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Fix #1583 - Index local refs in canonical types (#1593) 

* Fix #1583 - Index local refs in canonical types

* Add fix to pre-expansion

* Test fix

* Rework ID handling

* Test fixes

* Fix test
This commit is contained in:
James Agnew 2019-11-23 16:32:37 +01:00 committed by GitHub
parent f7f1ec26bc
commit a2f77b23d2
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24 changed files with 548 additions and 139 deletions
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76
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
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@ -22,10 +22,16 @@ package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.api.IIdentifiableElement;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ISupportsUndeclaredExtensions;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import org.apache.commons.lang3.StringUtils;
@ -35,7 +41,13 @@ import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.hl7.fhir.instance.model.api.*;
import javax.annotation.Nullable;
import java.io.*;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.io.StringWriter;
import java.io.Writer;
import java.lang.reflect.Modifier;
import java.util.*;
import java.util.stream.Collectors;
@ -530,11 +542,6 @@ public abstract class BaseParser implements IParser {
return tags;
}
@Override
public Boolean getOverrideResourceIdWithBundleEntryFullUrl() {
return myOverrideResourceIdWithBundleEntryFullUrl;
}
@Override
public List<Class<? extends IBaseResource>> getPreferTypes() {
return myPreferTypes;
@ -705,39 +712,38 @@ public abstract class BaseParser implements IParser {
RuntimeResourceDefinition def = myContext.getResourceDefinition(retVal);
if ("Bundle".equals(def.getName())) {
BaseRuntimeChildDefinition entryChild = def.getChildByName("entry");
BaseRuntimeElementCompositeDefinition<?> entryDef = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
List<IBase> entries = entryChild.getAccessor().getValues(retVal);
if (entries != null) {
for (IBase nextEntry : entries) {
/**
* If Bundle.entry.fullUrl is populated, set the resource ID to that
*/
// TODO: should emit a warning and maybe notify the error handler if the resource ID doesn't match the
// fullUrl idPart
BaseRuntimeChildDefinition fullUrlChild = entryDef.getChildByName("fullUrl");
if (fullUrlChild == null) {
continue; // TODO: remove this once the data model in tinder plugin catches up to 1.2
}
if (isOverrideResourceIdWithBundleEntryFullUrl()) {
List<IBase> fullUrl = fullUrlChild.getAccessor().getValues(nextEntry);
if (fullUrl != null && !fullUrl.isEmpty()) {
IPrimitiveType<?> value = (IPrimitiveType<?>) fullUrl.get(0);
if (value.isEmpty() == false) {
List<IBase> entryResources = entryDef.getChildByName("resource").getAccessor().getValues(nextEntry);
if (entryResources != null && entryResources.size() > 0) {
IBaseResource res = (IBaseResource) entryResources.get(0);
String versionId = res.getIdElement().getVersionIdPart();
res.setId(value.getValueAsString());
if (isNotBlank(versionId) && res.getIdElement().hasVersionIdPart() == false) {
res.setId(res.getIdElement().withVersion(versionId));
if (isOverrideResourceIdWithBundleEntryFullUrl()) {
BundleUtil.processEntries(myContext, (IBaseBundle) retVal, t -> {
String fullUrl = t.getFullUrl();
if (fullUrl != null) {
IBaseResource resource = t.getResource();
if (resource != null) {
IIdType resourceId = resource.getIdElement();
if (isBlank(resourceId.getValue())) {
resourceId.setValue(fullUrl);
} else {
if (fullUrl.startsWith("urn:") && fullUrl.endsWith(":" + resourceId.getIdPart())) {
resourceId.setValue(fullUrl);
} else {
IIdType fullUrlId = myContext.getVersion().newIdType();
fullUrlId.setValue(fullUrl);
if (myContext.getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) {
IIdType newId = fullUrlId;
if (!newId.hasVersionIdPart() && resourceId.hasVersionIdPart()) {
newId = newId.withVersion(resourceId.getVersionIdPart());
}
resourceId.setValue(newId.getValue());
} else if (StringUtils.equals(fullUrlId.getIdPart(), resourceId.getIdPart())) {
if (fullUrlId.hasBaseUrl()) {
IIdType newResourceId = resourceId.withServerBase(fullUrlId.getBaseUrl(), resourceId.getResourceType());
resourceId.setValue(newResourceId.getValue());
}
}
}
}
}
}
}
});
}
}

13
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/IParser.java
View File

@ -92,19 +92,6 @@ public interface IParser {
*/
Boolean getStripVersionsFromReferences();
/**
* If set to <code>true</code> (which is the default), the Bundle.entry.fullUrl will override the Bundle.entry.resource's
* resource id if the fullUrl is defined. This behavior happens when parsing the source data into a Bundle object. Set this
* to <code>false</code> if this is not the desired behavior (e.g. the client code wishes to perform additional
* validation checks between the fullUrl and the resource id).
*
* @return Returns the parser instance's configuration setting for overriding resource ids with Bundle.entry.fullUrl when
* parsing the source data into a Bundle object. This method will return <code>null</code> if no value is set, in
* which case the value from the {@link ParserOptions} will be used (default is <code>true</code>)
* @see ParserOptions
*/
Boolean getOverrideResourceIdWithBundleEntryFullUrl();
/**
* Is the parser in "summary mode"? See {@link #setSummaryMode(boolean)} for information
*

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleUtil.java
View File

@ -168,6 +168,8 @@ public class BundleUtil {
BaseRuntimeElementCompositeDefinition<?> entryChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
BaseRuntimeChildDefinition fullUrlChildDef = entryChildContentsDef.getChildByName("fullUrl");
BaseRuntimeChildDefinition resourceChildDef = entryChildContentsDef.getChildByName("resource");
BaseRuntimeChildDefinition requestChildDef = entryChildContentsDef.getChildByName("request");
BaseRuntimeElementCompositeDefinition<?> requestChildContentsDef = (BaseRuntimeElementCompositeDefinition<?>) requestChildDef.getChildByName("request");
@ -180,6 +182,11 @@ public class BundleUtil {
String url = null;
RequestTypeEnum requestType = null;
String conditionalUrl = null;
String fullUrl = fullUrlChildDef
.getAccessor()
.getFirstValueOrNull(nextEntry)
.map(t->((IPrimitiveType<?>)t).getValueAsString())
.orElse(null);
for (IBase nextResource : resourceChildDef.getAccessor().getValues(nextEntry)) {
resource = (IBaseResource) nextResource;
@ -217,7 +224,7 @@ public class BundleUtil {
* order in the original bundle.
*/
BundleEntryMutator mutator = new BundleEntryMutator(nextEntry, requestChildDef, requestChildContentsDef);
ModifiableBundleEntry entry = new ModifiableBundleEntry(new BundleEntryParts(requestType, url, resource, conditionalUrl), mutator);
ModifiableBundleEntry entry = new ModifiableBundleEntry(new BundleEntryParts(fullUrl, requestType, url, resource, conditionalUrl), mutator);
theProcessor.accept(entry);
}
}

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/bundle/BundleEntryParts.java
View File

@ -28,15 +28,21 @@ public class BundleEntryParts {
private final IBaseResource myResource;
private final String myUrl;
private final String myConditionalUrl;
private final String myFullUrl;
public BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
public BundleEntryParts(String theFullUrl, RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource, String theConditionalUrl) {
super();
myFullUrl = theFullUrl;
myRequestType = theRequestType;
myUrl = theUrl;
myResource = theResource;
myConditionalUrl = theConditionalUrl;
}
public String getFullUrl() {
return myFullUrl;
}
public RequestTypeEnum getRequestType() {
return myRequestType;
}

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/bundle/ModifiableBundleEntry.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.util.bundle;
*/
import ca.uhn.fhir.context.FhirContext;
import org.hl7.fhir.instance.model.api.IBaseResource;
public class ModifiableBundleEntry {
private final BundleEntryParts myBundleEntryParts;
@ -39,7 +40,15 @@ public class ModifiableBundleEntry {
myBundleEntryMutator.setRequestUrl(theFhirContext, theRequestUrl);
}
public String getFullUrl() {
return myBundleEntryParts.getFullUrl();
}
public String getRequestUrl() {
return myBundleEntryParts.getUrl();
}
public IBaseResource getResource() {
return myBundleEntryParts.getResource();
}
}

2
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/ConditionalParamBinder.java
View File

@ -44,7 +44,7 @@ class ConditionalParamBinder implements IParameter {
@Override
public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
if (theOuterCollectionType != null || theInnerCollectionType != null || theParameterType.equals(String.class) == false) {
throw new ConfigurationException("Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName() + " must be of type String, found incorrect parameteter in method \"" + theMethod + "\"");
throw new ConfigurationException("Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName() + " must be of type String, found incorrect parameter in method \"" + theMethod + "\"");
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IValueSetConceptAccumulator.java
View File

@ -31,7 +31,7 @@ public interface IValueSetConceptAccumulator {
void includeConcept(String theSystem, String theCode, String theDisplay);
void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations);
void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, @Nullable Collection<TermConceptDesignation> theDesignations);
void excludeConcept(String theSystem, String theCode);

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
View File

@ -34,7 +34,9 @@ import java.util.Collection;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.isAnyBlank;
import static org.apache.commons.lang3.StringUtils.isNoneBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetConceptAccumulator.class);
@ -71,8 +73,10 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
@Override
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection<TermConceptDesignation> theDesignations) {
TermValueSetConcept concept = saveConcept(theSystem, theCode, theDisplay);
for (TermConceptDesignation designation : theDesignations) {
saveConceptDesignation(concept, designation);
if (theDesignations != null) {
for (TermConceptDesignation designation : theDesignations) {
saveConceptDesignation(concept, designation);
}
}
}

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
@ -2154,6 +2155,27 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testSearchResourceLinkOnCanonical() {
Questionnaire q = new Questionnaire();
q.setId("Q");
myQuestionnaireDao.update(q);
QuestionnaireResponse qr = new QuestionnaireResponse();
qr.setId("QR");
qr.setQuestionnaire("Questionnaire/Q");
String qrId = myQuestionnaireResponseDao.update(qr).getId().toUnqualifiedVersionless().getValue();
List<QuestionnaireResponse> result = toList(myQuestionnaireResponseDao
.search(new SearchParameterMap().setLoadSynchronous(true).add(QuestionnaireResponse.SP_QUESTIONNAIRE, new ReferenceParam("Questionnaire/Q"))));
assertEquals(1, result.size());
assertEquals(qrId, result.get(0).getIdElement().toUnqualifiedVersionless().getValue());
}
@Test
public void testSearchResourceLinkWithChain() {
Patient patient = new Patient();

35
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java
View File

@ -10,6 +10,8 @@ import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
@ -116,6 +118,8 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
private IResourceReindexingSvc myResourceReindexingSvc;
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
@Autowired
private ITermReadSvc myTermSvc;
@Before
@Transactional()
@ -190,6 +194,36 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
}
}
@Test
public void testExpandValueSet() {
CodeSystem cs = new CodeSystem();
cs.setUrl("http://fooCS");
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.addConcept().setCode("CODEA");
cs.addConcept().setCode("CODEB");
myCodeSystemDao.create(cs);
ValueSet vs = new ValueSet();
vs.setUrl("http://fooVS");
vs.getCompose()
.addInclude()
.setSystem("http://fooCS")
.addConcept(new ValueSet.ConceptReferenceComponent().setCode("CODEA"));
// Explicit expand
ValueSet outcome = myValueSetDao.expand(vs, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("CODEA", outcome.getExpansion().getContains().get(0).getCode());
// Deferred expand
IIdType id = myValueSetDao.create(vs).getId().toUnqualifiedVersionless();
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
outcome = myValueSetDao.expand(id, null, mySrd);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
assertEquals("CODEA", outcome.getExpansion().getContains().get(0).getCode());
}
@Test
public void testSearchByCodeIn() {
CodeSystem cs = new CodeSystem();
@ -207,6 +241,7 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
.addConcept(new ValueSet.ConceptReferenceComponent().setCode("CODEA"));
myValueSetDao.create(vs);
Observation obs = new Observation();
obs.getCode().addCoding().setSystem("http://fooCS").setCode("CODEA");
String obs1id = myObservationDao.create(obs).getId().toUnqualifiedVersionless().getValue();

2
hapi-fhir-jpaserver-base/src/test/resources/david_big_bundle.json
View File

@ -2666,7 +2666,7 @@
"fullUrl": "http://fhirtest.uhn.ca/baseDstu3/Practitioner/A45515",
"resource": {
"resourceType": "Practitioner",
"id": "45515",
"id": "A45515",
"meta": {
"versionId": "1",
"lastUpdated": "2016-05-07T11:45:53.918-04:00"

30
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
View File

@ -51,6 +51,7 @@ import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.IdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
@ -151,7 +152,31 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
String nextType = toRootTypeName(value);
switch (nextType) {
case "uri":
case "canonical":
String typeName = toTypeName(value);
// Canonical has a root type of "uri"
if ("canonical".equals(typeName)) {
IPrimitiveType<?> valuePrimitive = (IPrimitiveType<?>) value;
IBaseReference fakeReference = (IBaseReference) myContext.getElementDefinition("Reference").newInstance();
fakeReference.setReference(valuePrimitive.getValueAsString());
/*
* See #1583
* Technically canonical fields should not allow local references (e.g.
* Questionnaire/123) but it seems reasonable for us to interpret a canonical
* containing a local reference for what it is, and allow people to seaerch
* based on that.
*/
IIdType parsed = fakeReference.getReferenceElement();
if (parsed.hasIdPart() && parsed.hasResourceType() && !parsed.isAbsolute()) {
PathAndRef ref = new PathAndRef(searchParam.getName(), path, fakeReference);
params.add(ref);
break;
}
}
params.addWarning("Ignoring canonical reference (indexing canonical is not yet supported)");
break;
case "reference":
@ -789,6 +814,11 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
return rootParentDefinition.getName();
}
private String toTypeName(IBase nextObject) {
BaseRuntimeElementDefinition<?> elementDefinition = getContext().getElementDefinition(nextObject.getClass());
return elementDefinition.getName();
}
@SuppressWarnings("unchecked")
private void addDateTimeTypes(String theResourceType, Set<ResourceIndexedSearchParamDate> theParams, RuntimeSearchParam theSearchParam, IBase theValue) {
IPrimitiveType<Date> nextBaseDateTime = (IPrimitiveType<Date>) theValue;

2
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/ConditionalParamBinder.java
View File

@ -47,7 +47,7 @@ class ConditionalParamBinder implements IParameter {
public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
if (theOuterCollectionType != null || theInnerCollectionType != null || theParameterType.equals(String.class) == false) {
throw new ConfigurationException(
"Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName() + " must be of type String, found incorrect parameteter in method \"" + theMethod + "\"");
"Parameters annotated with @" + ConditionalUrlParam.class.getSimpleName() + " must be of type String, found incorrect parameter in method \"" + theMethod + "\"");
}
}

10
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/OperationMethodBinding.java
View File

@ -28,6 +28,8 @@ import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
@ -91,6 +93,14 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
myDescription = null;
}
for (Annotation[] nextParamAnnotations : theMethod.getParameterAnnotations()) {
for (Annotation nextParam : nextParamAnnotations) {
if (nextParam instanceof OptionalParam || nextParam instanceof RequiredParam) {
throw new ConfigurationException("Illegal method parameter annotation @" + nextParam.annotationType().getSimpleName() + " on method: " + theMethod.toString());
}
}
}
if (isBlank(theOperationName)) {
throw new ConfigurationException("Method '" + theMethod.getName() + "' on type " + theMethod.getDeclaringClass().getName() + " is annotated with @" + Operation.class.getSimpleName()
+ " but this annotation has no name defined");

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -150,7 +150,7 @@
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>3.0.1</version>
<version>3.1.0</version>
<optional>true</optional>
</dependency>

29
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -23,6 +23,7 @@ import java.util.Set;
import java.util.concurrent.TimeUnit;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.hamcrest.core.IsNot.not;
import static org.junit.Assert.*;
import static org.mockito.Mockito.mock;
@ -174,6 +175,34 @@ public class JsonParserR4Test extends BaseTest {
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\">Copy © 1999</div>", p.getText().getDivAsString());
}
@Test
public void testEncodeAndParseBundleWithFullUrlAndResourceIdMismatch() {
MessageHeader header = new MessageHeader();
header.setId("1.1.1.1");
header.setDefinition("Hello");
Bundle input = new Bundle();
input
.addEntry()
.setFullUrl("urn:uuid:0.0.0.0")
.setResource(header);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
ourLog.info("Encoded: {}", encoded);
assertThat(encoded, stringContainsInOrder(
"\"fullUrl\": \"urn:uuid:0.0.0.0\"",
"\"id\": \"1.1.1.1\""
));
input = ourCtx.newJsonParser().parseResource(Bundle.class, encoded);
assertEquals("urn:uuid:0.0.0.0", input.getEntry().get(0).getFullUrl());
assertEquals("MessageHeader/1.1.1.1", input.getEntry().get(0).getResource().getId());
}
@Test
public void testEncodeBinary() {
Binary b = new Binary();

35
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/XmlParserR4Test.java
View File

@ -1,8 +1,13 @@
package ca.uhn.fhir.parser;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertThat;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.MessageHeader;
import org.hl7.fhir.r4.model.Narrative;
import org.junit.Test;
import org.slf4j.Logger;
@ -41,5 +46,33 @@ public class XmlParserR4Test {
int idx = encoded.indexOf(sectionText);
assertNotEquals(-1, idx);
}
@Test
public void testEncodeAndParseBundleWithFullUrlAndResourceIdMismatch() {
MessageHeader header = new MessageHeader();
header.setId("1.1.1.1");
header.setDefinition("Hello");
Bundle input = new Bundle();
input
.addEntry()
.setFullUrl("urn:uuid:0.0.0.0")
.setResource(header);
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input);
ourLog.info("Encoded: {}", encoded);
assertThat(encoded, stringContainsInOrder(
"<fullUrl value=\"urn:uuid:0.0.0.0\"/>",
"<id value=\"1.1.1.1\"/>"
));
input = ourCtx.newXmlParser().parseResource(Bundle.class, encoded);
assertEquals("urn:uuid:0.0.0.0", input.getEntry().get(0).getFullUrl());
assertEquals("MessageHeader/1.1.1.1", input.getEntry().get(0).getResource().getId());
}
}

113
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/BlockingContentR4Test.java Normal file
View File

@ -0,0 +1,113 @@
package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.Transaction;
import ca.uhn.fhir.rest.annotation.TransactionParam;
import ca.uhn.fhir.test.utilities.server.ResourceProviderRule;
import ca.uhn.fhir.test.utilities.server.RestfulServerRule;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpEntity;
import org.apache.http.client.config.RequestConfig;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.InputStreamEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.junit.ClassRule;
import org.junit.Rule;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
import java.util.concurrent.TimeUnit;
public class BlockingContentR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(BlockingContentR4Test.class);
private static FhirContext ourCtx = FhirContext.forR4();
@ClassRule
public static RestfulServerRule ourServerRule = new RestfulServerRule(ourCtx);
@Rule
public ResourceProviderRule myPatientProviderRule = new ResourceProviderRule(ourServerRule, new SystemProvider());
@Test
public void testCreateWith100Continue() throws Exception {
Patient patient = new Patient();
patient.setActive(true);
Bundle input = new Bundle();
input.setType(Bundle.BundleType.TRANSACTION);
input.addEntry().setResource(patient).setFullUrl("Patient/").getRequest().setMethod(Bundle.HTTPVerb.POST);
RequestConfig config = RequestConfig.custom().setExpectContinueEnabled(true).build();
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
builder.setDefaultRequestConfig(config);
try (CloseableHttpClient client = builder.build()) {
String resourceAsString = ourCtx.newJsonParser().encodeResourceToString(input);
// InputStream inputStream = new BlockingInputStream(resourceAsString.getBytes(Charsets.UTF_8));
byte[] bytes = resourceAsString.getBytes(Charsets.UTF_8);
InputStream inputStream = new ByteArrayInputStream(bytes);
HttpEntity entity = new InputStreamEntity(inputStream, ContentType.parse("application/fhir+json")){
@Override
public long getContentLength() {
return bytes.length + 100;
}
};
HttpPost post = new HttpPost("http://localhost:" + ourServerRule.getPort() + "/");
post.setEntity(entity);
try (CloseableHttpResponse resp = client.execute(post)) {
ourLog.info(Arrays.asList(resp.getAllHeaders()).toString().replace(", ", "\n"));
ourLog.info(resp.toString());
ourLog.info(IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8));
}
}
}
private static class BlockingInputStream extends InputStream {
private final ByteArrayInputStream myWrap;
private int myByteCount = 0;
public BlockingInputStream(byte[] theBytes) {
myWrap = new ByteArrayInputStream(theBytes);
}
@Override
public int read() throws IOException {
if (myByteCount++ == 10) {
ourLog.info("About to block...");
try {
Thread.sleep(30000);
} catch (InterruptedException e) {
ourLog.warn("Interrupted", e);
}
}
return myWrap.read();
}
}
public static class SystemProvider {
@Transaction
public Bundle transaction(@TransactionParam Bundle theInput) {
return theInput;
}
}
}

74
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/ServerInvalidDefinitionDstu2Test.java → hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerInvalidDefinitionR4Test.java
View File

@ -1,30 +1,30 @@
package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.TestUtil;
import org.hamcrest.core.StringContains;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.AfterClass;
import org.junit.Test;
import javax.servlet.ServletException;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import javax.servlet.ServletException;
public class ServerInvalidDefinitionR4Test {
import org.hamcrest.core.StringContains;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.TestUtil;
public class ServerInvalidDefinitionDstu2Test {
private static FhirContext ourCtx = FhirContext.forDstu2();
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
private static FhirContext ourCtx = FhirContext.forR4();
@Test
public void testWrongConditionalUrlType() {
@ -38,7 +38,7 @@ public class ServerInvalidDefinitionDstu2Test {
} catch (ServletException e) {
assertThat(e.getCause().toString(), StringContains.containsString("ConfigurationException"));
assertThat(e.getCause().toString(), StringContains.containsString(
"Parameters annotated with @ConditionalUrlParam must be of type String, found incorrect parameteter in method \"public ca.uhn.fhir.rest.api.MethodOutcome ca.uhn.fhir.rest.server.ServerInvalidDefinitionDstu2Test$UpdateWithWrongConditionalUrlType.update(ca.uhn.fhir.rest.param.TokenParam,ca.uhn.fhir.model.dstu2.resource.Patient)"));
"Parameters annotated with @ConditionalUrlParam must be of type String, found incorrect parameter in method \"public ca.uhn.fhir.rest.api.MethodOutcome ca.uhn.fhir.rest.server.ServerInvalidDefinitionR4Test$UpdateWithWrongConditionalUrlType.update(ca.uhn.fhir.rest.param.TokenParam,org.hl7.fhir.r4.model.Patient)"));
}
}
@ -54,7 +54,7 @@ public class ServerInvalidDefinitionDstu2Test {
} catch (ServletException e) {
assertThat(e.getCause().toString(), StringContains.containsString("ConfigurationException"));
assertThat(e.getCause().toString(), StringContains
.containsString("Method 'update' is annotated with @ResourceParam but has a type that is not an implemtation of org.hl7.fhir.instance.model.api.IBaseResource or String or byte[]"));
.containsString("Method 'update' is annotated with @ResourceParam but has a type that is not an implemtation of org.hl7.fhir.instance.model.api.IBaseResource or String or byte[]"));
}
}
@ -88,6 +88,29 @@ public class ServerInvalidDefinitionDstu2Test {
}
}
@Test
public void testWrongParameterAnnotationOnOperation() {
class MyProvider {
@Operation(name = "foo")
public MethodOutcome update(@OptionalParam(name = "foo") StringType theFoo) {
return null;
}
}
RestfulServer srv = new RestfulServer(ourCtx);
srv.setFhirContext(ourCtx);
srv.registerProvider(new MyProvider());
try {
srv.init();
fail();
} catch (ServletException e) {
assertThat(e.getCause().toString(), StringContains.containsString("Failure scanning class MyProvider: Illegal method parameter annotation @OptionalParam on method: public ca.uhn.fhir.rest.api.MethodOutcome ca.uhn.fhir.rest.server.ServerInvalidDefinitionR4Test$1MyProvider.update(org.hl7.fhir.r4.model.StringType)"));
}
}
public static class UpdateWithWrongConditionalUrlType implements IResourceProvider {
@Override
@ -144,4 +167,9 @@ public class ServerInvalidDefinitionDstu2Test {
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

111
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerMimetypeR4Test.java
View File

@ -1,18 +1,17 @@
package ca.uhn.fhir.rest.server;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import java.io.IOException;
import java.net.URI;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.CloseableHttpResponse;
@ -40,18 +39,18 @@ import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.MyPatientWithExtensions;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.TestUtil;
import java.io.IOException;
import java.net.URI;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
public class ServerMimetypeR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ServerMimetypeR4Test.class);
@ -406,45 +405,16 @@ public class ServerMimetypeR4Test {
return retVal;
}
@AfterClass
public static void afterClassClearContext() throws Exception {
JettyUtil.closeServer(ourServer);
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void beforeClass() throws Exception {
ourServer = new Server(0);
PatientProvider patientProvider = new PatientProvider();
ServletHandler proxyHandler = new ServletHandler();
ourServlet = new RestfulServer(ourCtx);
ourServlet.setResourceProviders(patientProvider);
ServletHolder servletHolder = new ServletHolder(ourServlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
public static class PatientProvider implements IResourceProvider {
@Create()
public MethodOutcome create(@ResourceParam Patient theIdParam) {
OperationOutcome oo = new OperationOutcome();
oo.addIssue().setDiagnostics(theIdParam.getNameFirstRep().getFamily());
theIdParam.setId("1");
theIdParam.getMeta().setVersionId("1");
return new MethodOutcome(new IdType("Patient", "1"), true).setOperationOutcome(oo).setResource(theIdParam);
}
@ -480,4 +450,33 @@ public class ServerMimetypeR4Test {
}
@AfterClass
public static void afterClassClearContext() throws Exception {
JettyUtil.closeServer(ourServer);
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void beforeClass() throws Exception {
ourServer = new Server(0);
PatientProvider patientProvider = new PatientProvider();
ServletHandler proxyHandler = new ServletHandler();
ourServlet = new RestfulServer(ourCtx);
ourServlet.setResourceProviders(patientProvider);
ServletHolder servletHolder = new ServletHolder(ourServlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
}

55
hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/server/ResourceProviderRule.java Normal file
View File

@ -0,0 +1,55 @@
package ca.uhn.fhir.test.utilities.server;
/*-
* #%L
* HAPI FHIR Test Utilities
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.junit.rules.TestRule;
import org.junit.runner.Description;
import org.junit.runners.model.Statement;
public class ResourceProviderRule implements TestRule {
private final RestfulServerRule myRestfulServerRule;
private Object myProvider;
/**
* Constructor
*/
public ResourceProviderRule(RestfulServerRule theRestfulServerRule, Object theProvider) {
myRestfulServerRule = theRestfulServerRule;
myProvider = theProvider;
}
@Override
public Statement apply(Statement base, Description description) {
return new Statement() {
@Override
public void evaluate() throws Throwable {
myRestfulServerRule.getRestfulServer().registerProvider(myProvider);
try {
base.evaluate();
} finally {
myRestfulServerRule.getRestfulServer().unregisterProvider(myProvider);
}
}
};
}
}

4
hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/server/RestfulServerRule.java
View File

@ -112,4 +112,8 @@ public class RestfulServerRule implements TestRule {
public RestfulServer getRestfulServer() {
return myServlet;
}
public int getPort() {
return myPort;
}
}

2
pom.xml
View File

@ -615,7 +615,7 @@
<jaxb_runtime_version>2.3.1</jaxb_runtime_version>
<jersey_version>2.25.1</jersey_version>
<!-- 9.4.17 seems to have issues -->
<jetty_version>9.4.14.v20181114</jetty_version>
<jetty_version>9.4.23.v20191118</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.4.6.Final</hibernate_version>

32
src/changes/changes.xml
View File

@ -6,6 +6,38 @@
<title>HAPI FHIR Changelog</title>
</properties>
<body>
<release version="4.2.0" date="TBD">
<action type="add">
The version of a few dependencies have been bumped to the
latest versions (dependent HAPI modules listed in brackets):
<![CDATA[
<ul>
<li>Jetty (CLI): 9.4.14.v20181114 -&gt; 9.4.23.v20191118</li>
</ul>
]]>
</action>
<action type="fix" issue="1583">
As of FHIR R4, some fields that were previously of type reference are now of type canonical.
One example is QuestionnaireResponse.questionnaire. Technically this means that this field
should no longer contain a relative reference, but as they are sometimes used that way, HAPI
FHIR will now try to be permissive and will index relative link canonical fields
such as (Questionnaire/123) as though it actually was a local relative link. Thanks to
Dean Atchley for reporting and providing a test case!
</action>
<action type="fix">
ValueSet PreCalculation did not successfully expand valuesets when Lucene was not enabled
in the JPA server. This has been corrected.
</action>
<action type="change">
When parsing Bundle resources containing other resources, XML/JSON parsers have an option called
"override resource ID with bundle entry fullUrl". This option previously caused any value
found in Bundle.entry.fullUrl to override any value found in
Bundle.entry.resource.id (meaning that the parsed resource would take its ID from
the fullUrl even if that ID disagreed with the ID found in the resource itself. As of
HAPI FHIR 4.1.0 the value in Bundle.entry.fullUrl will only be used to set the parsed resource
ID if the resource has no ID present.
</action>
</release>
<release version="4.1.0" date="2019-11-13" description="Jitterbug">
<action type="add">
The version of a few dependencies have been bumped to the