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Code Issues Packages Projects Releases Wiki Activity

Index canonical references (#1728) 

* Index canonical references

* Add changelog

* Fix compile error

* Add whitespace
This commit is contained in:
James Agnew 2020-02-25 21:45:46 -05:00 committed by GitHub
parent b2b0ff22b4
commit cb9906580e
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7 changed files with 129 additions and 39 deletions
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5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1728-index-canonical.yaml Normal file
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@ -0,0 +1,5 @@
---
type: add
issue: 1728
title: "Fields of type `canonical` were not previously indexed by the JPA server, meaning that some
default search parameters could not be honoured (e.g. StructureDefinition:valueset). This is now corrected."

62
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
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@ -3,7 +3,14 @@ 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.entity.Search;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@ -33,7 +40,11 @@ import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
import org.junit.*;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
@ -44,12 +55,30 @@ import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.util.*;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import java.util.stream.Collectors;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.Mockito.mock;
@SuppressWarnings({"unchecked", "Duplicates"})
@ -73,6 +102,28 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
public void testCanonicalReference() {
StructureDefinition sd = new StructureDefinition();
sd.getSnapshot().addElement().getBinding().setValueSet("http://foo");
String id = myStructureDefinitionDao.create(sd).getId().toUnqualifiedVersionless().getValue();
{
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add(StructureDefinition.SP_VALUESET, new ReferenceParam("http://foo"));
List<String> ids = toUnqualifiedVersionlessIdValues(myStructureDefinitionDao.search(map));
assertThat(ids, contains(id));
}
{
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add(StructureDefinition.SP_VALUESET, new ReferenceParam("http://foo2"));
List<String> ids = toUnqualifiedVersionlessIdValues(myStructureDefinitionDao.search(map));
assertThat(ids, empty());
}
}
@Test
public void testHasConditionAgeCompare() {
Patient patient = new Patient();
@ -4365,7 +4416,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
private String toStringMultiline(List<?> theResults) {
StringBuilder b = new StringBuilder();
for (Object next : theResults) {

53
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceLink.java
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@ -84,22 +84,6 @@ public class ResourceLink extends BaseResourceIndex {
super();
}
public ResourceLink(String theSourcePath, ResourceTable theSourceResource, IIdType theTargetResourceUrl, Date theUpdated) {
super();
setSourcePath(theSourcePath);
setSourceResource(theSourceResource);
setTargetResourceUrl(theTargetResourceUrl);
setUpdated(theUpdated);
}
public ResourceLink(String theSourcePath, ResourceTable theSourceResource, ResourceTable theTargetResource, Date theUpdated) {
super();
setSourcePath(theSourcePath);
setSourceResource(theSourceResource);
setTargetResource(theTargetResource);
setUpdated(theUpdated);
}
@Override
public boolean equals(Object theObj) {
if (this == theObj) {
@ -170,6 +154,13 @@ public class ResourceLink extends BaseResourceIndex {
myTargetResourceUrl = theTargetResourceUrl.getValue();
}
public void setTargetResourceUrlCanonical(String theTargetResourceUrl) {
Validate.notBlank(theTargetResourceUrl);
myTargetResourceType = "(unknown)";
myTargetResourceUrl = theTargetResourceUrl;
}
public Date getUpdated() {
return myUpdated;
}
@ -216,4 +207,34 @@ public class ResourceLink extends BaseResourceIndex {
return b.toString();
}
public static ResourceLink forAbsoluteReference(String theSourcePath, ResourceTable theSourceResource, IIdType theTargetResourceUrl, Date theUpdated) {
ResourceLink retVal = new ResourceLink();
retVal.setSourcePath(theSourcePath);
retVal.setSourceResource(theSourceResource);
retVal.setTargetResourceUrl(theTargetResourceUrl);
retVal.setUpdated(theUpdated);
return retVal;
}
/**
* Factory for canonical URL
*/
public static ResourceLink forLogicalReference(String theSourcePath, ResourceTable theSourceResource, String theTargetResourceUrl, Date theUpdated) {
ResourceLink retVal = new ResourceLink();
retVal.setSourcePath(theSourcePath);
retVal.setSourceResource(theSourceResource);
retVal.setTargetResourceUrlCanonical(theTargetResourceUrl);
retVal.setUpdated(theUpdated);
return retVal;
}
public static ResourceLink forLocalReference(String theSourcePath, ResourceTable theSourceResource, ResourceTable theTargetResource, Date theUpdated) {
ResourceLink retVal = new ResourceLink();
retVal.setSourcePath(theSourcePath);
retVal.setSourceResource(theSourceResource);
retVal.setTargetResource(theTargetResource);
retVal.setUpdated(theUpdated);
return retVal;
}
}

18
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
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@ -125,23 +125,29 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
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());
// Canonical has a root type of "uri"
if ("canonical".equals(typeName)) {
/*
* 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
* containing a local reference for what it is, and allow people to search
* based on that.
*/
IIdType parsed = fakeReference.getReferenceElement();
if (parsed.hasIdPart() && parsed.hasResourceType() && !parsed.isAbsolute()) {
PathAndRef ref = new PathAndRef(searchParam.getName(), path, fakeReference);
PathAndRef ref = new PathAndRef(searchParam.getName(), path, fakeReference, false);
params.add(ref);
break;
}
if (parsed.isAbsolute()) {
PathAndRef ref = new PathAndRef(searchParam.getName(), path, fakeReference, true);
params.add(ref);
break;
}
@ -165,7 +171,7 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
return;
}
PathAndRef ref = new PathAndRef(searchParam.getName(), path, valueRef);
PathAndRef ref = new PathAndRef(searchParam.getName(), path, valueRef, false);
params.add(ref);
break;
default:

8
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/PathAndRef.java
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@ -27,15 +27,21 @@ public class PathAndRef {
private final String myPath;
private final IBaseReference myRef;
private final String mySearchParamName;
private final boolean myCanonical;
/**
* Constructor
*/
public PathAndRef(String theSearchParamName, String thePath, IBaseReference theRef) {
public PathAndRef(String theSearchParamName, String thePath, IBaseReference theRef, boolean theCanonical) {
super();
mySearchParamName = theSearchParamName;
myPath = thePath;
myRef = theRef;
myCanonical = theCanonical;
}
public boolean isCanonical() {
return myCanonical;
}
public String getSearchParamName() {

10
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java
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@ -87,8 +87,10 @@ public class ResourceLinkExtractor {
theParams.myPopulatedResourceLinkParameters.add(thePathAndRef.getSearchParamName());
if (LogicalReferenceHelper.isLogicalReference(myModelConfig, nextId)) {
ResourceLink resourceLink = new ResourceLink(thePathAndRef.getPath(), theEntity, nextId, theUpdateTime);
boolean canonical = thePathAndRef.isCanonical();
if (LogicalReferenceHelper.isLogicalReference(myModelConfig, nextId) || canonical) {
String value = nextId.getValue();
ResourceLink resourceLink = ResourceLink.forLogicalReference(thePathAndRef.getPath(), theEntity, value, theUpdateTime);
if (theParams.myLinks.add(resourceLink)) {
ourLog.debug("Indexing remote resource reference URL: {}", nextId);
}
@ -130,7 +132,7 @@ public class ResourceLinkExtractor {
String msg = myContext.getLocalizer().getMessage(BaseSearchParamExtractor.class, "externalReferenceNotAllowed", nextId.getValue());
throw new InvalidRequestException(msg);
} else {
ResourceLink resourceLink = new ResourceLink(thePathAndRef.getPath(), theEntity, nextId, theUpdateTime);
ResourceLink resourceLink = ResourceLink.forAbsoluteReference(thePathAndRef.getPath(), theEntity, nextId, theUpdateTime);
if (theParams.myLinks.add(resourceLink)) {
ourLog.debug("Indexing remote resource reference URL: {}", nextId);
}
@ -165,7 +167,7 @@ public class ResourceLinkExtractor {
return null;
}
return new ResourceLink(nextPathAndRef.getPath(), theEntity, targetResource, theUpdateTime);
return ResourceLink.forLocalReference(nextPathAndRef.getPath(), theEntity, targetResource, theUpdateTime);
}
}

2
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParamsTest.java
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@ -32,7 +32,7 @@ public class ResourceIndexedSearchParamsTest {
myTarget.setResourceType("Organization");
myParams = new ResourceIndexedSearchParams(source);
ResourceLink link = new ResourceLink("organization", source, myTarget, new Date());
ResourceLink link = ResourceLink.forLocalReference("organization", source, myTarget, new Date());
myParams.getResourceLinks().add(link);
}