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Fix #147 - no duplicates in 'everything' operation

This commit is contained in:
jamesagnew 2015-04-04 23:36:04 -04:00
parent 461fdb50ce
commit 8c37973a78
11 changed files with 624 additions and 49 deletions
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27
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/GenericClient.java
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@ -101,7 +101,6 @@ import ca.uhn.fhir.rest.method.DeleteMethodBinding;
import ca.uhn.fhir.rest.method.HistoryMethodBinding;
import ca.uhn.fhir.rest.method.HttpDeleteClientInvocation;
import ca.uhn.fhir.rest.method.HttpGetClientInvocation;
import ca.uhn.fhir.rest.method.HttpPostClientInvocation;
import ca.uhn.fhir.rest.method.HttpSimpleGetClientInvocation;
import ca.uhn.fhir.rest.method.IClientResponseHandler;
import ca.uhn.fhir.rest.method.MethodUtil;
@ -1538,6 +1537,7 @@ public class GenericClient extends BaseClient implements IGenericClient {
private Bundle myBundle;
private List<IResource> myResources;
private IBaseBundle myBaseBundle;
public TransactionExecutable(Bundle theResources) {
myBundle = theResources;
@ -1547,18 +1547,25 @@ public class GenericClient extends BaseClient implements IGenericClient {
myResources = theResources;
}
@SuppressWarnings("unchecked")
public TransactionExecutable(IBaseBundle theBundle) {
myBaseBundle = theBundle;
}
@SuppressWarnings({ "unchecked", "rawtypes" })
@Override
public T execute() {
Map<String, List<String>> params = new HashMap<String, List<String>>();
if (myResources != null) {
ResourceListResponseHandler binding = new ResourceListResponseHandler(null);
BaseHttpClientInvocation invocation = TransactionMethodBinding.createTransactionInvocation(myResources, myContext);
Map<String, List<String>> params = new HashMap<String, List<String>>();
return (T) invoke(params, binding, invocation);
} else if (myBaseBundle != null) {
ResourceResponseHandler binding = new ResourceResponseHandler(myBaseBundle.getClass(),null);
BaseHttpClientInvocation invocation = TransactionMethodBinding.createTransactionInvocation(myBaseBundle, myContext);
return (T) invoke(params, binding, invocation);
} else {
BundleResponseHandler binding = new BundleResponseHandler(null);
BaseHttpClientInvocation invocation = TransactionMethodBinding.createTransactionInvocation(myBundle, myContext);
Map<String, List<String>> params = new HashMap<String, List<String>>();
return (T) invoke(params, binding, invocation);
}
}
@ -1568,15 +1575,23 @@ public class GenericClient extends BaseClient implements IGenericClient {
private final class TransactionInternal implements ITransaction {
@Override
public ITransactionTyped<Bundle> withBundle(Bundle theResources) {
return new TransactionExecutable<Bundle>(theResources);
public ITransactionTyped<Bundle> withBundle(Bundle theBundle) {
Validate.notNull(theBundle, "theBundle must not be null");
return new TransactionExecutable<Bundle>(theBundle);
}
@Override
public ITransactionTyped<List<IResource>> withResources(List<IResource> theResources) {
Validate.notNull(theResources, "theResources must not be null");
return new TransactionExecutable<List<IResource>>(theResources);
}
@Override
public <T extends IBaseBundle> ITransactionTyped<T> withBundle(T theBundle) {
Validate.notNull(theBundle, "theBundle must not be null");
return new TransactionExecutable<T>(theBundle);
}
}
private class UpdateInternal extends BaseClientExecutable<IUpdateExecutable, MethodOutcome> implements IUpdate, IUpdateTyped, IUpdateExecutable, IUpdateWithQuery, IUpdateWithQueryTyped {

15
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/gclient/ITransaction.java
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@ -22,14 +22,27 @@ package ca.uhn.fhir.rest.gclient;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.IResource;
public interface ITransaction {
/**
* Use a list of resources as the transaction input
*/
ITransactionTyped<List<IResource>> withResources(List<IResource> theResources);
ITransactionTyped<Bundle> withBundle(Bundle theResources);
/**
* Use a DSTU1 Bundle (Atom) as the transaction input
*/
ITransactionTyped<Bundle> withBundle(Bundle theBundle);
/**
* Use a DSTU2+ Bundle resource as the transaction input
*/
<T extends IBaseBundle> ITransactionTyped<T> withBundle(T theBundleResource);
// *****
// TODO: add withString version

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/HttpPostClientInvocation.java
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@ -40,6 +40,10 @@ public class HttpPostClientInvocation extends BaseHttpClientInvocationWithConten
super(theContext, theResource, theUrlExtension);
}
public HttpPostClientInvocation(FhirContext theContext, IBaseResource theResource) {
super(theContext, theResource, null);
}
public HttpPostClientInvocation(FhirContext theContext, TagList theTagList, String... theUrlExtension) {
super(theContext, theTagList, theUrlExtension);
}

67
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/TransactionMethodBinding.java
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@ -27,6 +27,8 @@ import java.lang.reflect.Method;
import java.util.IdentityHashMap;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Bundle;
@ -73,6 +75,21 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
}
}
@Override
public RestfulOperationTypeEnum getResourceOperationType() {
return null;
}
@Override
protected BundleTypeEnum getResponseBundleType() {
return BundleTypeEnum.TRANSACTION_RESPONSE;
}
@Override
public ReturnTypeEnum getReturnType() {
return ReturnTypeEnum.BUNDLE;
}
@Override
public RestfulOperationSystemEnum getSystemOperationType() {
return RestfulOperationSystemEnum.TRANSACTION;
@ -93,26 +110,33 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
}
@Override
public ReturnTypeEnum getReturnType() {
return ReturnTypeEnum.BUNDLE;
public BaseHttpClientInvocation invokeClient(Object[] theArgs) throws InternalErrorException {
FhirContext context = getContext();
if (theArgs[myTransactionParamIndex] instanceof Bundle) {
Bundle bundle = (Bundle) theArgs[myTransactionParamIndex];
return createTransactionInvocation(bundle, context);
} else {
@SuppressWarnings("unchecked")
List<IResource> resources = (List<IResource>) theArgs[myTransactionParamIndex];
return createTransactionInvocation(resources, context);
}
}
@SuppressWarnings("unchecked")
@Override
public Object invokeServer(RequestDetails theRequest, Object[] theMethodParams) throws InvalidRequestException, InternalErrorException {
/*
* The design of HAPI's transaction method for DSTU1 support assumed that a
* transaction was just an update on a bunch of resources (because that's what
* it was), but in DSTU2 transaction has become much more broad, so we no longer
* hold the user's hand much here.
* The design of HAPI's transaction method for DSTU1 support assumed that a transaction was just an update on a
* bunch of resources (because that's what it was), but in DSTU2 transaction has become much more broad, so we
* no longer hold the user's hand much here.
*/
if (myTransactionParamStyle == ParamStyle.RESOURCE_BUNDLE) {
// This is the DSTU2 style
Object response = invokeServerMethod(theMethodParams);
return response;
}
// Grab the IDs of all of the resources in the transaction
List<IResource> resources;
if (theMethodParams[myTransactionParamIndex] instanceof Bundle) {
@ -162,35 +186,16 @@ public class TransactionMethodBinding extends BaseResourceReturningMethodBinding
return null; // This is parsed in TransactionParamBinder
}
@Override
public RestfulOperationTypeEnum getResourceOperationType() {
return null;
public static BaseHttpClientInvocation createTransactionInvocation(Bundle theBundle, FhirContext theContext) {
return new HttpPostClientInvocation(theContext, theBundle);
}
@Override
public BaseHttpClientInvocation invokeClient(Object[] theArgs) throws InternalErrorException {
FhirContext context = getContext();
if (theArgs[myTransactionParamIndex] instanceof Bundle) {
Bundle bundle = (Bundle) theArgs[myTransactionParamIndex];
return createTransactionInvocation(bundle, context);
} else {
@SuppressWarnings("unchecked")
List<IResource> resources = (List<IResource>) theArgs[myTransactionParamIndex];
return createTransactionInvocation(resources, context);
}
public static BaseHttpClientInvocation createTransactionInvocation(IBaseBundle theBundle, FhirContext theContext) {
return new HttpPostClientInvocation(theContext, theBundle);
}
public static BaseHttpClientInvocation createTransactionInvocation(List<IResource> theResources, FhirContext theContext) {
return new HttpPostClientInvocation(theContext, theResources, BundleTypeEnum.TRANSACTION);
}
public static BaseHttpClientInvocation createTransactionInvocation(Bundle theBundle, FhirContext theContext) {
return new HttpPostClientInvocation(theContext, theBundle);
}
@Override
protected BundleTypeEnum getResponseBundleType() {
return BundleTypeEnum.TRANSACTION_RESPONSE;
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirResourceDao.java
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@ -1366,6 +1366,9 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
*/
if (theParams.getIncludes() != null && theParams.getIncludes().isEmpty() == false) {
Set<IdDt> previouslyLoadedPids = new HashSet<IdDt>();
for (IResource next : retVal) {
previouslyLoadedPids.add(next.getId().toUnqualifiedVersionless());
}
Set<IdDt> includePids = new HashSet<IdDt>();
List<IResource> resources = retVal;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2.java
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@ -487,8 +487,9 @@ public class FhirSystemDaoDstu2 extends BaseFhirSystemDao<Bundle> {
private static void handleTransactionCreateOrUpdateOutcome(Map<IdDt, IdDt> idSubstitutions, Map<IdDt, DaoMethodOutcome> idToPersistedOutcome, IdDt nextResourceId, DaoMethodOutcome outcome, Entry newEntry) {
IdDt newId = outcome.getId().toUnqualifiedVersionless();
if (newId.equals(nextResourceId) == false) {
idSubstitutions.put(nextResourceId, newId);
IdDt resourceId = nextResourceId.toUnqualifiedVersionless();
if (newId.equals(resourceId) == false) {
idSubstitutions.put(resourceId, newId);
}
idToPersistedOutcome.put(newId, outcome);
if (outcome.getCreated().booleanValue()) {

14
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu2Test.java
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@ -488,12 +488,12 @@ public class FhirSystemDaoDstu2Test {
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
p.addName().addFamily("Hello");
p.setId(id);
p.setId("urn:"+methodName);
request.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.PUT).setUrl("Patient?identifier=urn%3Asystem%7C" + methodName);
Observation o = new Observation();
o.getCode().setText("Some Observation");
o.getSubject().setReference(id);
o.getSubject().setReference("Patient/urn:"+methodName);
request.addEntry().setResource(o).getTransaction().setMethod(HTTPVerbEnum.POST);
Bundle resp = ourSystemDao.transaction(request);
@ -501,18 +501,16 @@ public class FhirSystemDaoDstu2Test {
Entry nextEntry = resp.getEntry().get(1);
assertEquals(Constants.STATUS_HTTP_201_CREATED + "", nextEntry.getTransactionResponse().getStatus());
IdDt patientId = new IdDt(nextEntry.getTransactionResponse().getLocation());
assertThat(nextEntry.getTransactionResponse().getLocation(), not(containsString("test")));
assertNotEquals(id.toVersionless(), new IdDt(nextEntry.getTransactionResponse().getLocation()).toVersionless());
assertNotEquals(id.toVersionless(), patientId.toVersionless());
assertThat(nextEntry.getTransactionResponse().getLocation(), endsWith("/_history/1"));
nextEntry = resp.getEntry().get(1);
assertEquals("" + Constants.STATUS_HTTP_201_CREATED, nextEntry.getTransactionResponse().getStatus());
assertThat(patientId.getValue(), endsWith("/_history/1"));
nextEntry = resp.getEntry().get(2);
o = ourObservationDao.read(new IdDt(nextEntry.getTransactionResponse().getLocation()));
assertEquals(id.toVersionless(), o.getSubject().getReference());
assertEquals(patientId.toVersionless(), o.getSubject().getReference());
}

35
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
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@ -9,6 +9,7 @@ import static org.hamcrest.Matchers.startsWith;
import static org.junit.Assert.*;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
@ -35,6 +36,7 @@ import org.junit.BeforeClass;
import org.junit.Test;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import ch.qos.logback.core.util.FileUtil;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
@ -345,14 +347,45 @@ public class ResourceProviderDstu2Test {
ids.add(next.getResource().getId());
}
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(patientId, devId, obsId, encId, orgId1, orgId2));
// _revinclude's are counted but not _include's
assertEquals(3, b.getTotal().intValue());
ourLog.info(ids.toString());
}
/**
* See #147
*/
@Test
public void testEverythingDoesnRepeatPatient() throws Exception {
ca.uhn.fhir.model.dstu2.resource.Bundle b;
b = ourFhirCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, new InputStreamReader(ResourceProviderDstu2Test.class.getResourceAsStream("/bug147-bundle.json")));
ca.uhn.fhir.model.dstu2.resource.Bundle resp = ourClient.transaction().withBundle(b).execute();
ourLog.info(ourFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
IdDt patientId = new IdDt(resp.getEntry().get(1).getTransactionResponse().getLocation());
assertEquals("Patient", patientId.getResourceType());
Parameters output = ourClient.operation().onInstance(patientId).named("everything").withNoParameters(Parameters.class).execute();
b = (ca.uhn.fhir.model.dstu2.resource.Bundle) output.getParameterFirstRep().getResource();
List<IdDt> ids = new ArrayList<IdDt>();
boolean dupes = false;
for (Entry next : b.getEntry()) {
IdDt toAdd = next.getResource().getId().toUnqualifiedVersionless();
dupes = dupes | ids.contains(toAdd);
ids.add(toAdd);
}
ourLog.info(ids.toString());
assertFalse(ids.toString(), dupes);
}
@Test
public void testCountParam() throws Exception {

453
hapi-fhir-jpaserver-base/src/test/resources/bug147-bundle.json Normal file
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File diff suppressed because one or more lines are too long

41
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/GenericClientTestDstu2.java
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@ -614,6 +614,47 @@ public class GenericClientTestDstu2 {
// assertEquals("PATIENT2", p2.getName().get(0).getFamily().get(0).getValue());
}
@Test
public void testTransactionWithTransactionResource() throws Exception {
ca.uhn.fhir.model.dstu2.resource.Bundle resp = new ca.uhn.fhir.model.dstu2.resource.Bundle();
resp.addEntry().getTransactionResponse().setLocation("Patient/1/_history/1");
resp.addEntry().getTransactionResponse().setLocation("Patient/2/_history/2");
String respString = ourCtx.newJsonParser().encodeResourceToString(resp);
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
when(myHttpResponse.getStatusLine()).thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
when(myHttpResponse.getEntity().getContentType()).thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_JSON + "; charset=UTF-8"));
when(myHttpResponse.getEntity().getContent()).thenReturn(new ReaderInputStream(new StringReader(respString), Charset.forName("UTF-8")));
IGenericClient client = ourCtx.newRestfulGenericClient("http://example.com/fhir");
ca.uhn.fhir.model.dstu2.resource.Bundle input = new ca.uhn.fhir.model.dstu2.resource.Bundle();
Patient p1 = new Patient(); // No ID
p1.addName().addFamily("PATIENT1");
input.addEntry().setResource(p1);
Patient p2 = new Patient(); // Yes ID
p2.addName().addFamily("PATIENT2");
p2.setId("Patient/2");
input.addEntry().setResource(p2);
//@formatter:off
ca.uhn.fhir.model.dstu2.resource.Bundle response = client.transaction()
.withBundle(input)
.encodedJson()
.execute();
//@formatter:on
assertEquals("http://example.com/fhir?_format=json", capt.getValue().getURI().toString());
assertEquals(2, response.getEntry().size());
assertEquals("Patient/1/_history/1", response.getEntry().get(0).getTransactionResponse().getLocation());
assertEquals("Patient/2/_history/2", response.getEntry().get(1).getTransactionResponse().getLocation());
}
@Test
public void testDeleteConditional() throws Exception {
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);

9
src/changes/changes.xml
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@ -114,6 +114,15 @@
for all of their help in tracking this issue down and developing
useful unit tests to demonstrate it.
</action>
<action type="add">
Client now supports invoking transcation using a DSTU2-style
Bundle resource as the input.
</action>
<action type="fix" issue="147">
JPA Server $everything operation could sometimes include a duplicate copy of
the main focus resource if it was referred to in a deep chain. Thanks
to David Hay for reporting!
</action>
</release>
<release version="0.9" date="2015-Mar-14">
<action type="add">