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Merge branch 'master' into ja_20200206_multitenancy

This commit is contained in:
jamesagnew 2020-04-15 22:12:20 -04:00
parent 982b54df57 f95f619bdc
commit d822867a4a
41 changed files with 698 additions and 402 deletions
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34
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseErrorHandler.java Normal file
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@ -0,0 +1,34 @@
package ca.uhn.fhir.parser;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* 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%
*/
class BaseErrorHandler {
String describeLocation(IParserErrorHandler.IParseLocation theLocation) {
if (theLocation == null) {
return "";
} else {
return theLocation.toString() + " ";
}
}
}

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
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@ -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"));

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
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@ -1387,10 +1387,6 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
}
private static void write(JsonLikeWriter theWriter, String theName, String theValue) throws IOException {
theWriter.write(theName, theValue);
}
private class HeldExtension implements Comparable<HeldExtension> {
private CompositeChildElement myChildElem;
@ -1574,4 +1570,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
theEventWriter.endObject();
}
}
private static void write(JsonLikeWriter theWriter, String theName, String theValue) throws IOException {
theWriter.write(theName, theValue);
}
}

14
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/LenientErrorHandler.java
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@ -38,7 +38,7 @@ import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
* @see IParser#setParserErrorHandler(IParserErrorHandler)
* @see FhirContext#setParserErrorHandler(IParserErrorHandler)
*/
public class LenientErrorHandler implements IParserErrorHandler {
public class LenientErrorHandler extends BaseErrorHandler implements IParserErrorHandler {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(LenientErrorHandler.class);
private static final StrictErrorHandler STRICT_ERROR_HANDLER = new StrictErrorHandler();
@ -84,7 +84,7 @@ public class LenientErrorHandler implements IParserErrorHandler {
public void invalidValue(IParseLocation theLocation, String theValue, String theError) {
if (isBlank(theValue) || myErrorOnInvalidValue == false) {
if (myLogErrors) {
ourLog.warn("Invalid attribute value \"{}\": {}", theValue, theError);
ourLog.warn("{}Invalid attribute value \"{}\": {}", describeLocation(theLocation), theValue, theError);
}
} else {
STRICT_ERROR_HANDLER.invalidValue(theLocation, theValue, theError);
@ -133,35 +133,35 @@ public class LenientErrorHandler implements IParserErrorHandler {
@Override
public void unexpectedRepeatingElement(IParseLocation theLocation, String theElementName) {
if (myLogErrors) {
ourLog.warn("Multiple repetitions of non-repeatable element '{}' found while parsing", theElementName);
ourLog.warn("{}Multiple repetitions of non-repeatable element '{}' found while parsing", describeLocation(theLocation), theElementName);
}
}
@Override
public void unknownAttribute(IParseLocation theLocation, String theElementName) {
if (myLogErrors) {
ourLog.warn("Unknown attribute '{}' found while parsing", theElementName);
ourLog.warn("{}Unknown attribute '{}' found while parsing",describeLocation(theLocation), theElementName);
}
}
@Override
public void unknownElement(IParseLocation theLocation, String theElementName) {
if (myLogErrors) {
ourLog.warn("Unknown element '{}' found while parsing", theElementName);
ourLog.warn("{}Unknown element '{}' found while parsing", describeLocation(theLocation), theElementName);
}
}
@Override
public void unknownReference(IParseLocation theLocation, String theReference) {
if (myLogErrors) {
ourLog.warn("Resource has invalid reference: {}", theReference);
ourLog.warn("{}Resource has invalid reference: {}", describeLocation(theLocation), theReference);
}
}
@Override
public void extensionContainsValueAndNestedExtensions(IParseLocation theLocation) {
if (myLogErrors) {
ourLog.warn("Extension contains both a value and nested extensions: {}", theLocation);
ourLog.warn("{}Extension contains both a value and nested extensions", describeLocation(theLocation));
}
}

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParseLocation.java
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@ -54,6 +54,13 @@ class ParseLocation implements IParseLocation {
@Override
public String toString() {
return defaultString(myParentElementName);
return "[element=\"" + defaultString(myParentElementName) + "\"]";
}
/**
* Factory method
*/
static ParseLocation fromElementName(String theChildName) {
return new ParseLocation(theChildName);
}
}

71
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
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@ -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.*;
@ -191,7 +192,7 @@ class ParserState<T> {
return thePrimitiveTarget.newInstance(theDefinition.getInstanceConstructorArguments());
}
public IPrimitiveType<?> getPrimitiveInstance(BaseRuntimeChildDefinition theChild, RuntimePrimitiveDatatypeDefinition thePrimitiveTarget) {
public IPrimitiveType<?> getPrimitiveInstance(BaseRuntimeChildDefinition theChild, RuntimePrimitiveDatatypeDefinition thePrimitiveTarget, String theChildName) {
return thePrimitiveTarget.newInstance(theChild.getInstanceConstructorArguments());
}
@ -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);
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);
@ -583,9 +584,9 @@ class ParserState<T> {
case PRIMITIVE_DATATYPE: {
RuntimePrimitiveDatatypeDefinition primitiveTarget = (RuntimePrimitiveDatatypeDefinition) target;
IPrimitiveType<?> newChildInstance;
newChildInstance = getPrimitiveInstance(child, primitiveTarget);
newChildInstance = getPrimitiveInstance(child, primitiveTarget, theChildName);
child.getMutator().addValue(myInstance, newChildInstance);
PrimitiveState newState = new PrimitiveState(getPreResourceState(), newChildInstance);
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);
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));
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));
push(new PrimitiveState(getPreResourceState(), profile, theLocalPart, "id"));
newProfiles.add(profile);
myMap.put(ResourceMetadataKeyEnum.PROFILES, Collections.unmodifiableList(newProfiles));
break;
@ -891,7 +892,7 @@ class ParserState<T> {
private class MetaVersionElementState extends BaseState {
private ResourceMetadataMap myMap;
private final ResourceMetadataMap myMap;
MetaVersionElementState(ParserState<T>.PreResourceState thePreResourceState, ResourceMetadataMap theMap) {
super(thePreResourceState);
@ -1048,6 +1049,8 @@ class ParserState<T> {
}
}
myInstance.setUserData(BaseParser.RESOURCE_CREATED_BY_PARSER, Boolean.TRUE);
populateTarget();
}
@ -1268,37 +1271,51 @@ class ParserState<T> {
}
private class PrimitiveState extends BaseState {
private final String myChildName;
private final String myTypeName;
private IPrimitiveType<?> myInstance;
PrimitiveState(PreResourceState thePreResourceState, IPrimitiveType<?> theInstance) {
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)) {
myErrorHandler.invalidValue(null, theValue, "Attribute values must not be empty (\"\")");
if ("".equals(value)) {
ParseLocation location = ParseLocation.fromElementName(myChildName);
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) {
myErrorHandler.invalidValue(null, theValue, e.getMessage());
ParseLocation location = ParseLocation.fromElementName(myChildName);
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 {
myErrorHandler.unknownAttribute(null, theName);
ParseLocation location = ParseLocation.fromElementName(myChildName);
myErrorHandler.unknownAttribute(location, theName);
}
} else {
super.attributeValue(theName, theValue);
super.attributeValue(theName, value);
}
}
@ -1343,7 +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()));
push(new PrimitiveState(getPreResourceState(), myInstance.getId(), theChildName, "id"));
} else if ("meta".equals(theChildName)) {
push(new MetaElementState(getPreResourceState(), myInstance.getResourceMetadata()));
} else {

15
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/StrictErrorHandler.java
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@ -3,6 +3,7 @@ package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.json.JsonLikeValue.ScalarType;
import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
import ca.uhn.fhir.util.UrlUtil;
/*
* #%L
@ -31,7 +32,7 @@ import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
* @see IParser#setParserErrorHandler(IParserErrorHandler)
* @see FhirContext#setParserErrorHandler(IParserErrorHandler)
*/
public class StrictErrorHandler implements IParserErrorHandler {
public class StrictErrorHandler extends BaseErrorHandler implements IParserErrorHandler {
@Override
public void containedResourceWithNoId(IParseLocation theLocation) {
@ -46,7 +47,7 @@ public class StrictErrorHandler implements IParserErrorHandler {
@Override
public void invalidValue(IParseLocation theLocation, String theValue, String theError) {
throw new DataFormatException("Invalid attribute value \"" + theValue + "\": " + theError);
throw new DataFormatException(describeLocation(theLocation) + "Invalid attribute value \"" + UrlUtil.sanitizeUrlPart(theValue) + "\": " + theError);
}
@Override
@ -65,27 +66,27 @@ public class StrictErrorHandler implements IParserErrorHandler {
@Override
public void unexpectedRepeatingElement(IParseLocation theLocation, String theElementName) {
throw new DataFormatException("Multiple repetitions of non-repeatable element '" + theElementName + "' found during parse");
throw new DataFormatException(describeLocation(theLocation) + "Multiple repetitions of non-repeatable element '" + theElementName + "' found during parse");
}
@Override
public void unknownAttribute(IParseLocation theLocation, String theAttributeName) {
throw new DataFormatException("Unknown attribute '" + theAttributeName + "' found during parse");
throw new DataFormatException(describeLocation(theLocation) + "Unknown attribute '" + theAttributeName + "' found during parse");
}
@Override
public void unknownElement(IParseLocation theLocation, String theElementName) {
throw new DataFormatException("Unknown element '" + theElementName + "' found during parse");
throw new DataFormatException(describeLocation(theLocation) + "Unknown element '" + theElementName + "' found during parse");
}
@Override
public void unknownReference(IParseLocation theLocation, String theReference) {
throw new DataFormatException("Resource has invalid reference: " + theReference);
throw new DataFormatException(describeLocation(theLocation) + "Resource has invalid reference: " + theReference);
}
@Override
public void extensionContainsValueAndNestedExtensions(IParseLocation theLocation) {
throw new DataFormatException("Extension contains both a value and nested extensions: " + theLocation);
throw new DataFormatException(describeLocation(theLocation) + "Extension contains both a value and nested extensions");
}
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/jackson/JacksonStructure.java
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@ -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_0/1793-report-attr-name-in-json-parse-errors.yaml Normal file
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@ -0,0 +1,7 @@
---
type: add
issue: 1793
title: "When parsing JSON resources, if an element contains an invalid value, the Parser Error Handler
did not have access to the actual name of the element being parsed. This meant that errors lacked useful
detail in order to diagnose the issue. This has been corrected. Thanks to GitHub user
@jwalter for reporting!"

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

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -17,6 +17,7 @@ import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperService;
import ca.uhn.fhir.jpa.partition.PartitionConfigSvcImpl;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.partition.RequestPartitionHelperService;
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;
@ -40,6 +41,9 @@ 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;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
import org.hibernate.jpa.HibernatePersistenceProvider;
@ -51,6 +55,7 @@ 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;
@ -163,6 +168,12 @@ public abstract class BaseConfig {
return new BinaryStorageInterceptor();
}
@Bean
@Primary
public IResourceLinkResolver daoResourceLinkResolver() {
return new DaoResourceLinkResolver();
}
@Bean
public ISearchCacheSvc searchCacheSvc() {
return new DatabaseSearchCacheSvcImpl();

22
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;
@ -23,7 +35,6 @@ 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;
@ -865,8 +876,9 @@ 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

@ -50,7 +50,6 @@ 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.config.PartitionConfig;
@ -35,7 +35,6 @@ 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;
@ -85,8 +84,6 @@ public class SearchParamWithInlineReferencesExtractor {
@Autowired
private SearchParamExtractorService mySearchParamExtractorService;
@Autowired
private ResourceLinkExtractor myResourceLinkExtractor;
@Autowired
private DaoResourceLinkResolver myDaoResourceLinkResolver;
@Autowired
private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
@ -97,19 +94,15 @@ public class SearchParamWithInlineReferencesExtractor {
protected EntityManager myEntityManager;
public void populateFromResource(PartitionConfig thePartitionConfig, 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(thePartitionConfig, 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());
}
}
}

6
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;
@ -368,8 +370,12 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@AfterClass
public static void afterClassClearContextBaseJpaDstu3Test() {
if (ourValueSetDao != null) {
ourValueSetDao.purgeCaches();
}
if (ourJpaValidationSupportChainDstu3 != null) {
ourJpaValidationSupportChainDstu3.invalidateCaches();
}
TestUtil.clearAllStaticFieldsForUnitTest();
}

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()

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/resthook/SubscriptionTriggeringDstu3Test.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.model.util.ProviderConstants;
import ca.uhn.fhir.jpa.provider.dstu3.BaseResourceProviderDstu3Test;
import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
import ca.uhn.fhir.jpa.subscription.triggering.ISubscriptionTriggeringSvc;
import ca.uhn.fhir.jpa.subscription.triggering.SubscriptionTriggeringSvcImpl;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.ResourceParam;
@ -17,6 +18,7 @@ import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.test.utilities.ProxyUtil;
import com.google.common.collect.Lists;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
@ -71,7 +73,7 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
@Autowired
private SubscriptionTestUtil mySubscriptionTestUtil;
@Autowired
private SubscriptionTriggeringSvcImpl mySubscriptionTriggeringSvc;
private ISubscriptionTriggeringSvc mySubscriptionTriggeringSvc;
@Autowired
private ISchedulerService mySchedulerService;
@ -93,8 +95,9 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
mySubscriptionTestUtil.unregisterSubscriptionInterceptor();
mySubscriptionTriggeringSvc.cancelAll();
mySubscriptionTriggeringSvc.setMaxSubmitPerPass(null);
SubscriptionTriggeringSvcImpl svc = ProxyUtil.getSingletonTarget(mySubscriptionTriggeringSvc, SubscriptionTriggeringSvcImpl.class);
svc.cancelAll();
svc.setMaxSubmitPerPass(null);
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
}
@ -224,7 +227,8 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
waitForSize(50, ourUpdatedPatients);
beforeReset();
mySubscriptionTriggeringSvc.setMaxSubmitPerPass(33);
SubscriptionTriggeringSvcImpl svc = ProxyUtil.getSingletonTarget(mySubscriptionTriggeringSvc, SubscriptionTriggeringSvcImpl.class);
svc.setMaxSubmitPerPass(33);
Parameters response = ourClient
.operation()
@ -294,7 +298,9 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
mySubscriptionTriggeringSvc.runDeliveryPass();
mySubscriptionTriggeringSvc.runDeliveryPass();
mySubscriptionTriggeringSvc.runDeliveryPass();
assertEquals(0, mySubscriptionTriggeringSvc.getActiveJobCount());
SubscriptionTriggeringSvcImpl svc = ProxyUtil.getSingletonTarget(mySubscriptionTriggeringSvc, SubscriptionTriggeringSvcImpl.class);
assertEquals(0, svc.getActiveJobCount());
assertEquals(0, ourCreatedPatients.size());
await().until(() -> ourUpdatedPatients.size() == 3);
@ -361,7 +367,8 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
waitForSize(50, ourUpdatedPatients);
beforeReset();
mySubscriptionTriggeringSvc.setMaxSubmitPerPass(33);
SubscriptionTriggeringSvcImpl svc = ProxyUtil.getSingletonTarget(mySubscriptionTriggeringSvc, SubscriptionTriggeringSvcImpl.class);
svc.setMaxSubmitPerPass(33);
Parameters response = ourClient
.operation()
@ -427,7 +434,8 @@ public class SubscriptionTriggeringDstu3Test extends BaseResourceProviderDstu3Te
waitForSize(0, ourUpdatedPatients);
beforeReset();
mySubscriptionTriggeringSvc.setMaxSubmitPerPass(50);
SubscriptionTriggeringSvcImpl svc = ProxyUtil.getSingletonTarget(mySubscriptionTriggeringSvc, SubscriptionTriggeringSvcImpl.class);
svc.setMaxSubmitPerPass(50);
Parameters response = ourClient
.operation()

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

@ -1054,6 +1054,10 @@ 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;
}

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

@ -114,7 +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);

202
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ResourceLinkExtractor.java
View File

@ -1,202 +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.config.PartitionConfig;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.PartitionId;
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 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 PartitionConfig myPartitionConfig;
@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) {
// If we're allowing references across partitions, we just don't include the partition ID when resolving the target
PartitionId targetPartitionId = theEntity.getPartitionId();
if (myPartitionConfig.isAllowReferencesAcrossPartitions()) {
targetPartitionId = null;
}
targetResource = theResourceLinkResolver.findTargetResource(targetPartitionId, 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;
}
}

55
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/matcher/InlineResourceLinkResolver.java
View File

@ -1,55 +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.PartitionId;
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(PartitionId thePartitionId, 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);
}
}

9
hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java
View File

@ -13,6 +13,7 @@ import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Matchers.eq;
import static org.mockito.Matchers.isNull;
import static org.mockito.Mockito.mock;
@ -1098,8 +1099,8 @@ public class JsonParserDstu2_1Test {
assertEquals(null, parsed.getGenderElement().getValueAsString());
ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).invalidValue(isNull(IParseLocation.class), eq(""), msgCaptor.capture());
assertEquals("Attribute values must not be empty (\"\")", msgCaptor.getValue());
verify(errorHandler, times(1)).invalidValue(any(IParseLocation.class), eq(""), msgCaptor.capture());
assertEquals("Attribute value must not be empty (\"\")", msgCaptor.getValue());
String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);
assertEquals("{\"resourceType\":\"Patient\"}", encoded);
@ -1118,7 +1119,7 @@ public class JsonParserDstu2_1Test {
assertEquals("foo", parsed.getGenderElement().getValueAsString());
ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).invalidValue(isNull(IParseLocation.class), eq("foo"), msgCaptor.capture());
verify(errorHandler, times(1)).invalidValue(any(IParseLocation.class), eq("foo"), msgCaptor.capture());
assertEquals("Unknown AdministrativeGender code 'foo'", msgCaptor.getValue());
String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);
@ -1138,7 +1139,7 @@ public class JsonParserDstu2_1Test {
assertEquals("foo", parsed.getValueDateTimeType().getValueAsString());
ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).invalidValue(isNull(IParseLocation.class), eq("foo"), msgCaptor.capture());
verify(errorHandler, times(1)).invalidValue(any(IParseLocation.class), eq("foo"), msgCaptor.capture());
assertEquals("Invalid date/time format: \"foo\"", msgCaptor.getValue());
String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);

2
hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2_1Test.java
View File

@ -2379,7 +2379,7 @@ public class XmlParserDstu2_1Test {
p.parseResource(resource);
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"1\": Invalid boolean string: '1'", e.getMessage());
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: [element=\"active\"] Invalid attribute value \"1\": Invalid boolean string: '1'", e.getMessage());
}
LenientErrorHandler errorHandler = new LenientErrorHandler();

2
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/validation/ResourceValidatorDstu2Test.java
View File

@ -82,7 +82,7 @@ public class ResourceValidatorDstu2Test {
parser.parseResource(encoded);
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: [element=\"birthDate\"] Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
}
}

26
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -58,6 +58,24 @@ public class JsonParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
@Test
public void testEncodedResourceWithIncorrectRepresentationOfDecimalTypeToJson() {
DecimalType decimalType = new DecimalType();
decimalType.setValueAsString(".5");
MedicationRequest mr = new MedicationRequest();
Dosage dosage = new Dosage();
dosage.setDose(new SimpleQuantity()
.setValue(decimalType.getValue())
.setUnit("{tablet}")
.setSystem("http://unitsofmeasure.org")
.setCode("{tablet}"));
mr.addDosageInstruction(dosage);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(mr);
ourLog.info(encoded);
mr = ourCtx.newJsonParser().parseResource(MedicationRequest.class, encoded);
assertEquals(BigDecimal.valueOf(0.5), mr.getDosageInstructionFirstRep().getDoseSimpleQuantity().getValue());
assertTrue(encoded.contains("0.5"));
}
/**
* See #563
@ -1504,7 +1522,7 @@ public class JsonParserDstu3Test {
assertEquals("foo", parsed.getValueDateTimeType().getValueAsString());
ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).invalidValue(isNull(), eq("foo"), msgCaptor.capture());
verify(errorHandler, times(1)).invalidValue(any(), eq("foo"), msgCaptor.capture());
assertEquals("Invalid date/time format: \"foo\"", msgCaptor.getValue());
String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);
@ -1536,8 +1554,8 @@ public class JsonParserDstu3Test {
assertEquals(null, parsed.getGenderElement().getValueAsString());
ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).invalidValue(isNull(), eq(""), msgCaptor.capture());
assertEquals("Attribute values must not be empty (\"\")", msgCaptor.getValue());
verify(errorHandler, times(1)).invalidValue(any(), eq(""), msgCaptor.capture());
assertEquals("Attribute value must not be empty (\"\")", msgCaptor.getValue());
String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);
assertEquals("{\"resourceType\":\"Patient\"}", encoded);
@ -1556,7 +1574,7 @@ public class JsonParserDstu3Test {
assertEquals("foo", parsed.getGenderElement().getValueAsString());
ArgumentCaptor<String> msgCaptor = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).invalidValue(isNull(), eq("foo"), msgCaptor.capture());
verify(errorHandler, times(1)).invalidValue(any(), eq("foo"), msgCaptor.capture());
assertEquals("Unknown AdministrativeGender code 'foo'", msgCaptor.getValue());
String encoded = ourCtx.newJsonParser().encodeResourceToString(parsed);

24
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
View File

@ -45,6 +45,7 @@ import org.xmlunit.diff.ElementSelectors;
import java.io.IOException;
import java.io.StringReader;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.text.SimpleDateFormat;
import java.util.*;
@ -70,6 +71,25 @@ public class XmlParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
@Test
public void testEncodedResourceWithIncorrectRepresentationOfDecimalTypeToXml() {
DecimalType decimalType = new DecimalType();
decimalType.setValueAsString(".5");
MedicationRequest mr = new MedicationRequest();
Dosage dosage = new Dosage();
dosage.setDose(new SimpleQuantity()
.setValue(decimalType.getValue())
.setUnit("{tablet}")
.setSystem("http://unitsofmeasure.org")
.setCode("{tablet}"));
mr.addDosageInstruction(dosage);
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(mr);
ourLog.info(encoded);
mr = ourCtx.newXmlParser().parseResource(MedicationRequest.class, encoded);
assertEquals(BigDecimal.valueOf(0.5), mr.getDosageInstructionFirstRep().getDoseSimpleQuantity().getValue());
assertTrue(encoded.contains("0.5"));
}
/**
* We specifically include extensions on CapabilityStatment even in
* summary mode, since this is behaviour that people depend on
@ -1542,7 +1562,7 @@ public class XmlParserDstu3Test {
parser.encodeResourceToString(p);
fail();
} catch (DataFormatException e) {
assertEquals("Extension contains both a value and nested extensions: Patient(res).extension", e.getMessage());
assertEquals("[element=\"Patient(res).extension\"] Extension contains both a value and nested extensions", e.getMessage());
}
}
@ -3119,7 +3139,7 @@ public class XmlParserDstu3Test {
p.parseResource(resource);
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"1\": Invalid boolean string: '1'", e.getMessage());
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: [element=\"active\"] Invalid attribute value \"1\": Invalid boolean string: '1'", e.getMessage());
}
LenientErrorHandler errorHandler = new LenientErrorHandler();

4
hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/rest/client/ClientServerValidationTestHl7OrgDstu2.java
View File

@ -100,7 +100,7 @@ public class ClientServerValidationTestHl7OrgDstu2 {
@Test
public void testServerReturnsWrongVersionForDstu2() throws Exception {
String wrongFhirVersion = "3.0.1";
String wrongFhirVersion = "3.0.2";
assertThat(wrongFhirVersion, is(FhirVersionEnum.DSTU3.getFhirVersionString())); // asserting that what we assume to be the DSTU3 FHIR version is still correct
Conformance conf = new Conformance();
conf.setFhirVersion(wrongFhirVersion);
@ -119,7 +119,7 @@ public class ClientServerValidationTestHl7OrgDstu2 {
myCtx.newRestfulGenericClient("http://foo").read(new UriDt("http://foo/Patient/1"));
fail();
} catch (FhirClientInappropriateForServerException e) {
assertThat(e.toString(), containsString("The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"3.0.1\" which corresponds to DSTU3, but this client is configured to use DSTU2_HL7ORG (via the FhirContext)"));
assertThat(e.toString(), containsString("The server at base URL \"http://foo/metadata\" returned a conformance statement indicating that it supports FHIR version \"3.0.2\" which corresponds to DSTU3, but this client is configured to use DSTU2_HL7ORG (via the FhirContext)"));
}
}

44
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));
@ -350,7 +350,7 @@ public class JsonParserR4Test extends BaseTest {
parser.encodeResourceToString(p);
fail();
} catch (DataFormatException e) {
assertEquals("Extension contains both a value and nested extensions: Patient(res).extension", e.getMessage());
assertEquals("[element=\"Patient(res).extension\"] Extension contains both a value and nested extensions", e.getMessage());
}
}
@ -569,6 +569,32 @@ public class JsonParserR4Test extends BaseTest {
}
/**
* See #1793
*/
@Test
public void testParseEmptyAttribute() {
String input = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"identifier\": [\n" +
" {\n" +
" \"system\": \"https://example.com\",\n" +
" \"value\": \"\"\n" +
" }\n" +
" ]\n" +
"}";
IParser jsonParser = ourCtx.newJsonParser();
jsonParser.setParserErrorHandler(new StrictErrorHandler());
try {
jsonParser.parseResource(Patient.class, input);
fail();
} catch (DataFormatException e) {
assertEquals("[element=\"value\"] Invalid attribute value \"\": Attribute value must not be empty (\"\")", e.getMessage());
}
}
@Test
public void testParseExtensionOnPrimitive() throws IOException {
String input = IOUtils.toString(JsonParserR4Test.class.getResourceAsStream("/extension-on-line.txt"), Constants.CHARSET_UTF8);

19
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/ResponseSizeCapturingInterceptorTest.java
View File

@ -1,8 +1,10 @@
package ca.uhn.fhir.rest.server.interceptor;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.test.utilities.server.HashMapResourceProviderRule;
import ca.uhn.fhir.test.utilities.server.RestfulServerRule;
import ca.uhn.test.concurrency.PointcutLatch;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Patient;
@ -28,13 +30,17 @@ import java.util.regex.Pattern;
import java.util.stream.Collectors;
import static org.awaitility.Awaitility.await;
import static org.awaitility.Awaitility.waitAtMost;
import static org.hamcrest.CoreMatchers.not;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.atMost;
import static org.mockito.Mockito.doAnswer;
import static org.mockito.Mockito.timeout;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
@ -63,11 +69,18 @@ public class ResponseSizeCapturingInterceptorTest {
}
@Test
public void testReadResource() {
public void testReadResource() throws InterruptedException {
PointcutLatch createLatch = new PointcutLatch(Pointcut.SERVER_PROCESSING_COMPLETED);
createLatch.setExpectedCount(1);
ourServerRule.getRestfulServer().getInterceptorService().registerAnonymousInterceptor(Pointcut.SERVER_PROCESSING_COMPLETED, createLatch);
Patient resource = new Patient();
resource.setActive(true);
IIdType id = ourServerRule.getFhirClient().create().resource(resource).execute().getId().toUnqualifiedVersionless();
createLatch.awaitExpected();
ourServerRule.getRestfulServer().getInterceptorService().unregisterInterceptor(createLatch);
myInterceptor.registerConsumer(myConsumer);
List<String> stacks = Collections.synchronizedList(new ArrayList<>());
@ -84,8 +97,8 @@ public class ResponseSizeCapturingInterceptorTest {
resource = ourServerRule.getFhirClient().read().resource(Patient.class).withId(id).execute();
assertEquals(true, resource.getActive());
await().until(()->stacks.size() > 0);
await().until(()->stacks.stream().collect(Collectors.joining("\n")), not(matchesPattern(Pattern.compile(".*INVOCATION.*INVOCATION.*", Pattern.MULTILINE | Pattern.DOTALL))));
verify(myConsumer, timeout(Duration.ofSeconds(10)).times(1)).accept(myResultCaptor.capture());
assertEquals(100, myResultCaptor.getValue().getWrittenChars());
}

17
hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ProxyUtil.java Normal file
View File

@ -0,0 +1,17 @@
package ca.uhn.fhir.test.utilities;
import org.apache.commons.lang3.Validate;
import org.springframework.aop.framework.AopProxyUtils;
public class ProxyUtil {
@SuppressWarnings("unchecked")
public static <T> T getSingletonTarget(Object theSource, Class<T> theSubscriptionTriggeringSvcClass) {
Validate.notNull(theSource);
if (theSubscriptionTriggeringSvcClass.isAssignableFrom(theSource.getClass())) {
return (T) theSource;
}
return (T) AopProxyUtils.getSingletonTarget(theSource);
}
}

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu2016may/hapi/validation/ResourceValidatorDstu2_1Test.java
View File

@ -72,7 +72,7 @@ public class ResourceValidatorDstu2_1Test {
parser.parseResource(encoded);
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: [element=\"birthDate\"] Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
}
}

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/ResourceValidatorDstu3Test.java
View File

@ -98,7 +98,7 @@ public class ResourceValidatorDstu3Test {
parser.parseResource(encoded);
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: [element=\"birthDate\"] Invalid attribute value \"2000-15-31\": Invalid date/time format: \"2000-15-31\"", e.getMessage());
}
}