
@ -1184,7 +1191,20 @@ public abstract class BaseParser implements IParser {
} else {
// TODO: make this configurable between the two below (and something else?)
// newId = new IdDt(UUID.randomUUID().toString());
newId = new IdDt(myNextContainedId++);
// Generally we won't even go into this loop once since
// our next ID shouldn't already exist, but there is
// always a chance that it does if someone is mixing
// manually assigned local IDs with HAPI assigned ones
// See JsonParser#testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalFirst
// and JsonParser#testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalLast
// for examples of where this is needed...
while (!myExistingLocalIds.add("#" + myNextContainedId)) {
myNextContainedId++;
}
newId = new IdDt(myNextContainedId);
myNextContainedId++;
}
myResourceToId.put(theResource, newId);
@ -1192,7 +1212,7 @@ public abstract class BaseParser implements IParser {
}
public void addContained(IIdType theId, IBaseResource theResource) {
if (!hasId(theId)) {
if (myExistingLocalIds.add(theId.getValue())) {
myResourceToId.put(theResource, theId);
myResources.add(theResource);
}
@ -1206,15 +1226,6 @@ public abstract class BaseParser implements IParser {
return myResourceToId.get(theNext);
}
public boolean hasId(IIdType theId) {
for (IIdType next : myResourceToId.values()) {
if (Objects.equals(next.getValue(), theId.getValue())) {
return true;
}
}
return false;
}
public boolean isEmpty() {
return myResourceToId.isEmpty();
}

30
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -152,6 +152,36 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
return input;
}
@Test
public void testTransactionUpdateTwoResourcesWithSameId() {
Bundle request = new Bundle();
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("DDD");
p.setId("Patient/ABC");
request.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.PUT)
.setUrl("Patient/ABC");
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("DDD");
p.setId("Patient/ABC");
request.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.PUT)
.setUrl("Patient/ABC");
try {
mySystemDao.transaction(mySrd, request);
fail();
} catch (InvalidRequestException e) {
assertThat(e.getMessage(), containsString("Transaction bundle contains multiple resources with ID: Patient/ABC"));
}
}
@SuppressWarnings("unchecked")
private <T extends org.hl7.fhir.dstu3.model.Resource> T find(Bundle theBundle, Class<T> theType, int theIndex) {
int count = 0;

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java
View File

@ -15,7 +15,6 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -696,6 +695,36 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
}
@Test
public void testTransactionUpdateTwoResourcesWithSameId() {
Bundle request = new Bundle();
Patient p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("DDD");
p.setId("Patient/ABC");
request.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.PUT)
.setUrl("Patient/ABC");
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue("DDD");
p.setId("Patient/ABC");
request.addEntry()
.setResource(p)
.getRequest()
.setMethod(HTTPVerb.PUT)
.setUrl("Patient/ABC");
try {
mySystemDao.transaction(mySrd, request);
fail();
} catch (InvalidRequestException e) {
assertThat(e.getMessage(), containsString("Transaction bundle contains multiple resources with ID: Patient/ABC"));
}
}
@Test
public void testTransactionCreateInlineMatchUrlWithOneMatch2() {
String methodName = "testTransactionCreateInlineMatchUrlWithOneMatch2";

64
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -36,6 +36,64 @@ public class JsonParserR4Test {
return b;
}
@Test
public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalFirst() {
Observation obs = new Observation();
Patient pt = new Patient();
pt.setId("#1");
pt.addName().setFamily("FAM");
obs.getSubject().setReference("#1");
obs.getContained().add(pt);
Encounter enc = new Encounter();
enc.setStatus(Encounter.EncounterStatus.ARRIVED);
obs.getContext().setResource(enc);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs);
ourLog.info(encoded);
obs = ourCtx.newJsonParser().parseResource(Observation.class, encoded);
assertEquals("#1", obs.getContained().get(0).getId());
assertEquals("#2", obs.getContained().get(1).getId());
pt = (Patient) obs.getSubject().getResource();
assertEquals("FAM", pt.getNameFirstRep().getFamily());
enc = (Encounter) obs.getContext().getResource();
assertEquals(Encounter.EncounterStatus.ARRIVED, enc.getStatus());
}
@Test
public void testEncodeResourceWithMixedManualAndAutomaticContainedResourcesLocalLast() {
Observation obs = new Observation();
Patient pt = new Patient();
pt.addName().setFamily("FAM");
obs.getSubject().setResource(pt);
Encounter enc = new Encounter();
enc.setId("#1");
enc.setStatus(Encounter.EncounterStatus.ARRIVED);
obs.getContext().setReference("#1");
obs.getContained().add(enc);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs);
ourLog.info(encoded);
obs = ourCtx.newJsonParser().parseResource(Observation.class, encoded);
assertEquals("#1", obs.getContained().get(0).getId());
assertEquals("#2", obs.getContained().get(1).getId());
pt = (Patient) obs.getSubject().getResource();
assertEquals("FAM", pt.getNameFirstRep().getFamily());
enc = (Encounter) obs.getContext().getResource();
assertEquals(Encounter.EncounterStatus.ARRIVED, enc.getStatus());
}
/**
* See #814
*/
@ -153,7 +211,7 @@ public class JsonParserR4Test {
b = parser.parseResource(Bundle.class, encoded);
assertEquals("BUNDLEID", b.getIdElement().getIdPart());
assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
assertEquals("Patient/PATIENTID", b.getEntry().get(0).getResource().getId());
assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
}
@ -179,7 +237,7 @@ public class JsonParserR4Test {
b = parser.parseResource(Bundle.class, encoded);
assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
assertEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
assertEquals("Patient/PATIENTID", b.getEntry().get(0).getResource().getId());
assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
}
@ -205,7 +263,7 @@ public class JsonParserR4Test {
b = parser.parseResource(Bundle.class, encoded);
assertNotEquals("BUNDLEID", b.getIdElement().getIdPart());
assertNotEquals("Patient/PATIENTID", ((Patient) b.getEntry().get(0).getResource()).getId());
assertNotEquals("Patient/PATIENTID", b.getEntry().get(0).getResource().getId());
assertEquals("GIVEN", ((Patient) b.getEntry().get(0).getResource()).getNameFirstRep().getGivenAsSingleString());
}

8
src/changes/changes.xml
View File

@ -45,6 +45,14 @@
This work was sponsored by the Regenstrief Institute. Thanks
to Regenstrief for their support!
</action>
<action type="fix">
When encoding a resource that had contained resources with user-supplied
local IDs (e.g. resource.setId("#1")) as well as contained resources
with no IDs (meaning HAPI should automatically assign a local ID
for these resources) it was possible for HAPI to generate
a local ID that already existed, making the resulting
serialization invalid. This has been corrected.
</action>
</release>
<release version="3.3.0" date="2018-03-29">
<action type="add">