honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Correct two JPA processing bugs (#1801) 

* Work on search params on contained

* Add workaround for stored decimals with leading decimal point

* Add changelog

* Cleanup

* Test fix

* Test fix

* One more test fix
This commit is contained in:
James Agnew 2020-04-15 14:22:47 -04:00 committed by GitHub
parent f2fa8659c4
commit f95f619bdc
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
25 changed files with 497 additions and 339 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -58,6 +58,14 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
@SuppressWarnings("WeakerAccess")
public abstract class BaseParser implements IParser {
/**
* Any resources that were created by the parser (i.e. by parsing a serialized resource) will have
* a {@link IBaseResource#getUserData(String) user data} property with this key.
*
* @since 5.0.0
*/
public static final String RESOURCE_CREATED_BY_PARSER = BaseParser.class.getName() + "_" + "RESOURCE_CREATED_BY_PARSER";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
private static final Set<String> notEncodeForContainedResource = new HashSet<>(Arrays.asList("security", "versionId", "lastUpdated"));

58
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
View File

@ -43,6 +43,7 @@ import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.XmlUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.*;
@ -456,7 +457,7 @@ class ParserState<T> {
RuntimePrimitiveDatatypeDefinition primitiveTarget = (RuntimePrimitiveDatatypeDefinition) target;
IPrimitiveType<?> newChildInstance = newPrimitiveInstance(myDefinition, primitiveTarget);
myDefinition.getMutator().addValue(myParentInstance, newChildInstance);
PrimitiveState newState = new PrimitiveState(getPreResourceState(), newChildInstance, theLocalPart);
PrimitiveState newState = new PrimitiveState(getPreResourceState(), newChildInstance, theLocalPart, primitiveTarget.getName());
push(newState);
return;
}
@ -495,10 +496,10 @@ class ParserState<T> {
private class ElementCompositeState extends BaseState {
private BaseRuntimeElementCompositeDefinition<?> myDefinition;
private IBase myInstance;
private Set<String> myParsedNonRepeatableNames = new HashSet<>();
private String myElementName;
private final BaseRuntimeElementCompositeDefinition<?> myDefinition;
private final IBase myInstance;
private final Set<String> myParsedNonRepeatableNames = new HashSet<>();
private final String myElementName;
ElementCompositeState(PreResourceState thePreResourceState, String theElementName, BaseRuntimeElementCompositeDefinition<?> theDef, IBase theInstance) {
super(thePreResourceState);
@ -585,7 +586,7 @@ class ParserState<T> {
IPrimitiveType<?> newChildInstance;
newChildInstance = getPrimitiveInstance(child, primitiveTarget, theChildName);
child.getMutator().addValue(myInstance, newChildInstance);
PrimitiveState newState = new PrimitiveState(getPreResourceState(), newChildInstance, theChildName);
PrimitiveState newState = new PrimitiveState(getPreResourceState(), newChildInstance, theChildName, primitiveTarget.getName());
push(newState);
return;
}
@ -668,7 +669,7 @@ class ParserState<T> {
public class ElementIdState extends BaseState {
private IBaseElement myElement;
private final IBaseElement myElement;
ElementIdState(ParserState<T>.PreResourceState thePreResourceState, IBaseElement theElement) {
super(thePreResourceState);
@ -689,7 +690,7 @@ class ParserState<T> {
private class ExtensionState extends BaseState {
private IBaseExtension<?, ?> myExtension;
private final IBaseExtension<?, ?> myExtension;
ExtensionState(PreResourceState thePreResourceState, IBaseExtension<?, ?> theExtension) {
super(thePreResourceState);
@ -752,7 +753,7 @@ class ParserState<T> {
RuntimePrimitiveDatatypeDefinition primitiveTarget = (RuntimePrimitiveDatatypeDefinition) target;
IPrimitiveType<?> newChildInstance = newInstance(primitiveTarget);
myExtension.setValue(newChildInstance);
PrimitiveState newState = new PrimitiveState(getPreResourceState(), newChildInstance, theLocalPart);
PrimitiveState newState = new PrimitiveState(getPreResourceState(), newChildInstance, theLocalPart, primitiveTarget.getName());
push(newState);
return;
}
@ -782,7 +783,7 @@ class ParserState<T> {
public class IdentifiableElementIdState extends BaseState {
private IIdentifiableElement myElement;
private final IIdentifiableElement myElement;
public IdentifiableElementIdState(ParserState<T>.PreResourceState thePreResourceState, IIdentifiableElement theElement) {
super(thePreResourceState);
@ -802,7 +803,7 @@ class ParserState<T> {
}
private class MetaElementState extends BaseState {
private ResourceMetadataMap myMap;
private final ResourceMetadataMap myMap;
public MetaElementState(ParserState<T>.PreResourceState thePreResourceState, ResourceMetadataMap theMap) {
super(thePreResourceState);
@ -824,7 +825,7 @@ class ParserState<T> {
break;
case "lastUpdated":
InstantDt updated = new InstantDt();
push(new PrimitiveState(getPreResourceState(), updated, theLocalPart));
push(new PrimitiveState(getPreResourceState(), updated, theLocalPart, "instant"));
myMap.put(ResourceMetadataKeyEnum.UPDATED, updated);
break;
case "security":
@ -850,7 +851,7 @@ class ParserState<T> {
newProfiles = new ArrayList<>(1);
}
IdDt profile = new IdDt();
push(new PrimitiveState(getPreResourceState(), profile, theLocalPart));
push(new PrimitiveState(getPreResourceState(), profile, theLocalPart, "id"));
newProfiles.add(profile);
myMap.put(ResourceMetadataKeyEnum.PROFILES, Collections.unmodifiableList(newProfiles));
break;
@ -1048,6 +1049,8 @@ class ParserState<T> {
}
}
myInstance.setUserData(BaseParser.RESOURCE_CREATED_BY_PARSER, Boolean.TRUE);
populateTarget();
}
@ -1269,41 +1272,50 @@ class ParserState<T> {
private class PrimitiveState extends BaseState {
private final String myChildName;
private final String myTypeName;
private IPrimitiveType<?> myInstance;
PrimitiveState(PreResourceState thePreResourceState, IPrimitiveType<?> theInstance, String theChildName) {
PrimitiveState(PreResourceState thePreResourceState, IPrimitiveType<?> theInstance, String theChildName, String theTypeName) {
super(thePreResourceState);
myInstance = theInstance;
myChildName = theChildName;
myTypeName = theTypeName;
}
@Override
public void attributeValue(String theName, String theValue) throws DataFormatException {
String value = theValue;
if ("value".equals(theName)) {
if ("".equals(theValue)) {
if ("".equals(value)) {
ParseLocation location = ParseLocation.fromElementName(myChildName);
myErrorHandler.invalidValue(location, theValue, "Attribute value must not be empty (\"\")");
myErrorHandler.invalidValue(location, value, "Attribute value must not be empty (\"\")");
} else {
if ("decimal".equals(myTypeName)) {
if (value != null && value.startsWith(".") && NumberUtils.isDigits(value.substring(1))) {
value = "0" + value;
}
}
try {
myInstance.setValueAsString(theValue);
myInstance.setValueAsString(value);
} catch (DataFormatException | IllegalArgumentException e) {
ParseLocation location = ParseLocation.fromElementName(myChildName);
myErrorHandler.invalidValue(location, theValue, e.getMessage());
myErrorHandler.invalidValue(location, value, e.getMessage());
}
}
} else if ("id".equals(theName)) {
if (myInstance instanceof IIdentifiableElement) {
((IIdentifiableElement) myInstance).setElementSpecificId(theValue);
((IIdentifiableElement) myInstance).setElementSpecificId(value);
} else if (myInstance instanceof IBaseElement) {
((IBaseElement) myInstance).setId(theValue);
((IBaseElement) myInstance).setId(value);
} else if (myInstance instanceof IBaseResource) {
new IdDt(theValue).applyTo((org.hl7.fhir.instance.model.api.IBaseResource) myInstance);
new IdDt(value).applyTo((org.hl7.fhir.instance.model.api.IBaseResource) myInstance);
} else {
ParseLocation location = ParseLocation.fromElementName(myChildName);
myErrorHandler.unknownAttribute(location, theName);
}
} else {
super.attributeValue(theName, theValue);
super.attributeValue(theName, value);
}
}
@ -1348,7 +1360,7 @@ class ParserState<T> {
@Override
public void enteringNewElement(String theNamespace, String theChildName) throws DataFormatException {
if ("id".equals(theChildName)) {
push(new PrimitiveState(getPreResourceState(), myInstance.getId(), theChildName));
push(new PrimitiveState(getPreResourceState(), myInstance.getId(), theChildName, "id"));
} else if ("meta".equals(theChildName)) {
push(new MetaElementState(getPreResourceState(), myInstance.getResourceMetadata()));
} else {

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonStructure.java
View File

@ -35,7 +35,6 @@ import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.DecimalNode;
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
import com.fasterxml.jackson.databind.node.ObjectNode;
import org.apache.jena.tdb.setup.BuilderStdDB;
import java.io.IOException;
import java.io.PushbackReader;

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1801-allow-parsing-contained-in-jpa.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: fix
issue: 1801
title: "When invoking JPA DAO methods programatically to store a resource (as opposed to using the FHIR REST API), if
the resource being stored had any contained resources, these would sometimes not be visible to the search parameter
indexer, leading to missing search params. This is a very fringe use case, but a workaround has been put in place to
solve it."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1801-handle-persisted-leading-decimals.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 1801
title: "In previous versions of HAPI FHIR, the server incorrectly silently accepted decimal numbers in JSON with no
leading numbers (e.g. `.123`). These will now be rejected by the JSON parser. Any values with this string that
have previously been stored in the JPA server database will now automatically convert the value to `0.123`."

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -11,6 +11,7 @@ import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
import ca.uhn.fhir.jpa.bulk.BulkDataExportSvcImpl;
import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.index.DaoResourceLinkResolver;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
import ca.uhn.fhir.jpa.interceptor.JpaConsentContextServices;
@ -33,6 +34,7 @@ import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
import ca.uhn.fhir.jpa.searchparam.config.SearchParamConfig;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -46,6 +48,7 @@ import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.FilterType;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.context.annotation.Scope;
import org.springframework.core.env.Environment;
import org.springframework.core.task.AsyncTaskExecutor;
@ -158,6 +161,12 @@ public abstract class BaseConfig {
return new BinaryStorageInterceptor();
}
@Bean
@Primary
public IResourceLinkResolver daoResourceLinkResolver() {
return new DaoResourceLinkResolver();
}
@Bean
public ISearchCacheSvc searchCacheSvc() {
return new DatabaseSearchCacheSvcImpl();

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -1,6 +1,13 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeChildResourceDefinition;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
@ -8,7 +15,12 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.dao.IJpaDao;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceProvenanceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
import ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
@ -22,7 +34,6 @@ import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
@ -78,7 +89,11 @@ import org.springframework.transaction.support.TransactionSynchronizationAdapter
import org.springframework.transaction.support.TransactionSynchronizationManager;
import javax.annotation.PostConstruct;
import javax.persistence.*;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Root;
@ -87,7 +102,12 @@ import javax.xml.stream.events.XMLEvent;
import java.util.*;
import java.util.Map.Entry;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.trim;
/*
* #%L
@ -850,8 +870,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
// 4. parse the text to FHIR
R retVal;
if (resourceEncoding != ResourceEncodingEnum.DEL) {
IParser parser = resourceEncoding.newParser(getContext(theEntity.getFhirVersion()));
parser.setParserErrorHandler(new LenientErrorHandler(false).setErrorOnInvalidValue(false));
LenientErrorHandler errorHandler = new LenientErrorHandler(false).setErrorOnInvalidValue(false);
IParser parser = new TolerantJsonParser(getContext(theEntity.getFhirVersion()), errorHandler);
try {
retVal = parser.parseResource(resourceType, resourceText);

57
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TolerantJsonParser.java Normal file
View File

@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParserErrorHandler;
import ca.uhn.fhir.parser.JsonParser;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.apache.commons.lang3.StringUtils.defaultString;
class TolerantJsonParser extends JsonParser {
private static final Logger ourLog = LoggerFactory.getLogger(TolerantJsonParser.class);
TolerantJsonParser(FhirContext theContext, IParserErrorHandler theParserErrorHandler) {
super(theContext, theParserErrorHandler);
}
@Override
public <T extends IBaseResource> T parseResource(Class<T> theResourceType, String theMessageString) {
try {
return super.parseResource(theResourceType, theMessageString);
} catch (DataFormatException e) {
if (defaultString(e.getMessage()).contains("Unexpected character ('.' (code 46))")) {
/*
* The following is a hacky and gross workaround until the following PR is hopefully merged:
* https://github.com/FasterXML/jackson-core/pull/611
*
* The issue this solves is that under Gson it was possible to store JSON containing
* decimal numbers with no leading integer, e.g. .123
*
* These don't parse in Jackson, meaning we can be stuck with data in the database
* that can't be loaded back out.
*
* Note that if we fix this in the future to rely on Jackson natively handing this
* nicely we may or may not be able to remove some code from
* ParserState.Primitive state too.
*/
Gson gson = new Gson();
JsonObject object = gson.fromJson(theMessageString, JsonObject.class);
String corrected = gson.toJson(object);
return super.parseResource(theResourceType, corrected);
}
throw e;
}
}
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
View File

@ -49,7 +49,6 @@ import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.util.Optional;
@Service
public class DaoResourceLinkResolver implements IResourceLinkResolver {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DaoResourceLinkResolver.class);
@PersistenceContext(type = PersistenceContextType.TRANSACTION)

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java
View File

@ -23,8 +23,8 @@ package ca.uhn.fhir.jpa.dao.index;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedCompositeStringUniqueDao;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
@ -34,7 +34,6 @@ import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceLinkExtractor;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorService;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.model.api.IQueryParameterType;
@ -84,8 +83,6 @@ public class SearchParamWithInlineReferencesExtractor {
@Autowired
private SearchParamExtractorService mySearchParamExtractorService;
@Autowired
private ResourceLinkExtractor myResourceLinkExtractor;
@Autowired
private DaoResourceLinkResolver myDaoResourceLinkResolver;
@Autowired
private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
@ -96,19 +93,15 @@ public class SearchParamWithInlineReferencesExtractor {
protected EntityManager myEntityManager;
public void populateFromResource(ResourceIndexedSearchParams theParams, Date theUpdateTime, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest) {
mySearchParamExtractorService.extractFromResource(theRequest, theParams, theEntity, theResource);
extractInlineReferences(theResource, theRequest);
mySearchParamExtractorService.extractFromResource(theRequest, theParams, theEntity, theResource, theUpdateTime, true);
Set<Map.Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).entrySet();
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
theParams.findMissingSearchParams(myDaoConfig.getModelConfig(), theEntity, activeSearchParams);
}
theParams.setUpdatedTime(theUpdateTime);
extractInlineReferences(theResource, theRequest);
myResourceLinkExtractor.extractResourceLinks(theParams, theEntity, theResource, theUpdateTime, myDaoResourceLinkResolver, true, theRequest);
/*
* If the existing resource already has links and those match links we still want, use them instead of removing them and re adding them
*/

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/xmlpatch/XmlPatchUtils.java
View File

@ -1,12 +1,14 @@
package ca.uhn.fhir.jpa.util.xmlpatch;
import java.io.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.github.dnault.xmlpatch.Patcher;
import org.hl7.fhir.instance.model.api.IBaseResource;
import com.github.dnault.xmlpatch.Patcher;
import ca.uhn.fhir.context.FhirContext;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
/*
* #%L
@ -28,9 +30,6 @@ import ca.uhn.fhir.context.FhirContext;
* #L%
*/
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
public class XmlPatchUtils {
public static <T extends IBaseResource> T apply(FhirContext theCtx, T theResourceToUpdate, String thePatchBody) {

50
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TolerantJsonParserR4Test.java Normal file
View File

@ -0,0 +1,50 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.LenientErrorHandler;
import org.hl7.fhir.r4.model.Observation;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
public class TolerantJsonParserR4Test {
private FhirContext myFhirContext = FhirContext.forR4();
@Test
public void testParseInvalidNumeric() {
String input = "{\n" +
"\"resourceType\": \"Observation\",\n" +
"\"valueQuantity\": {\n" +
" \"value\": .5\n" +
" }\n" +
"}";
TolerantJsonParser parser = new TolerantJsonParser(myFhirContext, new LenientErrorHandler());
Observation obs = parser.parseResource(Observation.class, input);
assertEquals("0.5", obs.getValueQuantity().getValueElement().getValueAsString());
}
@Test
public void testParseInvalidNumeric2() {
String input = "{\n" +
"\"resourceType\": \"Observation\",\n" +
"\"valueQuantity\": {\n" +
" \"value\": .\n" +
" }\n" +
"}";
TolerantJsonParser parser = new TolerantJsonParser(myFhirContext, new LenientErrorHandler());
try {
parser.parseResource(Observation.class, input);
} catch (DataFormatException e) {
assertEquals("[element=\"value\"] Invalid attribute value \".\": No digits found.", e.getMessage());
}
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -218,6 +218,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
protected IResourceIndexedSearchParamStringDao myResourceIndexedSearchParamStringDao;
@Autowired
protected IResourceIndexedSearchParamTokenDao myResourceIndexedSearchParamTokenDao;
@Autowired
protected IResourceTableDao myResourceTableDao;
@Autowired
protected IResourceTagDao myResourceTagDao;

45
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java
View File

@ -1,8 +1,10 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -20,6 +22,7 @@ import org.junit.Before;
import org.junit.Test;
import java.util.List;
import java.util.stream.Collectors;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
@ -1054,6 +1057,48 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
}
@Test
public void testProgramaticallyContainedByReferenceAreStillResolvable() {
SearchParameter sp = new SearchParameter();
sp.setUrl("http://hapifhir.io/fhir/StructureDefinition/sp-unique");
sp.setName("MEDICATIONADMINISTRATION-INGREDIENT-MEDICATION");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setCode("medicationadministration-ingredient-medication");
sp.addBase("MedicationAdministration");
sp.setType(Enumerations.SearchParamType.TOKEN);
sp.setExpression("MedicationAdministration.medication.resolve().ingredient.item.as(Reference).resolve().code");
mySearchParameterDao.create(sp);
mySearchParamRegistry.forceRefresh();
Medication ingredient = new Medication();
ingredient.getCode().addCoding().setSystem("system").setCode("code");
Medication medication = new Medication();
medication.addIngredient().setItem(new Reference(ingredient));
MedicationAdministration medAdmin = new MedicationAdministration();
medAdmin.setMedication(new Reference(medication));
myMedicationAdministrationDao.create(medAdmin);
runInTransaction(()->{
List<ResourceIndexedSearchParamToken> tokens = myResourceIndexedSearchParamTokenDao
.findAll()
.stream()
.filter(t -> t.getParamName().equals("medicationadministration-ingredient-medication"))
.collect(Collectors.toList());
ourLog.info("Tokens: {}", tokens);
assertEquals(tokens.toString(), 1, tokens.size());
});
SearchParameterMap map = new SearchParameterMap();
map.add("medicationadministration-ingredient-medication", new TokenParam("system","code"));
assertEquals(1, myMedicationAdministrationDao.search(map).size().intValue());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchCustomSearchParamTest.java
View File

@ -253,6 +253,7 @@ public class FhirResourceDaoR4SearchCustomSearchParamTest extends BaseJpaR4Test
MessageHeader messageHeader = new MessageHeader();
messageHeader.setId("123");
messageHeader.setDefinition("Hello");
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.MESSAGE);
bundle.addEntry()

14
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/config/SearchParamConfig.java
View File

@ -22,9 +22,7 @@ package ca.uhn.fhir.jpa.searchparam.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceLinkExtractor;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu2;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu3;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
@ -32,13 +30,11 @@ import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR5;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorService;
import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
import ca.uhn.fhir.jpa.searchparam.matcher.IndexedSearchParamExtractor;
import ca.uhn.fhir.jpa.searchparam.matcher.InlineResourceLinkResolver;
import ca.uhn.fhir.jpa.searchparam.matcher.SearchParamMatcher;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryImpl;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.scheduling.annotation.EnableScheduling;
@ -79,11 +75,6 @@ public class SearchParamConfig {
return new MatchUrlService();
}
@Bean
public ResourceLinkExtractor resourceLinkExtractor() {
return new ResourceLinkExtractor();
}
@Bean
@Lazy
public SearchParamExtractorService searchParamExtractorService(){
@ -95,11 +86,6 @@ public class SearchParamConfig {
return new IndexedSearchParamExtractor();
}
@Bean
public InlineResourceLinkResolver inlineResourceLinkResolver() {
return new InlineResourceLinkResolver();
}
@Bean
public InMemoryResourceMatcher InMemoryResourceMatcher() {
return new InMemoryResourceMatcher();

4
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
View File

@ -1015,6 +1015,10 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
systemAsString = myUseSystem;
}
if (value instanceof IIdType) {
valueAsString = ((IIdType) value).getIdPart();
}
BaseSearchParamExtractor.this.createTokenIndexIfNotBlank(myResourceTypeName, params, searchParam, systemAsString, valueAsString);
return;
}

14
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceIndexedSearchParams.java
View File

@ -26,18 +26,22 @@ import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.ReferenceParam;
import org.apache.commons.lang3.StringUtils;
import org.springframework.context.annotation.DependsOn;
import java.util.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.function.Predicate;
import static org.apache.commons.lang3.StringUtils.compare;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public final class ResourceIndexedSearchParams {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceIndexedSearchParams.class);
final public Collection<ResourceIndexedSearchParamString> myStringParams = new ArrayList<>();
final public Collection<ResourceIndexedSearchParamToken> myTokenParams = new HashSet<>();
final public Collection<ResourceIndexedSearchParamNumber> myNumberParams = new ArrayList<>();
@ -110,7 +114,7 @@ public final class ResourceIndexedSearchParams {
theEntity.setHasLinks(myLinks.isEmpty() == false);
}
public void setUpdatedTime(Date theUpdateTime) {
void setUpdatedTime(Date theUpdateTime) {
setUpdatedTime(myStringParams, theUpdateTime);
setUpdatedTime(myNumberParams, theUpdateTime);
setUpdatedTime(myQuantityParams, theUpdateTime);

192
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java
View File

@ -1,192 +0,0 @@
package ca.uhn.fhir.jpa.searchparam.extractor;
/*-
* #%L
* HAPI FHIR Search Parameters
* %%
* Copyright (C) 2014 - 2020 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 ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.commons.lang3.StringUtils;
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.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.Date;
import java.util.HashMap;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class ResourceLinkExtractor {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceLinkExtractor.class);
@Autowired
private ModelConfig myModelConfig;
@Autowired
private FhirContext myContext;
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
@Autowired
private ISearchParamExtractor mySearchParamExtractor;
@Autowired
private IInterceptorBroadcaster myInterceptorBroadcaster;
public void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, boolean theFailOnInvalidReference, RequestDetails theRequest) {
String resourceName = myContext.getResourceDefinition(theResource).getName();
ISearchParamExtractor.SearchParamSet<PathAndRef> refs = mySearchParamExtractor.extractResourceLinks(theResource);
SearchParamExtractorService.handleWarnings(theRequest, myInterceptorBroadcaster, refs);
Map<String, IResourceLookup> resourceIdToResolvedTarget = new HashMap<>();
for (PathAndRef nextPathAndRef : refs) {
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(resourceName, nextPathAndRef.getSearchParamName());
extractResourceLinks(theParams, theEntity, theUpdateTime, theResourceLinkResolver, searchParam, nextPathAndRef, theFailOnInvalidReference, theRequest, resourceIdToResolvedTarget);
}
theEntity.setHasLinks(theParams.myLinks.size() > 0);
}
private void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest, Map<String, IResourceLookup> theResourceIdToResolvedTarget) {
IBaseReference nextReference = thePathAndRef.getRef();
IIdType nextId = nextReference.getReferenceElement();
String path = thePathAndRef.getPath();
/*
* This can only really happen if the DAO is being called
* programmatically with a Bundle (not through the FHIR REST API)
* but Smile does this
*/
if (nextId.isEmpty() && nextReference.getResource() != null) {
nextId = nextReference.getResource().getIdElement();
}
theParams.myPopulatedResourceLinkParameters.add(thePathAndRef.getSearchParamName());
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);
}
return;
}
String baseUrl = nextId.getBaseUrl();
String typeString = nextId.getResourceType();
if (isBlank(typeString)) {
String msg = "Invalid resource reference found at path[" + path + "] - Does not contain resource type - " + nextId.getValue();
if (theFailOnInvalidReference) {
throw new InvalidRequestException(msg);
} else {
ourLog.debug(msg);
return;
}
}
RuntimeResourceDefinition resourceDefinition;
try {
resourceDefinition = myContext.getResourceDefinition(typeString);
} catch (DataFormatException e) {
String msg = "Invalid resource reference found at path[" + path + "] - Resource type is unknown or not supported on this server - " + nextId.getValue();
if (theFailOnInvalidReference) {
throw new InvalidRequestException(msg);
} else {
ourLog.debug(msg);
return;
}
}
if (theRuntimeSearchParam.hasTargets()) {
if (!theRuntimeSearchParam.getTargets().contains(typeString)) {
return;
}
}
if (isNotBlank(baseUrl)) {
if (!myModelConfig.getTreatBaseUrlsAsLocal().contains(baseUrl) && !myModelConfig.isAllowExternalReferences()) {
String msg = myContext.getLocalizer().getMessage(BaseSearchParamExtractor.class, "externalReferenceNotAllowed", nextId.getValue());
throw new InvalidRequestException(msg);
} else {
ResourceLink resourceLink = ResourceLink.forAbsoluteReference(thePathAndRef.getPath(), theEntity, nextId, theUpdateTime);
if (theParams.myLinks.add(resourceLink)) {
ourLog.debug("Indexing remote resource reference URL: {}", nextId);
}
return;
}
}
Class<? extends IBaseResource> type = resourceDefinition.getImplementingClass();
String id = nextId.getIdPart();
if (StringUtils.isBlank(id)) {
String msg = "Invalid resource reference found at path[" + path + "] - Does not contain resource ID - " + nextId.getValue();
if (theFailOnInvalidReference) {
throw new InvalidRequestException(msg);
} else {
ourLog.debug(msg);
return;
}
}
theResourceLinkResolver.validateTypeOrThrowException(type);
ResourceLink resourceLink = createResourceLink(theEntity, theUpdateTime, theResourceLinkResolver, theRuntimeSearchParam, path, thePathAndRef, nextId, typeString, type, nextReference, theRequest, theResourceIdToResolvedTarget);
if (resourceLink == null) {
return;
}
theParams.myLinks.add(resourceLink);
}
private ResourceLink createResourceLink(ResourceTable theEntity, Date theUpdateTime, IResourceLinkResolver theResourceLinkResolver, RuntimeSearchParam nextSpDef, String theNextPathsUnsplit, PathAndRef nextPathAndRef, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest, Map<String, IResourceLookup> theResourceIdToResolvedTarget) {
/*
* We keep a cache of resolved target resources. This is good since for some resource types, there
* are multiple search parameters that map to the same element path within a resource (e.g.
* Observation:patient and Observation.subject and we don't want to force a resolution of the
* target any more times than we have to.
*/
IResourceLookup targetResource = theResourceIdToResolvedTarget.get(theNextId.getValue());
if (targetResource == null) {
targetResource = theResourceLinkResolver.findTargetResource(nextSpDef, theNextPathsUnsplit, theNextId, theTypeString, theType, theReference, theRequest);
}
if (targetResource == null) {
return null;
}
theResourceIdToResolvedTarget.put(theNextId.getValue(), targetResource);
String targetResourceType = targetResource.getResourceType();
Long targetResourcePid = targetResource.getResourceId();
String targetResourceIdPart = theNextId.getIdPart();
return ResourceLink.forLocalReference(nextPathAndRef.getPath(), theEntity, targetResourceType, targetResourcePid, targetResourceIdPart, theUpdateTime);
}
}

220
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorService.java
View File

@ -20,21 +20,36 @@ package ca.uhn.fhir.jpa.searchparam.extractor;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.StringUtils;
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.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Lazy;
import org.springframework.stereotype.Service;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class SearchParamExtractorService {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamExtractorService.class);
@ -43,30 +58,60 @@ public class SearchParamExtractorService {
private ISearchParamExtractor mySearchParamExtractor;
@Autowired
private IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
private ModelConfig myModelConfig;
@Autowired
private FhirContext myContext;
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
@Autowired(required = false)
private IResourceLinkResolver myResourceLinkResolver;
public void extractFromResource(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource) {
/**
* This method is responsible for scanning a resource for all of the search parameter instances. I.e. for all search parameters defined for
* a given resource type, it extracts the associated indexes and populates {@literal theParams}.
*/
public void extractFromResource(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, Date theUpdateTime, boolean theFailOnInvalidReference) {
IBaseResource resource = normalizeResource(theResource);
// All search parameter types except Reference
extractSearchIndexParameters(theRequestDetails, theParams, resource, theEntity);
// Reference search parameters
extractResourceLinks(theParams, theEntity, resource, theUpdateTime, theFailOnInvalidReference, theRequestDetails);
theParams.setUpdatedTime(theUpdateTime);
}
private void extractSearchIndexParameters(RequestDetails theRequestDetails, ResourceIndexedSearchParams theParams, IBaseResource theResource, ResourceTable theEntity) {
// Strings
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamString> strings = extractSearchParamStrings(theResource);
handleWarnings(theRequestDetails, myInterceptorBroadcaster, strings);
theParams.myStringParams.addAll(strings);
// Numbers
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamNumber> numbers = extractSearchParamNumber(theResource);
handleWarnings(theRequestDetails, myInterceptorBroadcaster, numbers);
theParams.myNumberParams.addAll(numbers);
// Quantities
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamQuantity> quantities = extractSearchParamQuantity(theResource);
handleWarnings(theRequestDetails, myInterceptorBroadcaster, quantities);
theParams.myQuantityParams.addAll(quantities);
// Dates
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamDate> dates = extractSearchParamDates(theResource);
handleWarnings(theRequestDetails, myInterceptorBroadcaster, dates);
theParams.myDateParams.addAll(dates);
// URIs
ISearchParamExtractor.SearchParamSet<ResourceIndexedSearchParamUri> uris = extractSearchParamUri(theResource);
handleWarnings(theRequestDetails, myInterceptorBroadcaster, uris);
theParams.myUriParams.addAll(uris);
ourLog.trace("Storing date indexes: {}", theParams.myDateParams);
// Tokens (can result in both Token and String, as we index the display name for
// the types: Coding, CodeableConcept)
for (BaseResourceIndexedSearchParam next : extractSearchParamTokens(theResource)) {
if (next instanceof ResourceIndexedSearchParamToken) {
theParams.myTokenParams.add((ResourceIndexedSearchParamToken) next);
@ -77,21 +122,182 @@ public class SearchParamExtractorService {
}
}
// Specials
for (BaseResourceIndexedSearchParam next : extractSearchParamSpecial(theResource)) {
if (next instanceof ResourceIndexedSearchParamCoords) {
theParams.myCoordsParams.add((ResourceIndexedSearchParamCoords) next);
}
}
populateResourceTable(theParams.myStringParams, theEntity);
// Do this after, because we add to strings during both string and token processing
populateResourceTable(theParams.myNumberParams, theEntity);
populateResourceTable(theParams.myQuantityParams, theEntity);
populateResourceTable(theParams.myDateParams, theEntity);
populateResourceTable(theParams.myUriParams, theEntity);
populateResourceTable(theParams.myCoordsParams, theEntity);
populateResourceTable(theParams.myTokenParams, theEntity);
populateResourceTable(theParams.myStringParams, theEntity);
populateResourceTable(theParams.myCoordsParams, theEntity);
}
/**
* This is a bit hacky, but if someone has manually populated a resource (ie. my working directly with the model
* as opposed to by parsing a serialized instance) it's possible that they have put in contained resources
* using {@link IBaseReference#setResource(IBaseResource)}, and those contained resources have not yet
* ended up in the Resource.contained array, meaning that FHIRPath expressions won't be able to find them.
*
* As a result, we to a serialize-and-parse to normalize the object. This really only affects people who
* are calling the JPA DAOs directly, but there are a few of those...
*/
private IBaseResource normalizeResource(IBaseResource theResource) {
IParser parser = myContext.newJsonParser().setPrettyPrint(false);
theResource = parser.parseResource(parser.encodeResourceToString(theResource));
return theResource;
}
private void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, IBaseResource theResource, Date theUpdateTime, boolean theFailOnInvalidReference, RequestDetails theRequest) {
String resourceName = myContext.getResourceDefinition(theResource).getName();
ISearchParamExtractor.SearchParamSet<PathAndRef> refs = mySearchParamExtractor.extractResourceLinks(theResource);
SearchParamExtractorService.handleWarnings(theRequest, myInterceptorBroadcaster, refs);
Map<String, IResourceLookup> resourceIdToResolvedTarget = new HashMap<>();
for (PathAndRef nextPathAndRef : refs) {
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(resourceName, nextPathAndRef.getSearchParamName());
extractResourceLinks(theParams, theEntity, theUpdateTime, searchParam, nextPathAndRef, theFailOnInvalidReference, theRequest, resourceIdToResolvedTarget);
}
theEntity.setHasLinks(theParams.myLinks.size() > 0);
}
private void extractResourceLinks(ResourceIndexedSearchParams theParams, ResourceTable theEntity, Date theUpdateTime, RuntimeSearchParam theRuntimeSearchParam, PathAndRef thePathAndRef, boolean theFailOnInvalidReference, RequestDetails theRequest, Map<String, IResourceLookup> theResourceIdToResolvedTarget) {
IBaseReference nextReference = thePathAndRef.getRef();
IIdType nextId = nextReference.getReferenceElement();
String path = thePathAndRef.getPath();
/*
* This can only really happen if the DAO is being called
* programmatically with a Bundle (not through the FHIR REST API)
* but Smile does this
*/
if (nextId.isEmpty() && nextReference.getResource() != null) {
nextId = nextReference.getResource().getIdElement();
}
theParams.myPopulatedResourceLinkParameters.add(thePathAndRef.getSearchParamName());
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);
}
return;
}
String baseUrl = nextId.getBaseUrl();
String typeString = nextId.getResourceType();
if (isBlank(typeString)) {
String msg = "Invalid resource reference found at path[" + path + "] - Does not contain resource type - " + nextId.getValue();
if (theFailOnInvalidReference) {
throw new InvalidRequestException(msg);
} else {
ourLog.debug(msg);
return;
}
}
RuntimeResourceDefinition resourceDefinition;
try {
resourceDefinition = myContext.getResourceDefinition(typeString);
} catch (DataFormatException e) {
String msg = "Invalid resource reference found at path[" + path + "] - Resource type is unknown or not supported on this server - " + nextId.getValue();
if (theFailOnInvalidReference) {
throw new InvalidRequestException(msg);
} else {
ourLog.debug(msg);
return;
}
}
if (theRuntimeSearchParam.hasTargets()) {
if (!theRuntimeSearchParam.getTargets().contains(typeString)) {
return;
}
}
if (isNotBlank(baseUrl)) {
if (!myModelConfig.getTreatBaseUrlsAsLocal().contains(baseUrl) && !myModelConfig.isAllowExternalReferences()) {
String msg = myContext.getLocalizer().getMessage(BaseSearchParamExtractor.class, "externalReferenceNotAllowed", nextId.getValue());
throw new InvalidRequestException(msg);
} else {
ResourceLink resourceLink = ResourceLink.forAbsoluteReference(thePathAndRef.getPath(), theEntity, nextId, theUpdateTime);
if (theParams.myLinks.add(resourceLink)) {
ourLog.debug("Indexing remote resource reference URL: {}", nextId);
}
return;
}
}
Class<? extends IBaseResource> type = resourceDefinition.getImplementingClass();
String id = nextId.getIdPart();
if (StringUtils.isBlank(id)) {
String msg = "Invalid resource reference found at path[" + path + "] - Does not contain resource ID - " + nextId.getValue();
if (theFailOnInvalidReference) {
throw new InvalidRequestException(msg);
} else {
ourLog.debug(msg);
return;
}
}
ResourceLink resourceLink;
if (theFailOnInvalidReference) {
myResourceLinkResolver.validateTypeOrThrowException(type);
resourceLink = resolveTargetAndCreateResourceLinkOrReturnNull(theEntity, theUpdateTime, theRuntimeSearchParam, path, thePathAndRef, nextId, typeString, type, nextReference, theRequest, theResourceIdToResolvedTarget);
if (resourceLink == null) {
return;
}
} else {
ResourceTable target;
target = new ResourceTable();
target.setResourceType(typeString);
resourceLink = ResourceLink.forLocalReference(thePathAndRef.getPath(), theEntity, typeString, null, nextId.getIdPart(), theUpdateTime);
}
theParams.myLinks.add(resourceLink);
}
private ResourceLink resolveTargetAndCreateResourceLinkOrReturnNull(ResourceTable theEntity, Date theUpdateTime, RuntimeSearchParam nextSpDef, String theNextPathsUnsplit, PathAndRef nextPathAndRef, IIdType theNextId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest, Map<String, IResourceLookup> theResourceIdToResolvedTarget) {
/*
* We keep a cache of resolved target resources. This is good since for some resource types, there
* are multiple search parameters that map to the same element path within a resource (e.g.
* Observation:patient and Observation.subject and we don't want to force a resolution of the
* target any more times than we have to.
*/
IResourceLookup targetResource = theResourceIdToResolvedTarget.get(theNextId.getValue());
if (targetResource == null) {
targetResource = myResourceLinkResolver.findTargetResource(nextSpDef, theNextPathsUnsplit, theNextId, theTypeString, theType, theReference, theRequest);
}
if (targetResource == null) {
return null;
}
theResourceIdToResolvedTarget.put(theNextId.getValue(), targetResource);
String targetResourceType = targetResource.getResourceType();
Long targetResourcePid = targetResource.getResourceId();
String targetResourceIdPart = theNextId.getIdPart();
return ResourceLink.forLocalReference(nextPathAndRef.getPath(), theEntity, targetResourceType, targetResourcePid, targetResourceIdPart, theUpdateTime);
}
static void handleWarnings(RequestDetails theRequestDetails, IInterceptorBroadcaster theInterceptorBroadcaster, ISearchParamExtractor.SearchParamSet<?> theSearchParamSet) {
if (theSearchParamSet.getWarnings().isEmpty()) {
return;

9
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/IndexedSearchParamExtractor.java
View File

@ -23,30 +23,23 @@ package ca.uhn.fhir.jpa.searchparam.matcher;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceLinkExtractor;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorService;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
public class IndexedSearchParamExtractor {
@Autowired
private FhirContext myContext;
@Autowired
private SearchParamExtractorService mySearchParamExtractorService;
@Autowired
private ResourceLinkExtractor myResourceLinkExtractor;
@Autowired
private InlineResourceLinkResolver myInlineResourceLinkResolver;
public ResourceIndexedSearchParams extractIndexedSearchParams(IBaseResource theResource, RequestDetails theRequest) {
ResourceTable entity = new ResourceTable();
String resourceType = myContext.getResourceDefinition(theResource).getName();
entity.setResourceType(resourceType);
ResourceIndexedSearchParams resourceIndexedSearchParams = new ResourceIndexedSearchParams();
mySearchParamExtractorService.extractFromResource(theRequest, resourceIndexedSearchParams, entity, theResource);
myResourceLinkExtractor.extractResourceLinks(resourceIndexedSearchParams, entity, theResource, theResource.getMeta().getLastUpdated(), myInlineResourceLinkResolver, false, theRequest);
mySearchParamExtractorService.extractFromResource(theRequest, resourceIndexedSearchParams, entity, theResource, theResource.getMeta().getLastUpdated(), false);
return resourceIndexedSearchParams;
}
}

54
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InlineResourceLinkResolver.java
View File

@ -1,54 +0,0 @@
package ca.uhn.fhir.jpa.searchparam.matcher;
/*-
* #%L
* HAPI FHIR Search Parameters
* %%
* Copyright (C) 2014 - 2020 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 ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.cross.ResourceLookup;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.rest.api.server.RequestDetails;
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.springframework.stereotype.Service;
public class InlineResourceLinkResolver implements IResourceLinkResolver {
@Override
public IResourceLookup findTargetResource(RuntimeSearchParam theSearchParam, String theSourcePath, IIdType theSourceResourceId, String theTypeString, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest) {
/*
* TODO: JA - This gets used during runtime in-memory matching for subscription. It's not
* really clear if it's useful or not.
*/
ResourceTable target;
target = new ResourceTable();
target.setResourceType(theTypeString);
return new ResourceLookup(theTypeString, null, null);
}
@Override
public void validateTypeOrThrowException(Class<? extends IBaseResource> theType) {
// When resolving reference in-memory for a single resource, there's nothing to validate
}
}

2
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/SearchParamMatcher.java
View File

@ -33,7 +33,9 @@ public class SearchParamMatcher {
private InMemoryResourceMatcher myInMemoryResourceMatcher;
public InMemoryMatchResult match(String theCriteria, IBaseResource theResource, RequestDetails theRequest) {
ResourceIndexedSearchParams resourceIndexedSearchParams = myIndexedSearchParamExtractor.extractIndexedSearchParams(theResource, theRequest);
return myInMemoryResourceMatcher.match(theCriteria, theResource, resourceIndexedSearchParams);
}
}

1
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/IndexStressTest.java
View File

@ -41,6 +41,7 @@ public class IndexStressTest {
FhirContext ctx = FhirContext.forDstu3();
IValidationSupport mockValidationSupport = mock(IValidationSupport.class);
when(mockValidationSupport.getFhirContext()).thenReturn(ctx);
IValidationSupport validationSupport = new CachingValidationSupport(new ValidationSupportChain(new DefaultProfileValidationSupport(ctx), mockValidationSupport));
ISearchParamRegistry searchParamRegistry = mock(ISearchParamRegistry.class);
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ctx, validationSupport, searchParamRegistry);

16
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java
View File

@ -5,10 +5,7 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.test.BaseTest;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.Sets;
import com.google.common.io.Resources;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.output.NullWriter;
import org.apache.commons.lang.StringUtils;
@ -21,7 +18,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.net.URL;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
@ -30,8 +26,10 @@ 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;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
public class JsonParserR4Test extends BaseTest {
private static final Logger ourLog = LoggerFactory.getLogger(JsonParserR4Test.class);
@ -156,10 +154,12 @@ public class JsonParserR4Test extends BaseTest {
@Test
public void testParseBundleWithMultipleNestedContainedResources() throws Exception {
URL url = Resources.getResource("bundle-with-two-patient-resources.json");
String text = Resources.toString(url, Charsets.UTF_8);
String text = loadResource("/bundle-with-two-patient-resources.json");
Bundle bundle = ourCtx.newJsonParser().parseResource(Bundle.class, text);
assertEquals(Boolean.TRUE, bundle.getUserData(BaseParser.RESOURCE_CREATED_BY_PARSER));
assertEquals(Boolean.TRUE, bundle.getEntry().get(0).getResource().getUserData(BaseParser.RESOURCE_CREATED_BY_PARSER));
assertEquals(Boolean.TRUE, bundle.getEntry().get(1).getResource().getUserData(BaseParser.RESOURCE_CREATED_BY_PARSER));
assertEquals("12346", getPatientIdValue(bundle, 0));
assertEquals("12345", getPatientIdValue(bundle, 1));