Merge branch 'subscription_cleanup' of github.com:jamesagnew/hapi-fhir into subscription_cleanup
This commit is contained in:
jamesagnew
commit
10ecc9bdfe
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@ -3,10 +3,8 @@ package ca.uhn.fhir.jpa.config.dstu3;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.ParserOptions;
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import ca.uhn.fhir.jpa.config.BaseConfig;
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import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
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import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
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import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
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import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.dao.*;
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import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
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import ca.uhn.fhir.jpa.dao.dstu3.SearchParamExtractorDstu3;
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import ca.uhn.fhir.jpa.dao.dstu3.SearchParamRegistryDstu3;
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import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
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@ -21,6 +19,7 @@ import org.apache.commons.lang3.time.DateUtils;
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import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
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import org.hl7.fhir.dstu3.hapi.validation.CachingValidationSupport;
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import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.r4.utils.IResourceValidator;
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import org.springframework.beans.factory.annotation.Autowire;
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import org.springframework.context.annotation.Bean;
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@ -38,9 +37,9 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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@ -70,6 +69,16 @@ public class BaseDstu3Config extends BaseConfig {
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return retVal;
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}
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@Bean
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public TransactionProcessor.ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
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return new TransactionProcessorVersionAdapterDstu3();
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}
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@Bean
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public TransactionProcessor<Bundle, Bundle.BundleEntryComponent> transactionProcessor() {
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return new TransactionProcessor<>();
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}
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@Bean(name = "myInstanceValidatorDstu3")
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@Lazy
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public IValidatorModule instanceValidatorDstu3() {
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@ -3,12 +3,10 @@ package ca.uhn.fhir.jpa.config.r4;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.ParserOptions;
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import ca.uhn.fhir.jpa.config.BaseConfig;
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import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
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import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
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import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
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import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
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import ca.uhn.fhir.jpa.dao.*;
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import ca.uhn.fhir.jpa.dao.r4.SearchParamExtractorR4;
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import ca.uhn.fhir.jpa.dao.r4.SearchParamRegistryR4;
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import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
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import ca.uhn.fhir.jpa.graphql.JpaStorageServices;
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import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
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import ca.uhn.fhir.jpa.term.HapiTerminologySvcR4;
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@ -23,6 +21,7 @@ import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
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import org.hl7.fhir.r4.hapi.rest.server.GraphQLProvider;
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import org.hl7.fhir.r4.hapi.validation.CachingValidationSupport;
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import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.utils.GraphQLEngine;
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import org.hl7.fhir.r4.utils.IResourceValidator.BestPracticeWarningLevel;
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import org.springframework.beans.factory.annotation.Autowire;
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@ -73,6 +72,16 @@ public class BaseR4Config extends BaseConfig {
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return retVal;
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}
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@Bean
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public TransactionProcessor.ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
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return new TransactionProcessorVersionAdapterR4();
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}
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@Bean
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public TransactionProcessor<Bundle, Bundle.BundleEntryComponent> transactionProcessor() {
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return new TransactionProcessor<>();
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}
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@Bean(name = "myGraphQLProvider")
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@Lazy
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public GraphQLProvider graphQLProvider() {
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@ -206,7 +206,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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private ApplicationContext myApplicationContext;
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private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> myResourceTypeToDao;
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protected void clearRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
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public static void clearRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
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if (theRequestDetails != null) {
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theRequestDetails.getUserData().remove(PROCESSING_SUB_REQUEST);
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}
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@ -1156,7 +1156,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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return false;
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}
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protected void markRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
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public static void markRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
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if (theRequestDetails != null) {
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theRequestDetails.getUserData().put(PROCESSING_SUB_REQUEST, Boolean.TRUE);
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}
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@ -1170,7 +1170,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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return builder;
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}
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protected void notifyInterceptors(RestOperationTypeEnum theOperationType, ActionRequestDetails theRequestDetails) {
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public void notifyInterceptors(RestOperationTypeEnum theOperationType, ActionRequestDetails theRequestDetails) {
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if (theRequestDetails.getId() != null && theRequestDetails.getId().hasResourceType() && isNotBlank(theRequestDetails.getResourceType())) {
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if (theRequestDetails.getId().getResourceType().equals(theRequestDetails.getResourceType()) == false) {
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throw new InternalErrorException(
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@ -2288,7 +2288,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
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}
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}
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protected void validateDeleteConflictsEmptyOrThrowException(List<DeleteConflict> theDeleteConflicts) {
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public void validateDeleteConflictsEmptyOrThrowException(List<DeleteConflict> theDeleteConflicts) {
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if (theDeleteConflicts.isEmpty()) {
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return;
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}
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@ -0,0 +1,944 @@
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package ca.uhn.fhir.jpa.dao;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.RuntimeResourceDefinition;
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import ca.uhn.fhir.jpa.entity.ResourceTable;
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import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
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import ca.uhn.fhir.jpa.util.DeleteConflict;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.parser.DataFormatException;
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import ca.uhn.fhir.parser.IParser;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.rest.api.PreferReturnEnum;
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import ca.uhn.fhir.rest.api.RequestTypeEnum;
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import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.param.ParameterUtil;
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import ca.uhn.fhir.rest.server.RestfulServerUtils;
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import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
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import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
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import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
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import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
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import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
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import ca.uhn.fhir.util.FhirTerser;
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import ca.uhn.fhir.util.ResourceReferenceInfo;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.util.UrlUtil;
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import com.google.common.collect.ArrayListMultimap;
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import org.apache.commons.lang3.Validate;
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import org.apache.http.NameValuePair;
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import org.hibernate.Session;
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import org.hibernate.internal.SessionImpl;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.instance.model.api.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.transaction.TransactionDefinition;
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import org.springframework.transaction.support.TransactionCallback;
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import org.springframework.transaction.support.TransactionTemplate;
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import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import java.util.*;
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import static org.apache.commons.lang3.StringUtils.*;
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public class TransactionProcessor<BUNDLE extends IBaseBundle, BUNDLEENTRY> {
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public static final String URN_PREFIX = "urn:";
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private static final Logger ourLog = LoggerFactory.getLogger(TransactionProcessor.class);
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private BaseHapiFhirDao myDao;
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@Autowired
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private PlatformTransactionManager myTxManager;
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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private EntityManager myEntityManager;
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@Autowired
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private FhirContext myContext;
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@Autowired
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private ITransactionProcessorVersionAdapter<BUNDLE, BUNDLEENTRY> myVersionAdapter;
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public static boolean isPlaceholder(IIdType theId) {
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if (theId != null && theId.getValue() != null) {
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return theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:");
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}
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return false;
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}
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private static String toStatusString(int theStatusCode) {
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return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
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}
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private void populateEntryWithOperationOutcome(BaseServerResponseException caughtEx, BUNDLEENTRY nextEntry) {
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myVersionAdapter.populateEntryWithOperationOutcome(caughtEx, nextEntry);
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}
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private void handleTransactionCreateOrUpdateOutcome(Map<IIdType, IIdType> idSubstitutions, Map<IIdType, DaoMethodOutcome> idToPersistedOutcome, IIdType nextResourceId, DaoMethodOutcome outcome,
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BUNDLEENTRY newEntry, String theResourceType, IBaseResource theRes, ServletRequestDetails theRequestDetails) {
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IIdType newId = outcome.getId().toUnqualifiedVersionless();
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IIdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
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if (newId.equals(resourceId) == false) {
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idSubstitutions.put(resourceId, newId);
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if (isPlaceholder(resourceId)) {
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/*
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* The correct way for substitution IDs to be is to be with no resource type, but we'll accept the qualified kind too just to be lenient.
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*/
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IIdType id = myContext.getVersion().newIdType();
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id.setValue(theResourceType + '/' + resourceId.getValue());
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idSubstitutions.put(id, newId);
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}
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}
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idToPersistedOutcome.put(newId, outcome);
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if (outcome.getCreated().booleanValue()) {
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myVersionAdapter.setResponseStatus(newEntry, toStatusString(Constants.STATUS_HTTP_201_CREATED));
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} else {
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myVersionAdapter.setResponseStatus(newEntry, toStatusString(Constants.STATUS_HTTP_200_OK));
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}
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Date lastModifier = getLastModified(theRes);
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myVersionAdapter.setResponseLastModified(newEntry, lastModifier);
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if (theRequestDetails != null) {
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if (outcome.getResource() != null) {
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String prefer = theRequestDetails.getHeader(Constants.HEADER_PREFER);
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PreferReturnEnum preferReturn = RestfulServerUtils.parsePreferHeader(prefer);
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if (preferReturn != null) {
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if (preferReturn == PreferReturnEnum.REPRESENTATION) {
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myVersionAdapter.setResource(newEntry, outcome.getResource());
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}
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}
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}
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}
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}
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private Date getLastModified(IBaseResource theRes) {
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return theRes.getMeta().getLastUpdated();
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}
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private String performIdSubstitutionsInMatchUrl(Map<IIdType, IIdType> theIdSubstitutions, String theMatchUrl) {
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String matchUrl = theMatchUrl;
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if (isNotBlank(matchUrl)) {
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for (Map.Entry<IIdType, IIdType> nextSubstitutionEntry : theIdSubstitutions.entrySet()) {
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IIdType nextTemporaryId = nextSubstitutionEntry.getKey();
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IIdType nextReplacementId = nextSubstitutionEntry.getValue();
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String nextTemporaryIdPart = nextTemporaryId.getIdPart();
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String nextReplacementIdPart = nextReplacementId.getValueAsString();
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if (isUrn(nextTemporaryId) && nextTemporaryIdPart.length() > URN_PREFIX.length()) {
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matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
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matchUrl = matchUrl.replace(UrlUtil.escapeUrlParam(nextTemporaryIdPart), nextReplacementIdPart);
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}
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}
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}
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return matchUrl;
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}
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private boolean isUrn(IIdType theId) {
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return defaultString(theId.getValue()).startsWith(URN_PREFIX);
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}
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public void setDao(BaseHapiFhirDao theDao) {
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myDao = theDao;
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}
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public BUNDLE transaction(RequestDetails theRequestDetails, BUNDLE theRequest) {
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if (theRequestDetails != null) {
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IServerInterceptor.ActionRequestDetails requestDetails = new IServerInterceptor.ActionRequestDetails(theRequestDetails, theRequest, "Bundle", null);
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myDao.notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
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}
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String actionName = "Transaction";
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return processTransactionAsSubRequest((ServletRequestDetails) theRequestDetails, theRequest, actionName);
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}
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private BUNDLE processTransactionAsSubRequest(ServletRequestDetails theRequestDetails, BUNDLE theRequest, String theActionName) {
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BaseHapiFhirDao.markRequestAsProcessingSubRequest(theRequestDetails);
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try {
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return processTransaction(theRequestDetails, theRequest, theActionName);
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} finally {
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BaseHapiFhirDao.clearRequestAsProcessingSubRequest(theRequestDetails);
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}
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}
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private BUNDLE batch(final RequestDetails theRequestDetails, BUNDLE theRequest) {
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ourLog.info("Beginning batch with {} resources", myVersionAdapter.getEntries(theRequest).size());
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long start = System.currentTimeMillis();
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TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
|
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txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
|
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BUNDLE resp = myVersionAdapter.createBundle(org.hl7.fhir.r4.model.Bundle.BundleType.BATCHRESPONSE.toCode());
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/*
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* For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
|
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*/
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|
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for (final BUNDLEENTRY nextRequestEntry : myVersionAdapter.getEntries(theRequest)) {
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||||
|
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BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
|
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|
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TransactionCallback<BUNDLE> callback = theStatus -> {
|
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BUNDLE subRequestBundle = myVersionAdapter.createBundle(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION.toCode());
|
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myVersionAdapter.addEntry(subRequestBundle, nextRequestEntry);
|
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|
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BUNDLE subResponseBundle = processTransactionAsSubRequest((ServletRequestDetails) theRequestDetails, subRequestBundle, "Batch sub-request");
|
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return subResponseBundle;
|
||||
};
|
||||
|
||||
try {
|
||||
// FIXME: this doesn't need to be a callback
|
||||
BUNDLE nextResponseBundle = callback.doInTransaction(null);
|
||||
|
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BUNDLEENTRY subResponseEntry = myVersionAdapter.getEntries(nextResponseBundle).get(0);
|
||||
myVersionAdapter.addEntry(resp, subResponseEntry);
|
||||
|
||||
/*
|
||||
* If the individual entry didn't have a resource in its response, bring the sub-transaction's OperationOutcome across so the client can see it
|
||||
*/
|
||||
if (myVersionAdapter.getResource(subResponseEntry) == null) {
|
||||
BUNDLEENTRY nextResponseBundleFirstEntry = myVersionAdapter.getEntries(nextResponseBundle).get(0);
|
||||
myVersionAdapter.setResource(subResponseEntry, myVersionAdapter.getResource(nextResponseBundleFirstEntry));
|
||||
}
|
||||
|
||||
} catch (BaseServerResponseException e) {
|
||||
caughtEx.setException(e);
|
||||
} catch (Throwable t) {
|
||||
ourLog.error("Failure during BATCH sub transaction processing", t);
|
||||
caughtEx.setException(new InternalErrorException(t));
|
||||
}
|
||||
|
||||
if (caughtEx.getException() != null) {
|
||||
BUNDLEENTRY nextEntry = myVersionAdapter.addEntry(resp);
|
||||
|
||||
populateEntryWithOperationOutcome(caughtEx.getException(), nextEntry);
|
||||
|
||||
myVersionAdapter.setResponseStatus(nextEntry, toStatusString(caughtEx.getException().getStatusCode()));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
long delay = System.currentTimeMillis() - start;
|
||||
ourLog.info("Batch completed in {}ms", new Object[]{delay});
|
||||
|
||||
return resp;
|
||||
}
|
||||
|
||||
private BUNDLE processTransaction(final ServletRequestDetails theRequestDetails, final BUNDLE theRequest, final String theActionName) {
|
||||
validateDependencies();
|
||||
|
||||
String transactionType = myVersionAdapter.getBundleType(theRequest);
|
||||
if (org.hl7.fhir.r4.model.Bundle.BundleType.BATCH.toCode().equals(transactionType)) {
|
||||
return batch(theRequestDetails, theRequest);
|
||||
}
|
||||
|
||||
if (transactionType == null) {
|
||||
String message = "Transaction Bundle did not specify valid Bundle.type, assuming " + Bundle.BundleType.TRANSACTION.toCode();
|
||||
ourLog.warn(message);
|
||||
transactionType = org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION.toCode();
|
||||
}
|
||||
if (!org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION.toCode().equals(transactionType)) {
|
||||
throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType);
|
||||
}
|
||||
|
||||
ourLog.debug("Beginning {} with {} resources", theActionName, myVersionAdapter.getEntries(theRequest).size());
|
||||
|
||||
final Date updateTime = new Date();
|
||||
final StopWatch transactionStopWatch = new StopWatch();
|
||||
|
||||
final Set<IIdType> allIds = new LinkedHashSet<>();
|
||||
final Map<IIdType, IIdType> idSubstitutions = new HashMap<>();
|
||||
final Map<IIdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
|
||||
List<BUNDLEENTRY> requestEntries = myVersionAdapter.getEntries(theRequest);
|
||||
|
||||
// Do all entries have a verb?
|
||||
for (int i = 0; i < myVersionAdapter.getEntries(theRequest).size(); i++) {
|
||||
BUNDLEENTRY nextReqEntry = requestEntries.get(i);
|
||||
String verb = myVersionAdapter.getEntryRequestVerb(nextReqEntry);
|
||||
if (verb == null || !isValidVerb(verb)) {
|
||||
throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", verb, i));
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* We want to execute the transaction request bundle elements in the order
|
||||
* specified by the FHIR specification (see TransactionSorter) so we save the
|
||||
* original order in the request, then sort it.
|
||||
*
|
||||
* Entries with a type of GET are removed from the bundle so that they
|
||||
* can be processed at the very end. We do this because the incoming resources
|
||||
* are saved in a two-phase way in order to deal with interdependencies, and
|
||||
* we want the GET processing to use the final indexing state
|
||||
*/
|
||||
final BUNDLE response = myVersionAdapter.createBundle(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTIONRESPONSE.toCode());
|
||||
List<BUNDLEENTRY> getEntries = new ArrayList<>();
|
||||
final IdentityHashMap<BUNDLEENTRY, Integer> originalRequestOrder = new IdentityHashMap<>();
|
||||
for (int i = 0; i < requestEntries.size(); i++) {
|
||||
originalRequestOrder.put(requestEntries.get(i), i);
|
||||
myVersionAdapter.addEntry(response);
|
||||
if (myVersionAdapter.getEntryRequestVerb(requestEntries.get(i)).equals("GET")) {
|
||||
getEntries.add(requestEntries.get(i));
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* See FhirSystemDaoDstu3Test#testTransactionWithPlaceholderIdInMatchUrl
|
||||
* Basically if the resource has a match URL that references a placeholder,
|
||||
* we try to handle the resource with the placeholder first.
|
||||
*/
|
||||
Set<String> placeholderIds = new HashSet<>();
|
||||
final List<BUNDLEENTRY> entries = requestEntries;
|
||||
for (BUNDLEENTRY nextEntry : entries) {
|
||||
String fullUrl = myVersionAdapter.getFullUrl(nextEntry);
|
||||
if (isNotBlank(fullUrl) && fullUrl.startsWith(URN_PREFIX)) {
|
||||
placeholderIds.add(fullUrl);
|
||||
}
|
||||
}
|
||||
Collections.sort(entries, new TransactionSorter(placeholderIds));
|
||||
|
||||
/*
|
||||
* All of the write operations in the transaction (PUT, POST, etc.. basically anything
|
||||
* except GET) are performed in their own database transaction before we do the reads.
|
||||
* We do this because the reads (specifically the searches) often spawn their own
|
||||
* secondary database transaction and if we allow that within the primary
|
||||
* database transaction we can end up with deadlocks if the server is under
|
||||
* heavy load with lots of concurrent transactions using all available
|
||||
* database connections.
|
||||
*/
|
||||
TransactionTemplate txManager = new TransactionTemplate(myTxManager);
|
||||
Map<BUNDLEENTRY, ResourceTable> entriesToProcess = txManager.execute(status -> {
|
||||
Map<BUNDLEENTRY, ResourceTable> retVal = doTransactionWriteOperations(theRequestDetails, theActionName, updateTime, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder, entries, transactionStopWatch);
|
||||
|
||||
transactionStopWatch.startTask("Commit writes to database");
|
||||
return retVal;
|
||||
});
|
||||
transactionStopWatch.endCurrentTask();
|
||||
|
||||
for (Map.Entry<BUNDLEENTRY, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
|
||||
String responseLocation = nextEntry.getValue().getIdDt().toUnqualified().getValue();
|
||||
String responseEtag = nextEntry.getValue().getIdDt().getVersionIdPart();
|
||||
myVersionAdapter.setResponseLocation(nextEntry.getKey(), responseLocation);
|
||||
myVersionAdapter.setResponseETag(nextEntry.getKey(), responseEtag);
|
||||
}
|
||||
|
||||
/*
|
||||
* Loop through the request and process any entries of type GET
|
||||
*/
|
||||
if (getEntries.size() > 0) {
|
||||
transactionStopWatch.startTask("Process " + getEntries.size() + " GET entries");
|
||||
}
|
||||
for (BUNDLEENTRY nextReqEntry : getEntries) {
|
||||
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
|
||||
BUNDLEENTRY nextRespEntry = myVersionAdapter.getEntries(response).get(originalOrder);
|
||||
|
||||
ServletSubRequestDetails requestDetails = new ServletSubRequestDetails();
|
||||
requestDetails.setServletRequest(theRequestDetails.getServletRequest());
|
||||
requestDetails.setRequestType(RequestTypeEnum.GET);
|
||||
requestDetails.setServer(theRequestDetails.getServer());
|
||||
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, "GET");
|
||||
|
||||
int qIndex = url.indexOf('?');
|
||||
ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
|
||||
requestDetails.setParameters(new HashMap<>());
|
||||
if (qIndex != -1) {
|
||||
String params = url.substring(qIndex);
|
||||
List<NameValuePair> parameters = BaseHapiFhirDao.translateMatchUrl(params);
|
||||
for (NameValuePair next : parameters) {
|
||||
paramValues.put(next.getName(), next.getValue());
|
||||
}
|
||||
for (Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
|
||||
String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
|
||||
requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
|
||||
}
|
||||
url = url.substring(0, qIndex);
|
||||
}
|
||||
|
||||
requestDetails.setRequestPath(url);
|
||||
requestDetails.setFhirServerBase(theRequestDetails.getFhirServerBase());
|
||||
|
||||
theRequestDetails.getServer().populateRequestDetailsFromRequestPath(requestDetails, url);
|
||||
BaseMethodBinding<?> method = theRequestDetails.getServer().determineResourceMethod(requestDetails, url);
|
||||
if (method == null) {
|
||||
throw new IllegalArgumentException("Unable to handle GET " + url);
|
||||
}
|
||||
|
||||
if (isNotBlank(myVersionAdapter.getEntryRequestIfMatch(nextReqEntry))) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_MATCH, myVersionAdapter.getEntryRequestIfMatch(nextReqEntry));
|
||||
}
|
||||
if (isNotBlank(myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry))) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_NONE_EXIST, myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry));
|
||||
}
|
||||
if (isNotBlank(myVersionAdapter.getEntryRequestIfNoneMatch(nextReqEntry))) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, myVersionAdapter.getEntryRequestIfNoneMatch(nextReqEntry));
|
||||
}
|
||||
|
||||
Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {}", url);
|
||||
try {
|
||||
IBaseResource resource = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
|
||||
if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
|
||||
resource = filterNestedBundle(requestDetails, resource);
|
||||
}
|
||||
myVersionAdapter.setResource(nextRespEntry, resource);
|
||||
myVersionAdapter.setResponseStatus(nextRespEntry, toStatusString(Constants.STATUS_HTTP_200_OK));
|
||||
} catch (NotModifiedException e) {
|
||||
myVersionAdapter.setResponseStatus(nextRespEntry, toStatusString(Constants.STATUS_HTTP_304_NOT_MODIFIED));
|
||||
} catch (BaseServerResponseException e) {
|
||||
ourLog.info("Failure processing transaction GET {}: {}", url, e.toString());
|
||||
myVersionAdapter.setResponseStatus(nextRespEntry, toStatusString(e.getStatusCode()));
|
||||
populateEntryWithOperationOutcome(e, nextRespEntry);
|
||||
}
|
||||
|
||||
}
|
||||
transactionStopWatch.endCurrentTask();
|
||||
|
||||
ourLog.info("Transaction timing:\n{}", transactionStopWatch.formatTaskDurations());
|
||||
|
||||
return response;
|
||||
}
|
||||
|
||||
private boolean isValidVerb(String theVerb) {
|
||||
try {
|
||||
return org.hl7.fhir.r4.model.Bundle.HTTPVerb.fromCode(theVerb) != null;
|
||||
} catch (FHIRException theE) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* This method is called for nested bundles (e.g. if we received a transaction with an entry that
|
||||
* was a GET search, this method is called on the bundle for the search result, that will be placed in the
|
||||
* outer bundle). This method applies the _summary and _content parameters to the output of
|
||||
* that bundle.
|
||||
* <p>
|
||||
* TODO: This isn't the most efficient way of doing this.. hopefully we can come up with something better in the future.
|
||||
*/
|
||||
private IBaseResource filterNestedBundle(RequestDetails theRequestDetails, IBaseResource theResource) {
|
||||
IParser p = myContext.newJsonParser();
|
||||
RestfulServerUtils.configureResponseParser(theRequestDetails, p);
|
||||
return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
|
||||
}
|
||||
|
||||
public void setEntityManager(EntityManager theEntityManager) {
|
||||
myEntityManager = theEntityManager;
|
||||
}
|
||||
|
||||
private void validateDependencies() {
|
||||
Validate.notNull(myEntityManager);
|
||||
Validate.notNull(myContext);
|
||||
Validate.notNull(myDao);
|
||||
Validate.notNull(myTxManager);
|
||||
}
|
||||
|
||||
private IIdType newIdType(String theValue) {
|
||||
return myContext.getVersion().newIdType().setValue(theValue);
|
||||
}
|
||||
|
||||
private Map<BUNDLEENTRY, ResourceTable> doTransactionWriteOperations(ServletRequestDetails theRequestDetails, String theActionName, Date theUpdateTime, Set<IIdType> theAllIds,
|
||||
Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, BUNDLE theResponse, IdentityHashMap<BUNDLEENTRY, Integer> theOriginalRequestOrder, List<BUNDLEENTRY> theEntries, StopWatch theTransactionStopWatch) {
|
||||
Set<String> deletedResources = new HashSet<>();
|
||||
List<DeleteConflict> deleteConflicts = new ArrayList<>();
|
||||
Map<BUNDLEENTRY, ResourceTable> entriesToProcess = new IdentityHashMap<>();
|
||||
Set<ResourceTable> nonUpdatedEntities = new HashSet<>();
|
||||
Set<ResourceTable> updatedEntities = new HashSet<>();
|
||||
Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
|
||||
|
||||
/*
|
||||
* Loop through the request and process any entries of type
|
||||
* PUT, POST or DELETE
|
||||
*/
|
||||
for (int i = 0; i < theEntries.size(); i++) {
|
||||
|
||||
if (i % 100 == 0) {
|
||||
ourLog.debug("Processed {} non-GET entries out of {}", i, theEntries.size());
|
||||
}
|
||||
|
||||
BUNDLEENTRY nextReqEntry = theEntries.get(i);
|
||||
IBaseResource res = myVersionAdapter.getResource(nextReqEntry);
|
||||
IIdType nextResourceId = null;
|
||||
if (res != null) {
|
||||
|
||||
nextResourceId = res.getIdElement();
|
||||
|
||||
if (!nextResourceId.hasIdPart()) {
|
||||
if (isNotBlank(myVersionAdapter.getFullUrl(nextReqEntry))) {
|
||||
nextResourceId = newIdType(myVersionAdapter.getFullUrl(nextReqEntry));
|
||||
}
|
||||
}
|
||||
|
||||
if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+\\:.*") && !isPlaceholder(nextResourceId)) {
|
||||
throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
|
||||
}
|
||||
|
||||
if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
|
||||
nextResourceId = newIdType(toResourceName(res.getClass()), nextResourceId.getIdPart());
|
||||
res.setId(nextResourceId);
|
||||
}
|
||||
|
||||
/*
|
||||
* Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
|
||||
*/
|
||||
if (isPlaceholder(nextResourceId)) {
|
||||
if (!theAllIds.add(nextResourceId)) {
|
||||
throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextResourceId));
|
||||
}
|
||||
} else if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
|
||||
IIdType nextId = nextResourceId.toUnqualifiedVersionless();
|
||||
if (!theAllIds.add(nextId)) {
|
||||
throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextId));
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
String verb = myVersionAdapter.getEntryRequestVerb(nextReqEntry);
|
||||
String resourceType = res != null ? myContext.getResourceDefinition(res).getName() : null;
|
||||
Integer order = theOriginalRequestOrder.get(nextReqEntry);
|
||||
BUNDLEENTRY nextRespEntry = myVersionAdapter.getEntries(theResponse).get(order);
|
||||
|
||||
theTransactionStopWatch.startTask("Bundle.entry[" + i + "]: " + verb + " " + defaultString(resourceType));
|
||||
|
||||
switch (verb) {
|
||||
case "POST": {
|
||||
// CREATE
|
||||
@SuppressWarnings("rawtypes")
|
||||
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
|
||||
res.setId((String) null);
|
||||
DaoMethodOutcome outcome;
|
||||
String matchUrl = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
outcome = resourceDao.create(res, matchUrl, false, theRequestDetails);
|
||||
if (nextResourceId != null) {
|
||||
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
|
||||
}
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
if (outcome.getCreated() == false) {
|
||||
nonUpdatedEntities.add(outcome.getEntity());
|
||||
} else {
|
||||
if (isNotBlank(matchUrl)) {
|
||||
conditionalRequestUrls.put(matchUrl, res.getClass());
|
||||
}
|
||||
}
|
||||
|
||||
break;
|
||||
}
|
||||
case "DELETE": {
|
||||
// DELETE
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
|
||||
UrlUtil.UrlParts parts = UrlUtil.parseUrl(url);
|
||||
ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb, url);
|
||||
int status = Constants.STATUS_HTTP_204_NO_CONTENT;
|
||||
if (parts.getResourceId() != null) {
|
||||
IIdType deleteId = newIdType(parts.getResourceType(), parts.getResourceId());
|
||||
if (!deletedResources.contains(deleteId.getValueAsString())) {
|
||||
DaoMethodOutcome outcome = dao.delete(deleteId, deleteConflicts, theRequestDetails);
|
||||
if (outcome.getEntity() != null) {
|
||||
deletedResources.add(deleteId.getValueAsString());
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
}
|
||||
}
|
||||
} else {
|
||||
String matchUrl = parts.getResourceType() + '?' + parts.getParams();
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(matchUrl, deleteConflicts, theRequestDetails);
|
||||
List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
|
||||
for (ResourceTable deleted : allDeleted) {
|
||||
deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless().getValueAsString());
|
||||
}
|
||||
if (allDeleted.isEmpty()) {
|
||||
status = Constants.STATUS_HTTP_204_NO_CONTENT;
|
||||
}
|
||||
|
||||
myVersionAdapter.setResponseOutcome(nextRespEntry, deleteOutcome.getOperationOutcome());
|
||||
}
|
||||
|
||||
myVersionAdapter.setResponseStatus(nextRespEntry, toStatusString(status));
|
||||
|
||||
break;
|
||||
}
|
||||
case "PUT": {
|
||||
// UPDATE
|
||||
@SuppressWarnings("rawtypes")
|
||||
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
|
||||
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
|
||||
|
||||
DaoMethodOutcome outcome;
|
||||
UrlUtil.UrlParts parts = UrlUtil.parseUrl(url);
|
||||
if (isNotBlank(parts.getResourceId())) {
|
||||
String version = null;
|
||||
if (isNotBlank(myVersionAdapter.getEntryRequestIfMatch(nextReqEntry))) {
|
||||
version = ParameterUtil.parseETagValue(myVersionAdapter.getEntryRequestIfMatch(nextReqEntry));
|
||||
}
|
||||
res.setId(newIdType(parts.getResourceType(), parts.getResourceId(), version));
|
||||
outcome = resourceDao.update(res, null, false, theRequestDetails);
|
||||
} else {
|
||||
res.setId((String) null);
|
||||
String matchUrl;
|
||||
if (isNotBlank(parts.getParams())) {
|
||||
matchUrl = parts.getResourceType() + '?' + parts.getParams();
|
||||
} else {
|
||||
matchUrl = parts.getResourceType();
|
||||
}
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
outcome = resourceDao.update(res, matchUrl, false, theRequestDetails);
|
||||
if (Boolean.TRUE.equals(outcome.getCreated())) {
|
||||
conditionalRequestUrls.put(matchUrl, res.getClass());
|
||||
}
|
||||
}
|
||||
|
||||
if (outcome.getCreated() == Boolean.FALSE) {
|
||||
updatedEntities.add(outcome.getEntity());
|
||||
}
|
||||
|
||||
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
break;
|
||||
}
|
||||
case "GET":
|
||||
default:
|
||||
break;
|
||||
|
||||
}
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Make sure that there are no conflicts from deletions. E.g. we can't delete something
|
||||
* if something else has a reference to it.. Unless the thing that has a reference to it
|
||||
* was also deleted as a part of this transaction, which is why we check this now at the
|
||||
* end.
|
||||
*/
|
||||
|
||||
deleteConflicts.removeIf(next ->
|
||||
deletedResources.contains(next.getTargetId().toUnqualifiedVersionless().getValue()));
|
||||
myDao.validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
|
||||
|
||||
/*
|
||||
* Perform ID substitutions and then index each resource we have saved
|
||||
*/
|
||||
|
||||
FhirTerser terser = myContext.newTerser();
|
||||
theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
|
||||
for (DaoMethodOutcome nextOutcome : theIdToPersistedOutcome.values()) {
|
||||
IBaseResource nextResource = nextOutcome.getResource();
|
||||
if (nextResource == null) {
|
||||
continue;
|
||||
}
|
||||
|
||||
// References
|
||||
List<ResourceReferenceInfo> allRefs = terser.getAllResourceReferences(nextResource);
|
||||
for (ResourceReferenceInfo nextRef : allRefs) {
|
||||
IIdType nextId = nextRef.getResourceReference().getReferenceElement();
|
||||
if (!nextId.hasIdPart()) {
|
||||
continue;
|
||||
}
|
||||
if (theIdSubstitutions.containsKey(nextId)) {
|
||||
IIdType newId = theIdSubstitutions.get(nextId);
|
||||
ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
|
||||
nextRef.getResourceReference().setReference(newId.getValue());
|
||||
} else if (nextId.getValue().startsWith("urn:")) {
|
||||
throw new InvalidRequestException("Unable to satisfy placeholder ID " + nextId.getValue() + " found in element named '" + nextRef.getName() + "' within resource of type: " + nextResource.getIdElement().getResourceType());
|
||||
} else {
|
||||
ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
|
||||
}
|
||||
}
|
||||
|
||||
// URIs
|
||||
Class<? extends IPrimitiveType<?>> uriType = (Class<? extends IPrimitiveType<?>>) myContext.getElementDefinition("uri").getImplementingClass();
|
||||
List<? extends IPrimitiveType<?>> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, uriType);
|
||||
for (IPrimitiveType<?> nextRef : allUris) {
|
||||
if (nextRef instanceof IIdType) {
|
||||
continue; // No substitution on the resource ID itself!
|
||||
}
|
||||
IIdType nextUriString = newIdType(nextRef.getValueAsString());
|
||||
if (theIdSubstitutions.containsKey(nextUriString)) {
|
||||
IIdType newId = theIdSubstitutions.get(nextUriString);
|
||||
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
|
||||
nextRef.setValueAsString(newId.getValue());
|
||||
} else {
|
||||
ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
|
||||
}
|
||||
}
|
||||
|
||||
IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
|
||||
Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
|
||||
|
||||
if (updatedEntities.contains(nextOutcome.getEntity())) {
|
||||
myDao.updateInternal(theRequestDetails, nextResource, true, false, theRequestDetails, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
|
||||
} else if (!nonUpdatedEntities.contains(nextOutcome.getEntity())) {
|
||||
myDao.updateEntity(theRequestDetails, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
|
||||
}
|
||||
}
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
theTransactionStopWatch.startTask("Flush writes to database");
|
||||
|
||||
flushJpaSession();
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
if (conditionalRequestUrls.size() > 0) {
|
||||
theTransactionStopWatch.startTask("Check for conflicts in conditional resources");
|
||||
}
|
||||
|
||||
/*
|
||||
* Double check we didn't allow any duplicates we shouldn't have
|
||||
*/
|
||||
for (Map.Entry<String, Class<? extends IBaseResource>> nextEntry : conditionalRequestUrls.entrySet()) {
|
||||
String matchUrl = nextEntry.getKey();
|
||||
Class<? extends IBaseResource> resType = nextEntry.getValue();
|
||||
if (isNotBlank(matchUrl)) {
|
||||
IFhirResourceDao<?> resourceDao = myDao.getDao(resType);
|
||||
Set<Long> val = resourceDao.processMatchUrl(matchUrl);
|
||||
if (val.size() > 1) {
|
||||
throw new InvalidRequestException(
|
||||
"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
|
||||
for (IIdType next : theAllIds) {
|
||||
IIdType replacement = theIdSubstitutions.get(next);
|
||||
if (replacement == null) {
|
||||
continue;
|
||||
}
|
||||
if (replacement.equals(next)) {
|
||||
continue;
|
||||
}
|
||||
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
|
||||
}
|
||||
return entriesToProcess;
|
||||
}
|
||||
|
||||
private IIdType newIdType(String theResourceType, String theResourceId, String theVersion) {
|
||||
org.hl7.fhir.r4.model.IdType id = new org.hl7.fhir.r4.model.IdType(theResourceType, theResourceId, theVersion);
|
||||
return myContext.getVersion().newIdType().setValue(id.getValue());
|
||||
}
|
||||
|
||||
private IIdType newIdType(String theToResourceName, String theIdPart) {
|
||||
return newIdType(theToResourceName, theIdPart, null);
|
||||
}
|
||||
|
||||
private IFhirResourceDao getDaoOrThrowException(Class<? extends IBaseResource> theClass) {
|
||||
return myDao.getDaoOrThrowException(theClass);
|
||||
}
|
||||
|
||||
protected void flushJpaSession() {
|
||||
SessionImpl session = (SessionImpl) myEntityManager.unwrap(Session.class);
|
||||
int insertionCount = session.getActionQueue().numberOfInsertions();
|
||||
int updateCount = session.getActionQueue().numberOfUpdates();
|
||||
|
||||
StopWatch sw = new StopWatch();
|
||||
myEntityManager.flush();
|
||||
ourLog.debug("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
|
||||
}
|
||||
|
||||
protected String toResourceName(Class<? extends IBaseResource> theResourceType) {
|
||||
return myContext.getResourceDefinition(theResourceType).getName();
|
||||
}
|
||||
|
||||
public void setContext(FhirContext theContext) {
|
||||
myContext = theContext;
|
||||
}
|
||||
|
||||
private String extractTransactionUrlOrThrowException(BUNDLEENTRY nextEntry, String verb) {
|
||||
String url = myVersionAdapter.getEntryRequestUrl(nextEntry);
|
||||
if (isBlank(url)) {
|
||||
throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionMissingUrl", verb));
|
||||
}
|
||||
return url;
|
||||
}
|
||||
|
||||
private ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> toDao(UrlUtil.UrlParts theParts, String theVerb, String theUrl) {
|
||||
RuntimeResourceDefinition resType;
|
||||
try {
|
||||
resType = myContext.getResourceDefinition(theParts.getResourceType());
|
||||
} catch (DataFormatException e) {
|
||||
String msg = myContext.getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
throw new InvalidRequestException(msg);
|
||||
}
|
||||
IFhirResourceDao<? extends IBaseResource> dao = null;
|
||||
if (resType != null) {
|
||||
dao = myDao.getDao(resType.getImplementingClass());
|
||||
}
|
||||
if (dao == null) {
|
||||
String msg = myContext.getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
throw new InvalidRequestException(msg);
|
||||
}
|
||||
|
||||
// if (theParts.getResourceId() == null && theParts.getParams() == null) {
|
||||
// String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
// throw new InvalidRequestException(msg);
|
||||
// }
|
||||
|
||||
return dao;
|
||||
}
|
||||
|
||||
public interface ITransactionProcessorVersionAdapter<BUNDLE, BUNDLEENTRY> {
|
||||
|
||||
void setResponseStatus(BUNDLEENTRY theBundleEntry, String theStatus);
|
||||
|
||||
void setResponseLastModified(BUNDLEENTRY theBundleEntry, Date theLastModified);
|
||||
|
||||
void setResource(BUNDLEENTRY theBundleEntry, IBaseResource theResource);
|
||||
|
||||
IBaseResource getResource(BUNDLEENTRY theBundleEntry);
|
||||
|
||||
String getBundleType(BUNDLE theRequest);
|
||||
|
||||
void populateEntryWithOperationOutcome(BaseServerResponseException theCaughtEx, BUNDLEENTRY theEntry);
|
||||
|
||||
BUNDLE createBundle(String theBundleType);
|
||||
|
||||
List<BUNDLEENTRY> getEntries(BUNDLE theRequest);
|
||||
|
||||
void addEntry(BUNDLE theBundle, BUNDLEENTRY theEntry);
|
||||
|
||||
BUNDLEENTRY addEntry(BUNDLE theBundle);
|
||||
|
||||
String getEntryRequestVerb(BUNDLEENTRY theEntry);
|
||||
|
||||
String getFullUrl(BUNDLEENTRY theEntry);
|
||||
|
||||
String getEntryIfNoneExist(BUNDLEENTRY theEntry);
|
||||
|
||||
String getEntryRequestUrl(BUNDLEENTRY theEntry);
|
||||
|
||||
void setResponseLocation(BUNDLEENTRY theEntry, String theResponseLocation);
|
||||
|
||||
void setResponseETag(BUNDLEENTRY theEntry, String theEtag);
|
||||
|
||||
String getEntryRequestIfMatch(BUNDLEENTRY theEntry);
|
||||
|
||||
String getEntryRequestIfNoneExist(BUNDLEENTRY theEntry);
|
||||
|
||||
String getEntryRequestIfNoneMatch(BUNDLEENTRY theEntry);
|
||||
|
||||
void setResponseOutcome(BUNDLEENTRY theEntry, IBaseOperationOutcome theOperationOutcome);
|
||||
}
|
||||
|
||||
private static class BaseServerResponseExceptionHolder {
|
||||
private BaseServerResponseException myException;
|
||||
|
||||
public BaseServerResponseException getException() {
|
||||
return myException;
|
||||
}
|
||||
|
||||
public void setException(BaseServerResponseException myException) {
|
||||
this.myException = myException;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Transaction Order, per the spec:
|
||||
* <p>
|
||||
* Process any DELETE interactions
|
||||
* Process any POST interactions
|
||||
* Process any PUT interactions
|
||||
* Process any GET interactions
|
||||
*/
|
||||
//@formatter:off
|
||||
public class TransactionSorter implements Comparator<BUNDLEENTRY> {
|
||||
|
||||
private Set<String> myPlaceholderIds;
|
||||
|
||||
public TransactionSorter(Set<String> thePlaceholderIds) {
|
||||
myPlaceholderIds = thePlaceholderIds;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int compare(BUNDLEENTRY theO1, BUNDLEENTRY theO2) {
|
||||
int o1 = toOrder(theO1);
|
||||
int o2 = toOrder(theO2);
|
||||
|
||||
if (o1 == o2) {
|
||||
String matchUrl1 = toMatchUrl(theO1);
|
||||
String matchUrl2 = toMatchUrl(theO2);
|
||||
if (isBlank(matchUrl1) && isBlank(matchUrl2)) {
|
||||
return 0;
|
||||
}
|
||||
if (isBlank(matchUrl1)) {
|
||||
return -1;
|
||||
}
|
||||
if (isBlank(matchUrl2)) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
boolean match1containsSubstitutions = false;
|
||||
boolean match2containsSubstitutions = false;
|
||||
for (String nextPlaceholder : myPlaceholderIds) {
|
||||
if (matchUrl1.contains(nextPlaceholder)) {
|
||||
match1containsSubstitutions = true;
|
||||
}
|
||||
if (matchUrl2.contains(nextPlaceholder)) {
|
||||
match2containsSubstitutions = true;
|
||||
}
|
||||
}
|
||||
|
||||
if (match1containsSubstitutions && match2containsSubstitutions) {
|
||||
return 0;
|
||||
}
|
||||
if (!match1containsSubstitutions && !match2containsSubstitutions) {
|
||||
return 0;
|
||||
}
|
||||
if (match1containsSubstitutions) {
|
||||
return 1;
|
||||
} else {
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
return o1 - o2;
|
||||
}
|
||||
|
||||
private String toMatchUrl(BUNDLEENTRY theEntry) {
|
||||
String verb = myVersionAdapter.getEntryRequestVerb(theEntry);
|
||||
if (verb.equals("POST")) {
|
||||
return myVersionAdapter.getEntryIfNoneExist(theEntry);
|
||||
}
|
||||
if (verb.equals("PUT") || verb.equals("DELETE")) {
|
||||
String url = extractTransactionUrlOrThrowException(theEntry, verb);
|
||||
UrlUtil.UrlParts parts = UrlUtil.parseUrl(url);
|
||||
if (isBlank(parts.getResourceId())) {
|
||||
return parts.getResourceType() + '?' + parts.getParams();
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
private int toOrder(BUNDLEENTRY theO1) {
|
||||
int o1 = 0;
|
||||
if (myVersionAdapter.getEntryRequestVerb(theO1) != null) {
|
||||
switch (myVersionAdapter.getEntryRequestVerb(theO1)) {
|
||||
case "DELETE":
|
||||
o1 = 1;
|
||||
break;
|
||||
case "POST":
|
||||
o1 = 2;
|
||||
break;
|
||||
case "PUT":
|
||||
o1 = 3;
|
||||
break;
|
||||
case "GET":
|
||||
o1 = 4;
|
||||
break;
|
||||
default:
|
||||
o1 = 0;
|
||||
break;
|
||||
}
|
||||
}
|
||||
return o1;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao.dstu3;
|
|||
* 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.
|
||||
|
|
@ -20,610 +20,34 @@ package ca.uhn.fhir.jpa.dao.dstu3;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.context.RuntimeResourceDefinition;
|
||||
import ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao;
|
||||
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.DeleteMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
|
||||
import ca.uhn.fhir.jpa.entity.TagDefinition;
|
||||
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
|
||||
import ca.uhn.fhir.jpa.util.DeleteConflict;
|
||||
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
|
||||
import ca.uhn.fhir.parser.DataFormatException;
|
||||
import ca.uhn.fhir.parser.IParser;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
import ca.uhn.fhir.rest.api.PreferReturnEnum;
|
||||
import ca.uhn.fhir.rest.api.RequestTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.param.ParameterUtil;
|
||||
import ca.uhn.fhir.rest.server.RestfulServerUtils;
|
||||
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
|
||||
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
|
||||
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
|
||||
import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.FhirTerser;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil.UrlParts;
|
||||
import com.google.common.collect.ArrayListMultimap;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.apache.http.NameValuePair;
|
||||
import org.hl7.fhir.dstu3.model.*;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
|
||||
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryResponseComponent;
|
||||
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
|
||||
import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
|
||||
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
|
||||
import org.hl7.fhir.instance.model.api.*;
|
||||
import org.hl7.fhir.dstu3.model.Meta;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.transaction.PlatformTransactionManager;
|
||||
import org.springframework.transaction.TransactionDefinition;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
import org.springframework.transaction.annotation.Propagation;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
import org.springframework.transaction.support.TransactionCallback;
|
||||
import org.springframework.transaction.support.TransactionTemplate;
|
||||
|
||||
import javax.annotation.PostConstruct;
|
||||
import javax.persistence.TypedQuery;
|
||||
import java.util.*;
|
||||
import java.util.Map.Entry;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.*;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
|
||||
public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu3.class);
|
||||
|
||||
@Autowired
|
||||
private PlatformTransactionManager myTxManager;
|
||||
private TransactionProcessor<Bundle, BundleEntryComponent> myTransactionProcessor;
|
||||
|
||||
private Bundle batch(final RequestDetails theRequestDetails, Bundle theRequest) {
|
||||
ourLog.info("Beginning batch with {} resources", theRequest.getEntry().size());
|
||||
long start = System.currentTimeMillis();
|
||||
|
||||
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
|
||||
|
||||
Bundle resp = new Bundle();
|
||||
resp.setType(BundleType.BATCHRESPONSE);
|
||||
|
||||
/*
|
||||
* For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
|
||||
*/
|
||||
|
||||
for (final BundleEntryComponent nextRequestEntry : theRequest.getEntry()) {
|
||||
|
||||
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
|
||||
|
||||
TransactionCallback<Bundle> callback = new TransactionCallback<Bundle>() {
|
||||
@Override
|
||||
public Bundle doInTransaction(TransactionStatus theStatus) {
|
||||
Bundle subRequestBundle = new Bundle();
|
||||
subRequestBundle.setType(BundleType.TRANSACTION);
|
||||
subRequestBundle.addEntry(nextRequestEntry);
|
||||
|
||||
Bundle subResponseBundle = transaction((ServletRequestDetails) theRequestDetails, subRequestBundle, "Batch sub-request");
|
||||
return subResponseBundle;
|
||||
}
|
||||
};
|
||||
|
||||
try {
|
||||
Bundle nextResponseBundle = callback.doInTransaction(null);
|
||||
|
||||
BundleEntryComponent subResponseEntry = nextResponseBundle.getEntry().get(0);
|
||||
resp.addEntry(subResponseEntry);
|
||||
|
||||
/*
|
||||
* If the individual entry didn't have a resource in its response, bring the sub-transaction's OperationOutcome across so the client can see it
|
||||
*/
|
||||
if (subResponseEntry.getResource() == null) {
|
||||
subResponseEntry.setResource(nextResponseBundle.getEntry().get(0).getResource());
|
||||
}
|
||||
|
||||
} catch (BaseServerResponseException e) {
|
||||
caughtEx.setException(e);
|
||||
} catch (Throwable t) {
|
||||
ourLog.error("Failure during BATCH sub transaction processing", t);
|
||||
caughtEx.setException(new InternalErrorException(t));
|
||||
}
|
||||
|
||||
if (caughtEx.getException() != null) {
|
||||
BundleEntryComponent nextEntry = resp.addEntry();
|
||||
|
||||
populateEntryWithOperationOutcome(caughtEx.getException(), nextEntry);
|
||||
|
||||
BundleEntryResponseComponent nextEntryResp = nextEntry.getResponse();
|
||||
nextEntryResp.setStatus(toStatusString(caughtEx.getException().getStatusCode()));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
long delay = System.currentTimeMillis() - start;
|
||||
ourLog.info("Batch completed in {}ms", new Object[] {delay});
|
||||
|
||||
return resp;
|
||||
@PostConstruct
|
||||
public void start() {
|
||||
myTransactionProcessor.setDao(this);
|
||||
}
|
||||
|
||||
private Bundle doTransaction(final ServletRequestDetails theRequestDetails, final Bundle theRequest, final String theActionName) {
|
||||
BundleType transactionType = theRequest.getTypeElement().getValue();
|
||||
if (transactionType == BundleType.BATCH) {
|
||||
return batch(theRequestDetails, theRequest);
|
||||
}
|
||||
|
||||
if (transactionType == null) {
|
||||
String message = "Transaction Bundle did not specify valid Bundle.type, assuming " + BundleType.TRANSACTION.toCode();
|
||||
ourLog.warn(message);
|
||||
transactionType = BundleType.TRANSACTION;
|
||||
}
|
||||
if (transactionType != BundleType.TRANSACTION) {
|
||||
throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType.toCode());
|
||||
}
|
||||
|
||||
ourLog.debug("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
|
||||
|
||||
final Date updateTime = new Date();
|
||||
final StopWatch transactionStopWatch = new StopWatch();
|
||||
|
||||
final Set<IdType> allIds = new LinkedHashSet<>();
|
||||
final Map<IdType, IdType> idSubstitutions = new HashMap<>();
|
||||
final Map<IdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
|
||||
|
||||
// Do all entries have a verb?
|
||||
for (int i = 0; i < theRequest.getEntry().size(); i++) {
|
||||
BundleEntryComponent nextReqEntry = theRequest.getEntry().get(i);
|
||||
HTTPVerb verb = nextReqEntry.getRequest().getMethodElement().getValue();
|
||||
if (verb == null) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", nextReqEntry.getRequest().getMethod(), i));
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* We want to execute the transaction request bundle elements in the order
|
||||
* specified by the FHIR specification (see TransactionSorter) so we save the
|
||||
* original order in the request, then sort it.
|
||||
*
|
||||
* Entries with a type of GET are removed from the bundle so that they
|
||||
* can be processed at the very end. We do this because the incoming resources
|
||||
* are saved in a two-phase way in order to deal with interdependencies, and
|
||||
* we want the GET processing to use the final indexing state
|
||||
*/
|
||||
final Bundle response = new Bundle();
|
||||
List<BundleEntryComponent> getEntries = new ArrayList<BundleEntryComponent>();
|
||||
final IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder = new IdentityHashMap<Bundle.BundleEntryComponent, Integer>();
|
||||
for (int i = 0; i < theRequest.getEntry().size(); i++) {
|
||||
originalRequestOrder.put(theRequest.getEntry().get(i), i);
|
||||
response.addEntry();
|
||||
if (theRequest.getEntry().get(i).getRequest().getMethodElement().getValue() == HTTPVerb.GET) {
|
||||
getEntries.add(theRequest.getEntry().get(i));
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* See FhirSystemDaoDstu3Test#testTransactionWithPlaceholderIdInMatchUrl
|
||||
* Basically if the resource has a match URL that references a placeholder,
|
||||
* we try to handle the resource with the placeholder first.
|
||||
*/
|
||||
Set<String> placeholderIds = new HashSet<>();
|
||||
final List<BundleEntryComponent> entries = theRequest.getEntry();
|
||||
for (BundleEntryComponent nextEntry : entries) {
|
||||
if (isNotBlank(nextEntry.getFullUrl()) && nextEntry.getFullUrl().startsWith(IdType.URN_PREFIX)) {
|
||||
placeholderIds.add(nextEntry.getFullUrl());
|
||||
}
|
||||
}
|
||||
Collections.sort(entries, new TransactionSorter(placeholderIds));
|
||||
|
||||
/*
|
||||
* All of the write operations in the transaction (PUT, POST, etc.. basically anything
|
||||
* except GET) are performed in their own database transaction before we do the reads.
|
||||
* We do this because the reads (specifically the searches) often spawn their own
|
||||
* secondary database transaction and if we allow that within the primary
|
||||
* database transaction we can end up with deadlocks if the server is under
|
||||
* heavy load with lots of concurrent transactions using all available
|
||||
* database connections.
|
||||
*/
|
||||
TransactionTemplate txManager = new TransactionTemplate(myTxManager);
|
||||
Map<BundleEntryComponent, ResourceTable> entriesToProcess = txManager.execute(new TransactionCallback<Map<BundleEntryComponent, ResourceTable>>() {
|
||||
@Override
|
||||
public Map<BundleEntryComponent, ResourceTable> doInTransaction(TransactionStatus status) {
|
||||
Map<BundleEntryComponent, ResourceTable> retVal = doTransactionWriteOperations(theRequestDetails, theActionName, updateTime, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder, entries, transactionStopWatch);
|
||||
|
||||
transactionStopWatch.startTask("Commit writes to database");
|
||||
return retVal;
|
||||
}
|
||||
});
|
||||
transactionStopWatch.endCurrentTask();
|
||||
|
||||
for (Entry<BundleEntryComponent, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
|
||||
String responseLocation = nextEntry.getValue().getIdDt().toUnqualified().getValue();
|
||||
String responseEtag = nextEntry.getValue().getIdDt().getVersionIdPart();
|
||||
nextEntry.getKey().getResponse().setLocation(responseLocation);
|
||||
nextEntry.getKey().getResponse().setEtag(responseEtag);
|
||||
}
|
||||
|
||||
/*
|
||||
* Loop through the request and process any entries of type GET
|
||||
*/
|
||||
if (getEntries.size() > 0) {
|
||||
transactionStopWatch.startTask("Process " + getEntries.size() + " GET entries");
|
||||
}
|
||||
for (BundleEntryComponent nextReqEntry : getEntries) {
|
||||
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
|
||||
BundleEntryComponent nextRespEntry = response.getEntry().get(originalOrder);
|
||||
|
||||
ServletSubRequestDetails requestDetails = new ServletSubRequestDetails();
|
||||
requestDetails.setServletRequest(theRequestDetails.getServletRequest());
|
||||
requestDetails.setRequestType(RequestTypeEnum.GET);
|
||||
requestDetails.setServer(theRequestDetails.getServer());
|
||||
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, HTTPVerb.GET);
|
||||
|
||||
int qIndex = url.indexOf('?');
|
||||
ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
|
||||
requestDetails.setParameters(new HashMap<>());
|
||||
if (qIndex != -1) {
|
||||
String params = url.substring(qIndex);
|
||||
List<NameValuePair> parameters = translateMatchUrl(params);
|
||||
for (NameValuePair next : parameters) {
|
||||
paramValues.put(next.getName(), next.getValue());
|
||||
}
|
||||
for (Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
|
||||
String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
|
||||
requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
|
||||
}
|
||||
url = url.substring(0, qIndex);
|
||||
}
|
||||
|
||||
requestDetails.setRequestPath(url);
|
||||
requestDetails.setFhirServerBase(theRequestDetails.getFhirServerBase());
|
||||
|
||||
theRequestDetails.getServer().populateRequestDetailsFromRequestPath(requestDetails, url);
|
||||
BaseMethodBinding<?> method = theRequestDetails.getServer().determineResourceMethod(requestDetails, url);
|
||||
if (method == null) {
|
||||
throw new IllegalArgumentException("Unable to handle GET " + url);
|
||||
}
|
||||
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_MATCH, nextReqEntry.getRequest().getIfMatch());
|
||||
}
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfNoneExist())) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_NONE_EXIST, nextReqEntry.getRequest().getIfNoneExist());
|
||||
}
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfNoneMatch())) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, nextReqEntry.getRequest().getIfNoneMatch());
|
||||
}
|
||||
|
||||
Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {}", url);
|
||||
try {
|
||||
IBaseResource resource = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
|
||||
if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
|
||||
resource = filterNestedBundle(requestDetails, resource);
|
||||
}
|
||||
nextRespEntry.setResource((Resource) resource);
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
|
||||
} catch (NotModifiedException e) {
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_304_NOT_MODIFIED));
|
||||
} catch (BaseServerResponseException e) {
|
||||
ourLog.info("Failure processing transaction GET {}: {}", url, e.toString());
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(e.getStatusCode()));
|
||||
populateEntryWithOperationOutcome(e, nextRespEntry);
|
||||
}
|
||||
|
||||
}
|
||||
transactionStopWatch.endCurrentTask();
|
||||
|
||||
response.setType(BundleType.TRANSACTIONRESPONSE);
|
||||
|
||||
ourLog.info("Transaction timing:\n{}", transactionStopWatch.formatTaskDurations());
|
||||
|
||||
return response;
|
||||
}
|
||||
|
||||
private Map<BundleEntryComponent, ResourceTable> doTransactionWriteOperations(ServletRequestDetails theRequestDetails, String theActionName, Date theUpdateTime, Set<IdType> theAllIds,
|
||||
Map<IdType, IdType> theIdSubstitutions, Map<IdType, DaoMethodOutcome> theIdToPersistedOutcome, Bundle theResponse, IdentityHashMap<BundleEntryComponent, Integer> theOriginalRequestOrder, List<BundleEntryComponent> theEntries, StopWatch theTransactionStopWatch) {
|
||||
Set<String> deletedResources = new HashSet<>();
|
||||
List<DeleteConflict> deleteConflicts = new ArrayList<>();
|
||||
Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<>();
|
||||
Set<ResourceTable> nonUpdatedEntities = new HashSet<>();
|
||||
Set<ResourceTable> updatedEntities = new HashSet<>();
|
||||
Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
|
||||
|
||||
/*
|
||||
* Loop through the request and process any entries of type
|
||||
* PUT, POST or DELETE
|
||||
*/
|
||||
for (int i = 0; i < theEntries.size(); i++) {
|
||||
|
||||
if (i % 100 == 0) {
|
||||
ourLog.debug("Processed {} non-GET entries out of {}", i, theEntries.size());
|
||||
}
|
||||
|
||||
BundleEntryComponent nextReqEntry = theEntries.get(i);
|
||||
Resource res = nextReqEntry.getResource();
|
||||
IdType nextResourceId = null;
|
||||
if (res != null) {
|
||||
|
||||
nextResourceId = res.getIdElement();
|
||||
|
||||
if (!nextResourceId.hasIdPart()) {
|
||||
if (isNotBlank(nextReqEntry.getFullUrl())) {
|
||||
nextResourceId = new IdType(nextReqEntry.getFullUrl());
|
||||
}
|
||||
}
|
||||
|
||||
if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+\\:.*") && !isPlaceholder(nextResourceId)) {
|
||||
throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
|
||||
}
|
||||
|
||||
if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
|
||||
nextResourceId = new IdType(toResourceName(res.getClass()), nextResourceId.getIdPart());
|
||||
res.setId(nextResourceId);
|
||||
}
|
||||
|
||||
/*
|
||||
* Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
|
||||
*/
|
||||
if (isPlaceholder(nextResourceId)) {
|
||||
if (!theAllIds.add(nextResourceId)) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextResourceId));
|
||||
}
|
||||
} else if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
|
||||
IdType nextId = nextResourceId.toUnqualifiedVersionless();
|
||||
if (!theAllIds.add(nextId)) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextId));
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
HTTPVerb verb = nextReqEntry.getRequest().getMethodElement().getValue();
|
||||
String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
|
||||
BundleEntryComponent nextRespEntry = theResponse.getEntry().get(theOriginalRequestOrder.get(nextReqEntry));
|
||||
|
||||
theTransactionStopWatch.startTask("Bundle.entry[" + i + "]: " + verb.name() + " " + defaultString(resourceType));
|
||||
|
||||
switch (verb) {
|
||||
case POST: {
|
||||
// CREATE
|
||||
@SuppressWarnings("rawtypes")
|
||||
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
|
||||
res.setId((String) null);
|
||||
DaoMethodOutcome outcome;
|
||||
String matchUrl = nextReqEntry.getRequest().getIfNoneExist();
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
outcome = resourceDao.create(res, matchUrl, false, theRequestDetails);
|
||||
if (nextResourceId != null) {
|
||||
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
|
||||
}
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
if (outcome.getCreated() == false) {
|
||||
nonUpdatedEntities.add(outcome.getEntity());
|
||||
} else {
|
||||
if (isNotBlank(matchUrl)) {
|
||||
conditionalRequestUrls.put(matchUrl, res.getClass());
|
||||
}
|
||||
}
|
||||
|
||||
break;
|
||||
}
|
||||
case DELETE: {
|
||||
// DELETE
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
|
||||
UrlParts parts = UrlUtil.parseUrl(url);
|
||||
ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb.toCode(), url);
|
||||
int status = Constants.STATUS_HTTP_204_NO_CONTENT;
|
||||
if (parts.getResourceId() != null) {
|
||||
IdType deleteId = new IdType(parts.getResourceType(), parts.getResourceId());
|
||||
if (!deletedResources.contains(deleteId.getValueAsString())) {
|
||||
DaoMethodOutcome outcome = dao.delete(deleteId, deleteConflicts, theRequestDetails);
|
||||
if (outcome.getEntity() != null) {
|
||||
deletedResources.add(deleteId.getValueAsString());
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
}
|
||||
}
|
||||
} else {
|
||||
String matchUrl = parts.getResourceType() + '?' + parts.getParams();
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(matchUrl, deleteConflicts, theRequestDetails);
|
||||
List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
|
||||
for (ResourceTable deleted : allDeleted) {
|
||||
deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless().getValueAsString());
|
||||
}
|
||||
if (allDeleted.isEmpty()) {
|
||||
status = Constants.STATUS_HTTP_204_NO_CONTENT;
|
||||
}
|
||||
|
||||
nextRespEntry.getResponse().setOutcome((Resource) deleteOutcome.getOperationOutcome());
|
||||
}
|
||||
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(status));
|
||||
|
||||
break;
|
||||
}
|
||||
case PUT: {
|
||||
// UPDATE
|
||||
@SuppressWarnings("rawtypes")
|
||||
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
|
||||
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
|
||||
|
||||
DaoMethodOutcome outcome;
|
||||
UrlParts parts = UrlUtil.parseUrl(url);
|
||||
if (isNotBlank(parts.getResourceId())) {
|
||||
String version = null;
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
|
||||
version = ParameterUtil.parseETagValue(nextReqEntry.getRequest().getIfMatch());
|
||||
}
|
||||
res.setId(new IdType(parts.getResourceType(), parts.getResourceId(), version));
|
||||
outcome = resourceDao.update(res, null, false, theRequestDetails);
|
||||
} else {
|
||||
res.setId((String) null);
|
||||
String matchUrl;
|
||||
if (isNotBlank(parts.getParams())) {
|
||||
matchUrl = parts.getResourceType() + '?' + parts.getParams();
|
||||
} else {
|
||||
matchUrl = parts.getResourceType();
|
||||
}
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
outcome = resourceDao.update(res, matchUrl, false, theRequestDetails);
|
||||
if (Boolean.TRUE.equals(outcome.getCreated())) {
|
||||
conditionalRequestUrls.put(matchUrl, res.getClass());
|
||||
}
|
||||
}
|
||||
|
||||
if (outcome.getCreated() == Boolean.FALSE) {
|
||||
updatedEntities.add(outcome.getEntity());
|
||||
}
|
||||
|
||||
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
break;
|
||||
}
|
||||
case GET:
|
||||
case NULL:
|
||||
break;
|
||||
|
||||
}
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
}
|
||||
|
||||
/*
|
||||
* Make sure that there are no conflicts from deletions. E.g. we can't delete something
|
||||
* if something else has a reference to it.. Unless the thing that has a reference to it
|
||||
* was also deleted as a part of this transaction, which is why we check this now at the
|
||||
* end.
|
||||
*/
|
||||
|
||||
deleteConflicts.removeIf(next ->
|
||||
deletedResources.contains(next.getTargetId().toUnqualifiedVersionless().getValue()));
|
||||
validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
|
||||
|
||||
/*
|
||||
* Perform ID substitutions and then index each resource we have saved
|
||||
*/
|
||||
|
||||
FhirTerser terser = getContext().newTerser();
|
||||
theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
|
||||
for (DaoMethodOutcome nextOutcome : theIdToPersistedOutcome.values()) {
|
||||
IBaseResource nextResource = nextOutcome.getResource();
|
||||
if (nextResource == null) {
|
||||
continue;
|
||||
}
|
||||
|
||||
// References
|
||||
List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class);
|
||||
for (IBaseReference nextRef : allRefs) {
|
||||
IIdType nextId = nextRef.getReferenceElement();
|
||||
if (!nextId.hasIdPart()) {
|
||||
continue;
|
||||
}
|
||||
if (theIdSubstitutions.containsKey(nextId)) {
|
||||
IdType newId = theIdSubstitutions.get(nextId);
|
||||
ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
|
||||
nextRef.setReference(newId.getValue());
|
||||
} else if (nextId.getValue().startsWith("urn:")) {
|
||||
throw new InvalidRequestException("Unable to satisfy placeholder ID: " + nextId.getValue());
|
||||
} else {
|
||||
ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
|
||||
}
|
||||
}
|
||||
|
||||
// URIs
|
||||
List<UriType> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, UriType.class);
|
||||
for (UriType nextRef : allUris) {
|
||||
if (nextRef instanceof IIdType) {
|
||||
continue; // No substitution on the resource ID itself!
|
||||
}
|
||||
IdType nextUriString = new IdType(nextRef.getValueAsString());
|
||||
if (theIdSubstitutions.containsKey(nextUriString)) {
|
||||
IdType newId = theIdSubstitutions.get(nextUriString);
|
||||
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
|
||||
nextRef.setValue(newId.getValue());
|
||||
} else {
|
||||
ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
|
||||
}
|
||||
}
|
||||
|
||||
IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
|
||||
Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
|
||||
|
||||
if (updatedEntities.contains(nextOutcome.getEntity())) {
|
||||
updateInternal(theRequestDetails, nextResource, true, false, theRequestDetails, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
|
||||
} else if (!nonUpdatedEntities.contains(nextOutcome.getEntity())) {
|
||||
updateEntity(theRequestDetails, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
|
||||
}
|
||||
}
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
theTransactionStopWatch.startTask("Flush writes to database");
|
||||
|
||||
flushJpaSession();
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
if (conditionalRequestUrls.size() > 0) {
|
||||
theTransactionStopWatch.startTask("Check for conflicts in conditional resources");
|
||||
}
|
||||
|
||||
/*
|
||||
* Double check we didn't allow any duplicates we shouldn't have
|
||||
*/
|
||||
for (Entry<String, Class<? extends IBaseResource>> nextEntry : conditionalRequestUrls.entrySet()) {
|
||||
String matchUrl = nextEntry.getKey();
|
||||
Class<? extends IBaseResource> resType = nextEntry.getValue();
|
||||
if (isNotBlank(matchUrl)) {
|
||||
IFhirResourceDao<?> resourceDao = getDao(resType);
|
||||
Set<Long> val = resourceDao.processMatchUrl(matchUrl);
|
||||
if (val.size() > 1) {
|
||||
throw new InvalidRequestException(
|
||||
"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
theTransactionStopWatch.endCurrentTask();
|
||||
|
||||
for (IdType next : theAllIds) {
|
||||
IdType replacement = theIdSubstitutions.get(next);
|
||||
if (replacement == null) {
|
||||
continue;
|
||||
}
|
||||
if (replacement.equals(next)) {
|
||||
continue;
|
||||
}
|
||||
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
|
||||
}
|
||||
return entriesToProcess;
|
||||
}
|
||||
|
||||
private String extractTransactionUrlOrThrowException(BundleEntryComponent nextEntry, HTTPVerb verb) {
|
||||
String url = nextEntry.getRequest().getUrl();
|
||||
if (isBlank(url)) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionMissingUrl", verb.name()));
|
||||
}
|
||||
return url;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method is called for nested bundles (e.g. if we received a transaction with an entry that
|
||||
* was a GET search, this method is called on the bundle for the search result, that will be placed in the
|
||||
* outer bundle). This method applies the _summary and _content parameters to the output of
|
||||
* that bundle.
|
||||
* <p>
|
||||
* TODO: This isn't the most efficient way of doing this.. hopefully we can come up with something better in the future.
|
||||
*/
|
||||
private IBaseResource filterNestedBundle(RequestDetails theRequestDetails, IBaseResource theResource) {
|
||||
IParser p = getContext().newJsonParser();
|
||||
RestfulServerUtils.configureResponseParser(theRequestDetails, p);
|
||||
return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public Meta metaGetOperation(RequestDetails theRequestDetails) {
|
||||
// Notify interceptors
|
||||
|
|
@ -634,60 +58,10 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
|
|||
TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
|
||||
List<TagDefinition> tagDefinitions = q.getResultList();
|
||||
|
||||
Meta retVal = toMeta(tagDefinitions);
|
||||
|
||||
return retVal;
|
||||
return toMeta(tagDefinitions);
|
||||
}
|
||||
|
||||
private String performIdSubstitutionsInMatchUrl(Map<IdType, IdType> theIdSubstitutions, String theMatchUrl) {
|
||||
String matchUrl = theMatchUrl;
|
||||
if (isNotBlank(matchUrl)) {
|
||||
for (Entry<IdType, IdType> nextSubstitutionEntry : theIdSubstitutions.entrySet()) {
|
||||
IdType nextTemporaryId = nextSubstitutionEntry.getKey();
|
||||
IdType nextReplacementId = nextSubstitutionEntry.getValue();
|
||||
String nextTemporaryIdPart = nextTemporaryId.getIdPart();
|
||||
String nextReplacementIdPart = nextReplacementId.getValueAsString();
|
||||
if (nextTemporaryId.isUrn() && nextTemporaryIdPart.length() > IdType.URN_PREFIX.length()) {
|
||||
matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
|
||||
matchUrl = matchUrl.replace(UrlUtil.escapeUrlParam(nextTemporaryIdPart), nextReplacementIdPart);
|
||||
}
|
||||
}
|
||||
}
|
||||
return matchUrl;
|
||||
}
|
||||
|
||||
private void populateEntryWithOperationOutcome(BaseServerResponseException caughtEx, BundleEntryComponent nextEntry) {
|
||||
OperationOutcome oo = new OperationOutcome();
|
||||
oo.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics(caughtEx.getMessage());
|
||||
nextEntry.getResponse().setOutcome(oo);
|
||||
}
|
||||
|
||||
private ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> toDao(UrlParts theParts, String theVerb, String theUrl) {
|
||||
RuntimeResourceDefinition resType;
|
||||
try {
|
||||
resType = getContext().getResourceDefinition(theParts.getResourceType());
|
||||
} catch (DataFormatException e) {
|
||||
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
throw new InvalidRequestException(msg);
|
||||
}
|
||||
IFhirResourceDao<? extends IBaseResource> dao = null;
|
||||
if (resType != null) {
|
||||
dao = getDao(resType.getImplementingClass());
|
||||
}
|
||||
if (dao == null) {
|
||||
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
throw new InvalidRequestException(msg);
|
||||
}
|
||||
|
||||
// if (theParts.getResourceId() == null && theParts.getParams() == null) {
|
||||
// String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
// throw new InvalidRequestException(msg);
|
||||
// }
|
||||
|
||||
return dao;
|
||||
}
|
||||
|
||||
protected Meta toMeta(Collection<TagDefinition> tagDefinitions) {
|
||||
private Meta toMeta(Collection<TagDefinition> tagDefinitions) {
|
||||
Meta retVal = new Meta();
|
||||
for (TagDefinition next : tagDefinitions) {
|
||||
switch (next.getTagType()) {
|
||||
|
|
@ -708,187 +82,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
|
|||
@Transactional(propagation = Propagation.NEVER)
|
||||
@Override
|
||||
public Bundle transaction(RequestDetails theRequestDetails, Bundle theRequest) {
|
||||
if (theRequestDetails != null) {
|
||||
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theRequest, "Bundle", null);
|
||||
notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
|
||||
}
|
||||
|
||||
String actionName = "Transaction";
|
||||
return transaction((ServletRequestDetails) theRequestDetails, theRequest, actionName);
|
||||
return myTransactionProcessor.transaction(theRequestDetails, theRequest);
|
||||
}
|
||||
|
||||
private Bundle transaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
|
||||
super.markRequestAsProcessingSubRequest(theRequestDetails);
|
||||
try {
|
||||
return doTransaction(theRequestDetails, theRequest, theActionName);
|
||||
} finally {
|
||||
super.clearRequestAsProcessingSubRequest(theRequestDetails);
|
||||
}
|
||||
}
|
||||
|
||||
private static void handleTransactionCreateOrUpdateOutcome(Map<IdType, IdType> idSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, IdType nextResourceId, DaoMethodOutcome outcome,
|
||||
BundleEntryComponent newEntry, String theResourceType, IBaseResource theRes, ServletRequestDetails theRequestDetails) {
|
||||
IdType newId = (IdType) outcome.getId().toUnqualifiedVersionless();
|
||||
IdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
|
||||
if (newId.equals(resourceId) == false) {
|
||||
idSubstitutions.put(resourceId, newId);
|
||||
if (isPlaceholder(resourceId)) {
|
||||
/*
|
||||
* The correct way for substitution IDs to be is to be with no resource type, but we'll accept the qualified kind too just to be lenient.
|
||||
*/
|
||||
idSubstitutions.put(new IdType(theResourceType + '/' + resourceId.getValue()), newId);
|
||||
}
|
||||
}
|
||||
idToPersistedOutcome.put(newId, outcome);
|
||||
if (outcome.getCreated().booleanValue()) {
|
||||
newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_201_CREATED));
|
||||
} else {
|
||||
newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
|
||||
}
|
||||
newEntry.getResponse().setLastModified(((Resource) theRes).getMeta().getLastUpdated());
|
||||
|
||||
if (theRequestDetails != null) {
|
||||
if (outcome.getResource() != null) {
|
||||
String prefer = theRequestDetails.getHeader(Constants.HEADER_PREFER);
|
||||
PreferReturnEnum preferReturn = RestfulServerUtils.parsePreferHeader(prefer);
|
||||
if (preferReturn != null) {
|
||||
if (preferReturn == PreferReturnEnum.REPRESENTATION) {
|
||||
newEntry.setResource((Resource) outcome.getResource());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static boolean isPlaceholder(IdType theId) {
|
||||
if (theId != null && theId.getValue() != null) {
|
||||
if (theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:")) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
private static String toStatusString(int theStatusCode) {
|
||||
return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
|
||||
}
|
||||
|
||||
/**
|
||||
* Transaction Order, per the spec:
|
||||
* <p>
|
||||
* Process any DELETE interactions
|
||||
* Process any POST interactions
|
||||
* Process any PUT interactions
|
||||
* Process any GET interactions
|
||||
*/
|
||||
//@formatter:off
|
||||
public class TransactionSorter implements Comparator<BundleEntryComponent> {
|
||||
|
||||
private Set<String> myPlaceholderIds;
|
||||
|
||||
public TransactionSorter(Set<String> thePlaceholderIds) {
|
||||
myPlaceholderIds = thePlaceholderIds;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int compare(BundleEntryComponent theO1, BundleEntryComponent theO2) {
|
||||
int o1 = toOrder(theO1);
|
||||
int o2 = toOrder(theO2);
|
||||
|
||||
if (o1 == o2) {
|
||||
String matchUrl1 = toMatchUrl(theO1);
|
||||
String matchUrl2 = toMatchUrl(theO2);
|
||||
if (isBlank(matchUrl1) && isBlank(matchUrl2)) {
|
||||
return 0;
|
||||
}
|
||||
if (isBlank(matchUrl1)) {
|
||||
return -1;
|
||||
}
|
||||
if (isBlank(matchUrl2)) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
boolean match1containsSubstitutions = false;
|
||||
boolean match2containsSubstitutions = false;
|
||||
for (String nextPlaceholder : myPlaceholderIds) {
|
||||
if (matchUrl1.contains(nextPlaceholder)) {
|
||||
match1containsSubstitutions = true;
|
||||
}
|
||||
if (matchUrl2.contains(nextPlaceholder)) {
|
||||
match2containsSubstitutions = true;
|
||||
}
|
||||
}
|
||||
|
||||
if (match1containsSubstitutions && match2containsSubstitutions) {
|
||||
return 0;
|
||||
}
|
||||
if (!match1containsSubstitutions && !match2containsSubstitutions) {
|
||||
return 0;
|
||||
}
|
||||
if (match1containsSubstitutions) {
|
||||
return 1;
|
||||
} else {
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
return o1 - o2;
|
||||
}
|
||||
|
||||
private String toMatchUrl(BundleEntryComponent theEntry) {
|
||||
HTTPVerb verb = theEntry.getRequest().getMethod();
|
||||
if (verb == HTTPVerb.POST) {
|
||||
return theEntry.getRequest().getIfNoneExist();
|
||||
}
|
||||
if (verb == HTTPVerb.PUT || verb == HTTPVerb.DELETE) {
|
||||
String url = extractTransactionUrlOrThrowException(theEntry, verb);
|
||||
UrlParts parts = UrlUtil.parseUrl(url);
|
||||
if (isBlank(parts.getResourceId())) {
|
||||
return parts.getResourceType() + '?' + parts.getParams();
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
private int toOrder(BundleEntryComponent theO1) {
|
||||
int o1 = 0;
|
||||
if (theO1.getRequest().getMethodElement().getValue() != null) {
|
||||
switch (theO1.getRequest().getMethodElement().getValue()) {
|
||||
case DELETE:
|
||||
o1 = 1;
|
||||
break;
|
||||
case POST:
|
||||
o1 = 2;
|
||||
break;
|
||||
case PUT:
|
||||
o1 = 3;
|
||||
break;
|
||||
case GET:
|
||||
o1 = 4;
|
||||
break;
|
||||
case NULL:
|
||||
o1 = 0;
|
||||
break;
|
||||
}
|
||||
}
|
||||
return o1;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
//@formatter:off
|
||||
|
||||
private static class BaseServerResponseExceptionHolder {
|
||||
private BaseServerResponseException myException;
|
||||
|
||||
public BaseServerResponseException getException() {
|
||||
return myException;
|
||||
}
|
||||
|
||||
public void setException(BaseServerResponseException myException) {
|
||||
this.myException = myException;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,133 @@
|
|||
package ca.uhn.fhir.jpa.dao.dstu3;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
|
||||
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.OperationOutcome;
|
||||
import org.hl7.fhir.dstu3.model.Resource;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
public class TransactionProcessorVersionAdapterDstu3 implements TransactionProcessor.ITransactionProcessorVersionAdapter<Bundle, Bundle.BundleEntryComponent> {
|
||||
@Override
|
||||
public void setResponseStatus(Bundle.BundleEntryComponent theBundleEntry, String theStatus) {
|
||||
theBundleEntry.getResponse().setStatus(theStatus);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseLastModified(Bundle.BundleEntryComponent theBundleEntry, Date theLastModified) {
|
||||
theBundleEntry.getResponse().setLastModified(theLastModified);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResource(Bundle.BundleEntryComponent theBundleEntry, IBaseResource theResource) {
|
||||
theBundleEntry.setResource((Resource) theResource);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IBaseResource getResource(Bundle.BundleEntryComponent theBundleEntry) {
|
||||
return theBundleEntry.getResource();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getBundleType(Bundle theRequest) {
|
||||
if (theRequest.getType() == null) {
|
||||
return null;
|
||||
}
|
||||
return theRequest.getTypeElement().getValue().toCode();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void populateEntryWithOperationOutcome(BaseServerResponseException theCaughtEx, Bundle.BundleEntryComponent theEntry) {
|
||||
OperationOutcome oo = new OperationOutcome();
|
||||
oo.addIssue().setSeverity(OperationOutcome.IssueSeverity.ERROR).setDiagnostics(theCaughtEx.getMessage());
|
||||
theEntry.getResponse().setOutcome(oo);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Bundle createBundle(String theBundleType) {
|
||||
Bundle resp = new Bundle();
|
||||
try {
|
||||
resp.setType(Bundle.BundleType.fromCode(theBundleType));
|
||||
} catch (FHIRException theE) {
|
||||
throw new InternalErrorException("Unknown bundle type: " + theBundleType);
|
||||
}
|
||||
return resp;
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<Bundle.BundleEntryComponent> getEntries(Bundle theRequest) {
|
||||
return theRequest.getEntry();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void addEntry(Bundle theBundle, Bundle.BundleEntryComponent theEntry) {
|
||||
theBundle.addEntry(theEntry);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Bundle.BundleEntryComponent addEntry(Bundle theBundle) {
|
||||
return theBundle.addEntry();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestVerb(Bundle.BundleEntryComponent theEntry) {
|
||||
String retVal = null;
|
||||
Bundle.HTTPVerb value = theEntry.getRequest().getMethodElement().getValue();
|
||||
if (value != null) {
|
||||
retVal = value.toCode();
|
||||
}
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getFullUrl(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getFullUrl();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryIfNoneExist(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfNoneExist();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestUrl(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getUrl();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseLocation(Bundle.BundleEntryComponent theEntry, String theResponseLocation) {
|
||||
theEntry.getResponse().setLocation(theResponseLocation);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseETag(Bundle.BundleEntryComponent theEntry, String theEtag) {
|
||||
theEntry.getResponse().setEtag(theEtag);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestIfMatch(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfMatch();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestIfNoneExist(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfNoneExist();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestIfNoneMatch(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfNoneMatch();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseOutcome(Bundle.BundleEntryComponent theEntry, IBaseOperationOutcome theOperationOutcome) {
|
||||
theEntry.getResponse().setOutcome((Resource) theOperationOutcome);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -143,6 +143,10 @@ public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> i
|
|||
|
||||
translationMatch.setSource(new UriType(element.getConceptMapUrl()));
|
||||
|
||||
if (element.getConceptMapGroupElementTargets().size() == 1) {
|
||||
translationMatch.setEquivalence(new CodeType(element.getConceptMapGroupElementTargets().get(0).getEquivalence().toCode()));
|
||||
}
|
||||
|
||||
retVal.addMatch(translationMatch);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao.r4;
|
|||
* 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.
|
||||
|
|
@ -20,587 +20,34 @@ package ca.uhn.fhir.jpa.dao.r4;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.context.RuntimeResourceDefinition;
|
||||
import ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao;
|
||||
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.DeleteMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
|
||||
import ca.uhn.fhir.jpa.entity.TagDefinition;
|
||||
import ca.uhn.fhir.jpa.provider.ServletSubRequestDetails;
|
||||
import ca.uhn.fhir.jpa.util.DeleteConflict;
|
||||
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
|
||||
import ca.uhn.fhir.parser.DataFormatException;
|
||||
import ca.uhn.fhir.parser.IParser;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
import ca.uhn.fhir.rest.api.PreferReturnEnum;
|
||||
import ca.uhn.fhir.rest.api.RequestTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.param.ParameterUtil;
|
||||
import ca.uhn.fhir.rest.server.RestfulServerUtils;
|
||||
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.NotModifiedException;
|
||||
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
|
||||
import ca.uhn.fhir.rest.server.method.BaseMethodBinding;
|
||||
import ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.FhirTerser;
|
||||
import ca.uhn.fhir.util.UrlUtil;
|
||||
import ca.uhn.fhir.util.UrlUtil.UrlParts;
|
||||
import com.google.common.collect.ArrayListMultimap;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.apache.http.NameValuePair;
|
||||
import org.hl7.fhir.instance.model.api.*;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
|
||||
import org.hl7.fhir.r4.model.Bundle.BundleEntryResponseComponent;
|
||||
import org.hl7.fhir.r4.model.Bundle.BundleType;
|
||||
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
|
||||
import org.hl7.fhir.r4.model.Meta;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.transaction.PlatformTransactionManager;
|
||||
import org.springframework.transaction.TransactionDefinition;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
import org.springframework.transaction.annotation.Propagation;
|
||||
import org.springframework.transaction.annotation.Transactional;
|
||||
import org.springframework.transaction.support.TransactionCallback;
|
||||
import org.springframework.transaction.support.TransactionTemplate;
|
||||
|
||||
import javax.annotation.PostConstruct;
|
||||
import javax.persistence.TypedQuery;
|
||||
import java.util.*;
|
||||
import java.util.Map.Entry;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.*;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
|
||||
public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoR4.class);
|
||||
|
||||
@Autowired
|
||||
private PlatformTransactionManager myTxManager;
|
||||
private TransactionProcessor<Bundle, BundleEntryComponent> myTransactionProcessor;
|
||||
|
||||
private Bundle batch(final RequestDetails theRequestDetails, Bundle theRequest) {
|
||||
ourLog.info("Beginning batch with {} resources", theRequest.getEntry().size());
|
||||
long start = System.currentTimeMillis();
|
||||
|
||||
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
|
||||
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
|
||||
|
||||
Bundle resp = new Bundle();
|
||||
resp.setType(BundleType.BATCHRESPONSE);
|
||||
|
||||
/*
|
||||
* For batch, we handle each entry as a mini-transaction in its own database transaction so that if one fails, it doesn't prevent others
|
||||
*/
|
||||
|
||||
for (final BundleEntryComponent nextRequestEntry : theRequest.getEntry()) {
|
||||
|
||||
BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
|
||||
|
||||
TransactionCallback<Bundle> callback = new TransactionCallback<Bundle>() {
|
||||
@Override
|
||||
public Bundle doInTransaction(TransactionStatus theStatus) {
|
||||
Bundle subRequestBundle = new Bundle();
|
||||
subRequestBundle.setType(BundleType.TRANSACTION);
|
||||
subRequestBundle.addEntry(nextRequestEntry);
|
||||
|
||||
Bundle subResponseBundle = transaction((ServletRequestDetails) theRequestDetails, subRequestBundle, "Batch sub-request");
|
||||
return subResponseBundle;
|
||||
}
|
||||
};
|
||||
|
||||
try {
|
||||
Bundle nextResponseBundle = callback.doInTransaction(null);
|
||||
|
||||
BundleEntryComponent subResponseEntry = nextResponseBundle.getEntry().get(0);
|
||||
resp.addEntry(subResponseEntry);
|
||||
|
||||
/*
|
||||
* If the individual entry didn't have a resource in its response, bring the sub-transaction's OperationOutcome across so the client can see it
|
||||
*/
|
||||
if (subResponseEntry.getResource() == null) {
|
||||
subResponseEntry.setResource(nextResponseBundle.getEntry().get(0).getResource());
|
||||
}
|
||||
|
||||
} catch (BaseServerResponseException e) {
|
||||
caughtEx.setException(e);
|
||||
} catch (Throwable t) {
|
||||
ourLog.error("Failure during BATCH sub transaction processing", t);
|
||||
caughtEx.setException(new InternalErrorException(t));
|
||||
}
|
||||
|
||||
if (caughtEx.getException() != null) {
|
||||
BundleEntryComponent nextEntry = resp.addEntry();
|
||||
|
||||
populateEntryWithOperationOutcome(caughtEx.getException(), nextEntry);
|
||||
|
||||
BundleEntryResponseComponent nextEntryResp = nextEntry.getResponse();
|
||||
nextEntryResp.setStatus(toStatusString(caughtEx.getException().getStatusCode()));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
long delay = System.currentTimeMillis() - start;
|
||||
ourLog.info("Batch completed in {}ms", new Object[] {delay});
|
||||
|
||||
return resp;
|
||||
}
|
||||
|
||||
private Bundle doTransaction(final ServletRequestDetails theRequestDetails, final Bundle theRequest, final String theActionName) {
|
||||
BundleType transactionType = theRequest.getTypeElement().getValue();
|
||||
if (transactionType == BundleType.BATCH) {
|
||||
return batch(theRequestDetails, theRequest);
|
||||
}
|
||||
|
||||
if (transactionType == null) {
|
||||
String message = "Transaction Bundle did not specify valid Bundle.type, assuming " + BundleType.TRANSACTION.toCode();
|
||||
ourLog.warn(message);
|
||||
transactionType = BundleType.TRANSACTION;
|
||||
}
|
||||
if (transactionType != BundleType.TRANSACTION) {
|
||||
throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType.toCode());
|
||||
}
|
||||
|
||||
ourLog.debug("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
|
||||
|
||||
long start = System.currentTimeMillis();
|
||||
final Date updateTime = new Date();
|
||||
|
||||
final Set<IdType> allIds = new LinkedHashSet<>();
|
||||
final Map<IdType, IdType> idSubstitutions = new HashMap<>();
|
||||
final Map<IdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
|
||||
|
||||
// Do all entries have a verb?
|
||||
for (int i = 0; i < theRequest.getEntry().size(); i++) {
|
||||
BundleEntryComponent nextReqEntry = theRequest.getEntry().get(i);
|
||||
HTTPVerb verb = nextReqEntry.getRequest().getMethodElement().getValue();
|
||||
if (verb == null) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionEntryHasInvalidVerb", nextReqEntry.getRequest().getMethod(), i));
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* We want to execute the transaction request bundle elements in the order
|
||||
* specified by the FHIR specification (see TransactionSorter) so we save the
|
||||
* original order in the request, then sort it.
|
||||
*
|
||||
* Entries with a type of GET are removed from the bundle so that they
|
||||
* can be processed at the very end. We do this because the incoming resources
|
||||
* are saved in a two-phase way in order to deal with interdependencies, and
|
||||
* we want the GET processing to use the final indexing state
|
||||
*/
|
||||
final Bundle response = new Bundle();
|
||||
List<BundleEntryComponent> getEntries = new ArrayList<>();
|
||||
final IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder = new IdentityHashMap<>();
|
||||
for (int i = 0; i < theRequest.getEntry().size(); i++) {
|
||||
originalRequestOrder.put(theRequest.getEntry().get(i), i);
|
||||
response.addEntry();
|
||||
if (theRequest.getEntry().get(i).getRequest().getMethodElement().getValue() == HTTPVerb.GET) {
|
||||
getEntries.add(theRequest.getEntry().get(i));
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* See FhirSystemDaoR4Test#testTransactionWithPlaceholderIdInMatchUrl
|
||||
* Basically if the resource has a match URL that references a placeholder,
|
||||
* we try to handle the resource with the placeholder first.
|
||||
*/
|
||||
Set<String> placeholderIds = new HashSet<String>();
|
||||
final List<BundleEntryComponent> entries = theRequest.getEntry();
|
||||
for (BundleEntryComponent nextEntry : entries) {
|
||||
if (isNotBlank(nextEntry.getFullUrl()) && nextEntry.getFullUrl().startsWith(IdType.URN_PREFIX)) {
|
||||
placeholderIds.add(nextEntry.getFullUrl());
|
||||
}
|
||||
}
|
||||
Collections.sort(entries, new TransactionSorter(placeholderIds));
|
||||
|
||||
/*
|
||||
* All of the write operations in the transaction (PUT, POST, etc.. basically anything
|
||||
* except GET) are performed in their own database transaction before we do the reads.
|
||||
* We do this because the reads (specifically the searches) often spawn their own
|
||||
* secondary database transaction and if we allow that within the primary
|
||||
* database transaction we can end up with deadlocks if the server is under
|
||||
* heavy load with lots of concurrent transactions using all available
|
||||
* database connections.
|
||||
*/
|
||||
TransactionTemplate txManager = new TransactionTemplate(myTxManager);
|
||||
Map<BundleEntryComponent, ResourceTable> entriesToProcess = txManager.execute(new TransactionCallback<Map<BundleEntryComponent, ResourceTable>>() {
|
||||
@Override
|
||||
public Map<BundleEntryComponent, ResourceTable> doInTransaction(TransactionStatus status) {
|
||||
return doTransactionWriteOperations(theRequestDetails, theRequest, theActionName, updateTime, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder, entries);
|
||||
}
|
||||
});
|
||||
for (Entry<BundleEntryComponent, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
|
||||
String responseLocation = nextEntry.getValue().getIdDt().toUnqualified().getValue();
|
||||
String responseEtag = nextEntry.getValue().getIdDt().getVersionIdPart();
|
||||
nextEntry.getKey().getResponse().setLocation(responseLocation);
|
||||
nextEntry.getKey().getResponse().setEtag(responseEtag);
|
||||
}
|
||||
|
||||
/*
|
||||
* Loop through the request and process any entries of type GET
|
||||
*/
|
||||
for (int i = 0; i < getEntries.size(); i++) {
|
||||
BundleEntryComponent nextReqEntry = getEntries.get(i);
|
||||
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
|
||||
BundleEntryComponent nextRespEntry = response.getEntry().get(originalOrder);
|
||||
|
||||
ServletSubRequestDetails requestDetails = new ServletSubRequestDetails();
|
||||
requestDetails.setServletRequest(theRequestDetails.getServletRequest());
|
||||
requestDetails.setRequestType(RequestTypeEnum.GET);
|
||||
requestDetails.setServer(theRequestDetails.getServer());
|
||||
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, HTTPVerb.GET);
|
||||
|
||||
int qIndex = url.indexOf('?');
|
||||
ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
|
||||
requestDetails.setParameters(new HashMap<String, String[]>());
|
||||
if (qIndex != -1) {
|
||||
String params = url.substring(qIndex);
|
||||
List<NameValuePair> parameters = translateMatchUrl(params);
|
||||
for (NameValuePair next : parameters) {
|
||||
paramValues.put(next.getName(), next.getValue());
|
||||
}
|
||||
for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
|
||||
String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
|
||||
requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
|
||||
}
|
||||
url = url.substring(0, qIndex);
|
||||
}
|
||||
|
||||
requestDetails.setRequestPath(url);
|
||||
requestDetails.setFhirServerBase(theRequestDetails.getFhirServerBase());
|
||||
|
||||
theRequestDetails.getServer().populateRequestDetailsFromRequestPath(requestDetails, url);
|
||||
BaseMethodBinding<?> method = theRequestDetails.getServer().determineResourceMethod(requestDetails, url);
|
||||
if (method == null) {
|
||||
throw new IllegalArgumentException("Unable to handle GET " + url);
|
||||
}
|
||||
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_MATCH, nextReqEntry.getRequest().getIfMatch());
|
||||
}
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfNoneExist())) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_NONE_EXIST, nextReqEntry.getRequest().getIfNoneExist());
|
||||
}
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfNoneMatch())) {
|
||||
requestDetails.addHeader(Constants.HEADER_IF_NONE_MATCH, nextReqEntry.getRequest().getIfNoneMatch());
|
||||
}
|
||||
|
||||
Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {0}", url);
|
||||
try {
|
||||
IBaseResource resource = ((BaseResourceReturningMethodBinding) method).doInvokeServer(theRequestDetails.getServer(), requestDetails);
|
||||
if (paramValues.containsKey(Constants.PARAM_SUMMARY) || paramValues.containsKey(Constants.PARAM_CONTENT)) {
|
||||
resource = filterNestedBundle(requestDetails, resource);
|
||||
}
|
||||
nextRespEntry.setResource((Resource) resource);
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
|
||||
} catch (NotModifiedException e) {
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_304_NOT_MODIFIED));
|
||||
} catch (BaseServerResponseException e) {
|
||||
ourLog.info("Failure processing transaction GET {}: {}", url, e.toString());
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(e.getStatusCode()));
|
||||
populateEntryWithOperationOutcome(e, nextRespEntry);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
long delay = System.currentTimeMillis() - start;
|
||||
ourLog.info(theActionName + " completed in {}ms", new Object[] {delay});
|
||||
|
||||
response.setType(BundleType.TRANSACTIONRESPONSE);
|
||||
return response;
|
||||
}
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
private Map<BundleEntryComponent, ResourceTable> doTransactionWriteOperations(RequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date theUpdateTime, Set<IdType> theAllIds,
|
||||
Map<IdType, IdType> theIdSubstitutions, Map<IdType, DaoMethodOutcome> theIdToPersistedOutcome, Bundle theResponse, IdentityHashMap<BundleEntryComponent, Integer> theOriginalRequestOrder, List<BundleEntryComponent> theEntries) {
|
||||
Set<String> deletedResources = new HashSet<>();
|
||||
List<DeleteConflict> deleteConflicts = new ArrayList<>();
|
||||
Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<>();
|
||||
Set<ResourceTable> nonUpdatedEntities = new HashSet<>();
|
||||
Set<ResourceTable> updatedEntities = new HashSet<>();
|
||||
Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
|
||||
|
||||
/*
|
||||
* Loop through the request and process any entries of type
|
||||
* PUT, POST or DELETE
|
||||
*/
|
||||
for (int i = 0; i < theEntries.size(); i++) {
|
||||
|
||||
if (i % 100 == 0) {
|
||||
ourLog.debug("Processed {} non-GET entries out of {}", i, theEntries.size());
|
||||
}
|
||||
|
||||
BundleEntryComponent nextReqEntry = theEntries.get(i);
|
||||
Resource res = nextReqEntry.getResource();
|
||||
IdType nextResourceId = null;
|
||||
if (res != null) {
|
||||
|
||||
nextResourceId = res.getIdElement();
|
||||
|
||||
if (!nextResourceId.hasIdPart()) {
|
||||
if (isNotBlank(nextReqEntry.getFullUrl())) {
|
||||
nextResourceId = new IdType(nextReqEntry.getFullUrl());
|
||||
}
|
||||
}
|
||||
|
||||
if (nextResourceId.hasIdPart() && nextResourceId.getIdPart().matches("[a-zA-Z]+\\:.*") && !isPlaceholder(nextResourceId)) {
|
||||
throw new InvalidRequestException("Invalid placeholder ID found: " + nextResourceId.getIdPart() + " - Must be of the form 'urn:uuid:[uuid]' or 'urn:oid:[oid]'");
|
||||
}
|
||||
|
||||
if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
|
||||
nextResourceId = new IdType(toResourceName(res.getClass()), nextResourceId.getIdPart());
|
||||
res.setId(nextResourceId);
|
||||
}
|
||||
|
||||
/*
|
||||
* Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
|
||||
*/
|
||||
if (isPlaceholder(nextResourceId)) {
|
||||
if (!theAllIds.add(nextResourceId)) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextResourceId));
|
||||
}
|
||||
} else if (nextResourceId.hasResourceType() && nextResourceId.hasIdPart()) {
|
||||
IdType nextId = nextResourceId.toUnqualifiedVersionless();
|
||||
if (!theAllIds.add(nextId)) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionContainsMultipleWithDuplicateId", nextId));
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
HTTPVerb verb = nextReqEntry.getRequest().getMethodElement().getValue();
|
||||
|
||||
String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
|
||||
BundleEntryComponent nextRespEntry = theResponse.getEntry().get(theOriginalRequestOrder.get(nextReqEntry));
|
||||
|
||||
switch (verb) {
|
||||
case POST: {
|
||||
// CREATE
|
||||
@SuppressWarnings("rawtypes")
|
||||
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
|
||||
res.setId((String) null);
|
||||
DaoMethodOutcome outcome;
|
||||
String matchUrl = nextReqEntry.getRequest().getIfNoneExist();
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
outcome = resourceDao.create(res, matchUrl, false, theRequestDetails);
|
||||
if (nextResourceId != null) {
|
||||
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
|
||||
}
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
if (outcome.getCreated() == false) {
|
||||
nonUpdatedEntities.add(outcome.getEntity());
|
||||
} else {
|
||||
if (isNotBlank(matchUrl)) {
|
||||
conditionalRequestUrls.put(matchUrl, res.getClass());
|
||||
}
|
||||
}
|
||||
|
||||
break;
|
||||
}
|
||||
case DELETE: {
|
||||
// DELETE
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
|
||||
UrlParts parts = UrlUtil.parseUrl(url);
|
||||
ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> dao = toDao(parts, verb.toCode(), url);
|
||||
int status = Constants.STATUS_HTTP_204_NO_CONTENT;
|
||||
if (parts.getResourceId() != null) {
|
||||
IdType deleteId = new IdType(parts.getResourceType(), parts.getResourceId());
|
||||
if (!deletedResources.contains(deleteId.getValueAsString())) {
|
||||
DaoMethodOutcome outcome = dao.delete(deleteId, deleteConflicts, theRequestDetails);
|
||||
if (outcome.getEntity() != null) {
|
||||
deletedResources.add(deleteId.getValueAsString());
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
}
|
||||
}
|
||||
} else {
|
||||
String matchUrl = parts.getResourceType() + '?' + parts.getParams();
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
DeleteMethodOutcome deleteOutcome = dao.deleteByUrl(matchUrl, deleteConflicts, theRequestDetails);
|
||||
List<ResourceTable> allDeleted = deleteOutcome.getDeletedEntities();
|
||||
for (ResourceTable deleted : allDeleted) {
|
||||
deletedResources.add(deleted.getIdDt().toUnqualifiedVersionless().getValueAsString());
|
||||
}
|
||||
if (allDeleted.isEmpty()) {
|
||||
status = Constants.STATUS_HTTP_204_NO_CONTENT;
|
||||
}
|
||||
|
||||
nextRespEntry.getResponse().setOutcome((Resource) deleteOutcome.getOperationOutcome());
|
||||
}
|
||||
|
||||
nextRespEntry.getResponse().setStatus(toStatusString(status));
|
||||
|
||||
break;
|
||||
}
|
||||
case PUT: {
|
||||
// UPDATE
|
||||
@SuppressWarnings("rawtypes")
|
||||
IFhirResourceDao resourceDao = getDaoOrThrowException(res.getClass());
|
||||
|
||||
String url = extractTransactionUrlOrThrowException(nextReqEntry, verb);
|
||||
|
||||
DaoMethodOutcome outcome;
|
||||
UrlParts parts = UrlUtil.parseUrl(url);
|
||||
if (isNotBlank(parts.getResourceId())) {
|
||||
String version = null;
|
||||
if (isNotBlank(nextReqEntry.getRequest().getIfMatch())) {
|
||||
version = ParameterUtil.parseETagValue(nextReqEntry.getRequest().getIfMatch());
|
||||
}
|
||||
res.setId(new IdType(parts.getResourceType(), parts.getResourceId(), version));
|
||||
outcome = resourceDao.update(res, null, false, theRequestDetails);
|
||||
} else {
|
||||
res.setId((String) null);
|
||||
String matchUrl;
|
||||
if (isNotBlank(parts.getParams())) {
|
||||
matchUrl = parts.getResourceType() + '?' + parts.getParams();
|
||||
} else {
|
||||
matchUrl = parts.getResourceType();
|
||||
}
|
||||
matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
|
||||
outcome = resourceDao.update(res, matchUrl, false, theRequestDetails);
|
||||
if (Boolean.TRUE.equals(outcome.getCreated())) {
|
||||
conditionalRequestUrls.put(matchUrl, res.getClass());
|
||||
}
|
||||
}
|
||||
|
||||
if (outcome.getCreated() == Boolean.FALSE) {
|
||||
updatedEntities.add(outcome.getEntity());
|
||||
}
|
||||
|
||||
handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequestDetails);
|
||||
entriesToProcess.put(nextRespEntry, outcome.getEntity());
|
||||
break;
|
||||
}
|
||||
case GET:
|
||||
case NULL:
|
||||
case HEAD:
|
||||
case PATCH:
|
||||
break;
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* Make sure that there are no conflicts from deletions. E.g. we can't delete something
|
||||
* if something else has a reference to it.. Unless the thing that has a reference to it
|
||||
* was also deleted as a part of this transaction, which is why we check this now at the
|
||||
* end.
|
||||
*/
|
||||
|
||||
deleteConflicts.removeIf(next ->
|
||||
deletedResources.contains(next.getTargetId().toUnqualifiedVersionless().getValue()));
|
||||
validateDeleteConflictsEmptyOrThrowException(deleteConflicts);
|
||||
|
||||
/*
|
||||
* Perform ID substitutions and then index each resource we have saved
|
||||
*/
|
||||
|
||||
FhirTerser terser = getContext().newTerser();
|
||||
for (DaoMethodOutcome nextOutcome : theIdToPersistedOutcome.values()) {
|
||||
IBaseResource nextResource = nextOutcome.getResource();
|
||||
if (nextResource == null) {
|
||||
continue;
|
||||
}
|
||||
|
||||
// References
|
||||
List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(nextResource, IBaseReference.class);
|
||||
for (IBaseReference nextRef : allRefs) {
|
||||
IIdType nextId = nextRef.getReferenceElement();
|
||||
if (!nextId.hasIdPart()) {
|
||||
continue;
|
||||
}
|
||||
if (theIdSubstitutions.containsKey(nextId)) {
|
||||
IdType newId = theIdSubstitutions.get(nextId);
|
||||
ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
|
||||
nextRef.setReference(newId.getValue());
|
||||
} else if (nextId.getValue().startsWith("urn:")) {
|
||||
throw new InvalidRequestException("Unable to satisfy placeholder ID: " + nextId.getValue());
|
||||
} else {
|
||||
ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
|
||||
}
|
||||
}
|
||||
|
||||
// URIs
|
||||
List<UriType> allUris = terser.getAllPopulatedChildElementsOfType(nextResource, UriType.class);
|
||||
for (UriType nextRef : allUris) {
|
||||
if (nextRef instanceof IIdType) {
|
||||
continue; // No substitution on the resource ID itself!
|
||||
}
|
||||
IdType nextUriString = new IdType(nextRef.getValueAsString());
|
||||
if (theIdSubstitutions.containsKey(nextUriString)) {
|
||||
IdType newId = theIdSubstitutions.get(nextUriString);
|
||||
ourLog.debug(" * Replacing resource ref {} with {}", nextUriString, newId);
|
||||
nextRef.setValue(newId.getValue());
|
||||
} else {
|
||||
ourLog.debug(" * Reference [{}] does not exist in bundle", nextUriString);
|
||||
}
|
||||
}
|
||||
|
||||
IPrimitiveType<Date> deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get((IAnyResource) nextResource);
|
||||
Date deletedTimestampOrNull = deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
|
||||
|
||||
if (updatedEntities.contains(nextOutcome.getEntity())) {
|
||||
updateInternal(theRequestDetails, nextResource, true, false, theRequestDetails, nextOutcome.getEntity(), nextResource.getIdElement(), nextOutcome.getPreviousResource());
|
||||
} else if (!nonUpdatedEntities.contains(nextOutcome.getEntity())) {
|
||||
updateEntity(theRequestDetails, nextResource, nextOutcome.getEntity(), deletedTimestampOrNull, true, false, theUpdateTime, false, true);
|
||||
}
|
||||
}
|
||||
|
||||
flushJpaSession();
|
||||
|
||||
/*
|
||||
* Double check we didn't allow any duplicates we shouldn't have
|
||||
*/
|
||||
for (Entry<String, Class<? extends IBaseResource>> nextEntry : conditionalRequestUrls.entrySet()) {
|
||||
String matchUrl = nextEntry.getKey();
|
||||
Class<? extends IBaseResource> resType = nextEntry.getValue();
|
||||
if (isNotBlank(matchUrl)) {
|
||||
IFhirResourceDao<?> resourceDao = getDao(resType);
|
||||
Set<Long> val = resourceDao.processMatchUrl(matchUrl);
|
||||
if (val.size() > 1) {
|
||||
throw new InvalidRequestException(
|
||||
"Unable to process " + theActionName + " - Request would cause multiple resources to match URL: \"" + matchUrl + "\". Does transaction request contain duplicates?");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (IdType next : theAllIds) {
|
||||
IdType replacement = theIdSubstitutions.get(next);
|
||||
if (replacement == null) {
|
||||
continue;
|
||||
}
|
||||
if (replacement.equals(next)) {
|
||||
continue;
|
||||
}
|
||||
ourLog.debug("Placeholder resource ID \"{}\" was replaced with permanent ID \"{}\"", next, replacement);
|
||||
}
|
||||
return entriesToProcess;
|
||||
}
|
||||
|
||||
private String extractTransactionUrlOrThrowException(BundleEntryComponent nextEntry, HTTPVerb verb) {
|
||||
String url = nextEntry.getRequest().getUrl();
|
||||
if (isBlank(url)) {
|
||||
throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionMissingUrl", verb.name()));
|
||||
}
|
||||
return url;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method is called for nested bundles (e.g. if we received a transaction with an entry that
|
||||
* was a GET search, this method is called on the bundle for the search result, that will be placed in the
|
||||
* outer bundle). This method applies the _summary and _content parameters to the output of
|
||||
* that bundle.
|
||||
* <p>
|
||||
* TODO: This isn't the most efficient way of doing this.. hopefully we can come up with something better in the future.
|
||||
*/
|
||||
private IBaseResource filterNestedBundle(RequestDetails theRequestDetails, IBaseResource theResource) {
|
||||
IParser p = getContext().newJsonParser();
|
||||
RestfulServerUtils.configureResponseParser(theRequestDetails, p);
|
||||
return p.parseResource(theResource.getClass(), p.encodeResourceToString(theResource));
|
||||
@PostConstruct
|
||||
public void start() {
|
||||
myTransactionProcessor.setDao(this);
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -617,53 +64,6 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
|
|||
return toMeta(tagDefinitions);
|
||||
}
|
||||
|
||||
private String performIdSubstitutionsInMatchUrl(Map<IdType, IdType> theIdSubstitutions, String theMatchUrl) {
|
||||
String matchUrl = theMatchUrl;
|
||||
if (isNotBlank(matchUrl)) {
|
||||
for (Entry<IdType, IdType> nextSubstitutionEntry : theIdSubstitutions.entrySet()) {
|
||||
IdType nextTemporaryId = nextSubstitutionEntry.getKey();
|
||||
IdType nextReplacementId = nextSubstitutionEntry.getValue();
|
||||
String nextTemporaryIdPart = nextTemporaryId.getIdPart();
|
||||
String nextReplacementIdPart = nextReplacementId.getValueAsString();
|
||||
if (nextTemporaryId.isUrn() && nextTemporaryIdPart.length() > IdType.URN_PREFIX.length()) {
|
||||
matchUrl = matchUrl.replace(nextTemporaryIdPart, nextReplacementIdPart);
|
||||
matchUrl = matchUrl.replace(UrlUtil.escapeUrlParam(nextTemporaryIdPart), nextReplacementIdPart);
|
||||
}
|
||||
}
|
||||
}
|
||||
return matchUrl;
|
||||
}
|
||||
|
||||
private void populateEntryWithOperationOutcome(BaseServerResponseException caughtEx, BundleEntryComponent nextEntry) {
|
||||
OperationOutcome oo = new OperationOutcome();
|
||||
oo.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics(caughtEx.getMessage());
|
||||
nextEntry.getResponse().setOutcome(oo);
|
||||
}
|
||||
|
||||
private ca.uhn.fhir.jpa.dao.IFhirResourceDao<? extends IBaseResource> toDao(UrlParts theParts, String theVerb, String theUrl) {
|
||||
RuntimeResourceDefinition resType;
|
||||
try {
|
||||
resType = getContext().getResourceDefinition(theParts.getResourceType());
|
||||
} catch (DataFormatException e) {
|
||||
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
throw new InvalidRequestException(msg);
|
||||
}
|
||||
IFhirResourceDao<? extends IBaseResource> dao = null;
|
||||
if (resType != null) {
|
||||
dao = getDao(resType.getImplementingClass());
|
||||
}
|
||||
if (dao == null) {
|
||||
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
throw new InvalidRequestException(msg);
|
||||
}
|
||||
|
||||
// if (theParts.getResourceId() == null && theParts.getParams() == null) {
|
||||
// String msg = getContext().getLocalizer().getMessage(BaseHapiFhirSystemDao.class, "transactionInvalidUrl", theVerb, theUrl);
|
||||
// throw new InvalidRequestException(msg);
|
||||
// }
|
||||
|
||||
return dao;
|
||||
}
|
||||
|
||||
protected Meta toMeta(Collection<TagDefinition> tagDefinitions) {
|
||||
Meta retVal = new Meta();
|
||||
|
|
@ -686,193 +86,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
|
|||
@Transactional(propagation = Propagation.NEVER)
|
||||
@Override
|
||||
public Bundle transaction(RequestDetails theRequestDetails, Bundle theRequest) {
|
||||
if (theRequestDetails != null) {
|
||||
ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, theRequest, "Bundle", null);
|
||||
notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
|
||||
}
|
||||
|
||||
String actionName = "Transaction";
|
||||
return transaction((ServletRequestDetails) theRequestDetails, theRequest, actionName);
|
||||
}
|
||||
|
||||
private Bundle transaction(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName) {
|
||||
super.markRequestAsProcessingSubRequest(theRequestDetails);
|
||||
try {
|
||||
return doTransaction(theRequestDetails, theRequest, theActionName);
|
||||
} finally {
|
||||
super.clearRequestAsProcessingSubRequest(theRequestDetails);
|
||||
}
|
||||
}
|
||||
|
||||
private static void handleTransactionCreateOrUpdateOutcome(Map<IdType, IdType> idSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, IdType nextResourceId, DaoMethodOutcome outcome,
|
||||
BundleEntryComponent newEntry, String theResourceType, IBaseResource theRes, RequestDetails theRequestDetails) {
|
||||
IdType newId = (IdType) outcome.getId().toUnqualifiedVersionless();
|
||||
IdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
|
||||
if (newId.equals(resourceId) == false) {
|
||||
idSubstitutions.put(resourceId, newId);
|
||||
if (isPlaceholder(resourceId)) {
|
||||
/*
|
||||
* The correct way for substitution IDs to be is to be with no resource type, but we'll accept the qualified kind too just to be lenient.
|
||||
*/
|
||||
idSubstitutions.put(new IdType(theResourceType + '/' + resourceId.getValue()), newId);
|
||||
}
|
||||
}
|
||||
idToPersistedOutcome.put(newId, outcome);
|
||||
if (outcome.getCreated().booleanValue()) {
|
||||
newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_201_CREATED));
|
||||
} else {
|
||||
newEntry.getResponse().setStatus(toStatusString(Constants.STATUS_HTTP_200_OK));
|
||||
}
|
||||
newEntry.getResponse().setLastModified(((Resource) theRes).getMeta().getLastUpdated());
|
||||
|
||||
if (theRequestDetails != null) {
|
||||
if (outcome.getResource() != null) {
|
||||
String prefer = theRequestDetails.getHeader(Constants.HEADER_PREFER);
|
||||
PreferReturnEnum preferReturn = RestfulServerUtils.parsePreferHeader(prefer);
|
||||
if (preferReturn != null) {
|
||||
if (preferReturn == PreferReturnEnum.REPRESENTATION) {
|
||||
newEntry.setResource((Resource) outcome.getResource());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static boolean isPlaceholder(IdType theId) {
|
||||
if (theId != null && theId.getValue() != null) {
|
||||
if (theId.getValue().startsWith("urn:oid:") || theId.getValue().startsWith("urn:uuid:")) {
|
||||
return true;
|
||||
}
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
private static String toStatusString(int theStatusCode) {
|
||||
return Integer.toString(theStatusCode) + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
|
||||
}
|
||||
|
||||
/**
|
||||
* Transaction Order, per the spec:
|
||||
* <p>
|
||||
* Process any DELETE interactions
|
||||
* Process any POST interactions
|
||||
* Process any PUT interactions
|
||||
* Process any GET interactions
|
||||
*/
|
||||
//@formatter:off
|
||||
public class TransactionSorter implements Comparator<BundleEntryComponent> {
|
||||
|
||||
private Set<String> myPlaceholderIds;
|
||||
|
||||
public TransactionSorter(Set<String> thePlaceholderIds) {
|
||||
myPlaceholderIds = thePlaceholderIds;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int compare(BundleEntryComponent theO1, BundleEntryComponent theO2) {
|
||||
int o1 = toOrder(theO1);
|
||||
int o2 = toOrder(theO2);
|
||||
|
||||
if (o1 == o2) {
|
||||
String matchUrl1 = toMatchUrl(theO1);
|
||||
String matchUrl2 = toMatchUrl(theO2);
|
||||
if (isBlank(matchUrl1) && isBlank(matchUrl2)) {
|
||||
return 0;
|
||||
}
|
||||
if (isBlank(matchUrl1)) {
|
||||
return -1;
|
||||
}
|
||||
if (isBlank(matchUrl2)) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
boolean match1containsSubstitutions = false;
|
||||
boolean match2containsSubstitutions = false;
|
||||
for (String nextPlaceholder : myPlaceholderIds) {
|
||||
if (matchUrl1.contains(nextPlaceholder)) {
|
||||
match1containsSubstitutions = true;
|
||||
}
|
||||
if (matchUrl2.contains(nextPlaceholder)) {
|
||||
match2containsSubstitutions = true;
|
||||
}
|
||||
}
|
||||
|
||||
if (match1containsSubstitutions && match2containsSubstitutions) {
|
||||
return 0;
|
||||
}
|
||||
if (!match1containsSubstitutions && !match2containsSubstitutions) {
|
||||
return 0;
|
||||
}
|
||||
if (match1containsSubstitutions) {
|
||||
return 1;
|
||||
} else {
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
return o1 - o2;
|
||||
}
|
||||
|
||||
private String toMatchUrl(BundleEntryComponent theEntry) {
|
||||
HTTPVerb verb = theEntry.getRequest().getMethod();
|
||||
if (verb == HTTPVerb.POST) {
|
||||
return theEntry.getRequest().getIfNoneExist();
|
||||
}
|
||||
if (verb == HTTPVerb.PUT || verb == HTTPVerb.DELETE) {
|
||||
String url = extractTransactionUrlOrThrowException(theEntry, verb);
|
||||
UrlParts parts = UrlUtil.parseUrl(url);
|
||||
if (isBlank(parts.getResourceId())) {
|
||||
return parts.getResourceType() + '?' + parts.getParams();
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
private int toOrder(BundleEntryComponent theO1) {
|
||||
int o1 = 0;
|
||||
if (theO1.getRequest().getMethodElement().getValue() != null) {
|
||||
switch (theO1.getRequest().getMethodElement().getValue()) {
|
||||
case DELETE:
|
||||
o1 = 1;
|
||||
break;
|
||||
case POST:
|
||||
o1 = 2;
|
||||
break;
|
||||
case PUT:
|
||||
o1 = 3;
|
||||
break;
|
||||
case PATCH:
|
||||
o1 = 4;
|
||||
break;
|
||||
case HEAD:
|
||||
o1 = 5;
|
||||
break;
|
||||
case GET:
|
||||
o1 = 6;
|
||||
break;
|
||||
case NULL:
|
||||
o1 = 0;
|
||||
break;
|
||||
}
|
||||
}
|
||||
return o1;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
//@formatter:off
|
||||
|
||||
private static class BaseServerResponseExceptionHolder {
|
||||
private BaseServerResponseException myException;
|
||||
|
||||
public BaseServerResponseException getException() {
|
||||
return myException;
|
||||
}
|
||||
|
||||
public void setException(BaseServerResponseException myException) {
|
||||
this.myException = myException;
|
||||
}
|
||||
return myTransactionProcessor.transaction(theRequestDetails, theRequest);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,133 @@
|
|||
package ca.uhn.fhir.jpa.dao.r4;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
|
||||
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.model.OperationOutcome;
|
||||
import org.hl7.fhir.r4.model.Resource;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
public class TransactionProcessorVersionAdapterR4 implements TransactionProcessor.ITransactionProcessorVersionAdapter<Bundle, Bundle.BundleEntryComponent> {
|
||||
@Override
|
||||
public void setResponseStatus(Bundle.BundleEntryComponent theBundleEntry, String theStatus) {
|
||||
theBundleEntry.getResponse().setStatus(theStatus);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseLastModified(Bundle.BundleEntryComponent theBundleEntry, Date theLastModified) {
|
||||
theBundleEntry.getResponse().setLastModified(theLastModified);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResource(Bundle.BundleEntryComponent theBundleEntry, IBaseResource theResource) {
|
||||
theBundleEntry.setResource((Resource) theResource);
|
||||
}
|
||||
|
||||
@Override
|
||||
public IBaseResource getResource(Bundle.BundleEntryComponent theBundleEntry) {
|
||||
return theBundleEntry.getResource();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getBundleType(Bundle theRequest) {
|
||||
if (theRequest.getType() == null) {
|
||||
return null;
|
||||
}
|
||||
return theRequest.getTypeElement().getValue().toCode();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void populateEntryWithOperationOutcome(BaseServerResponseException theCaughtEx, Bundle.BundleEntryComponent theEntry) {
|
||||
OperationOutcome oo = new OperationOutcome();
|
||||
oo.addIssue().setSeverity(OperationOutcome.IssueSeverity.ERROR).setDiagnostics(theCaughtEx.getMessage());
|
||||
theEntry.getResponse().setOutcome(oo);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Bundle createBundle(String theBundleType) {
|
||||
Bundle resp = new Bundle();
|
||||
try {
|
||||
resp.setType(Bundle.BundleType.fromCode(theBundleType));
|
||||
} catch (FHIRException theE) {
|
||||
throw new InternalErrorException("Unknown bundle type: " + theBundleType);
|
||||
}
|
||||
return resp;
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<Bundle.BundleEntryComponent> getEntries(Bundle theRequest) {
|
||||
return theRequest.getEntry();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void addEntry(Bundle theBundle, Bundle.BundleEntryComponent theEntry) {
|
||||
theBundle.addEntry(theEntry);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Bundle.BundleEntryComponent addEntry(Bundle theBundle) {
|
||||
return theBundle.addEntry();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestVerb(Bundle.BundleEntryComponent theEntry) {
|
||||
String retVal = null;
|
||||
Bundle.HTTPVerb value = theEntry.getRequest().getMethodElement().getValue();
|
||||
if (value != null) {
|
||||
retVal = value.toCode();
|
||||
}
|
||||
return retVal;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getFullUrl(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getFullUrl();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryIfNoneExist(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfNoneExist();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestUrl(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getUrl();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseLocation(Bundle.BundleEntryComponent theEntry, String theResponseLocation) {
|
||||
theEntry.getResponse().setLocation(theResponseLocation);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseETag(Bundle.BundleEntryComponent theEntry, String theEtag) {
|
||||
theEntry.getResponse().setEtag(theEtag);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestIfMatch(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfMatch();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestIfNoneExist(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfNoneExist();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getEntryRequestIfNoneMatch(Bundle.BundleEntryComponent theEntry) {
|
||||
return theEntry.getRequest().getIfNoneMatch();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void setResponseOutcome(Bundle.BundleEntryComponent theEntry, IBaseOperationOutcome theOperationOutcome) {
|
||||
theEntry.getResponse().setOutcome((Resource) theOperationOutcome);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1343,14 +1343,18 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
predicates = new ArrayList<>();
|
||||
|
||||
coding = translationQuery.getCoding();
|
||||
String targetCode = null;
|
||||
String targetCodeSystem = null;
|
||||
if (coding.hasCode()) {
|
||||
predicates.add(criteriaBuilder.equal(targetJoin.get("myCode"), coding.getCode()));
|
||||
targetCode = coding.getCode();
|
||||
} else {
|
||||
throw new InvalidRequestException("A code must be provided for translation to occur.");
|
||||
}
|
||||
|
||||
if (coding.hasSystem()) {
|
||||
predicates.add(criteriaBuilder.equal(groupJoin.get("myTarget"), coding.getSystem()));
|
||||
targetCodeSystem = coding.getSystem();
|
||||
}
|
||||
|
||||
if (coding.hasVersion()) {
|
||||
|
|
@ -1384,7 +1388,24 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
Iterator<TermConceptMapGroupElement> scrollableResultsIterator = new ScrollableResultsIterator<>(scrollableResults);
|
||||
|
||||
while (scrollableResultsIterator.hasNext()) {
|
||||
elements.add(scrollableResultsIterator.next());
|
||||
TermConceptMapGroupElement nextElement = scrollableResultsIterator.next();
|
||||
nextElement.getConceptMapGroupElementTargets().size();
|
||||
myEntityManager.detach(nextElement);
|
||||
|
||||
if (isNotBlank(targetCode) && isNotBlank(targetCodeSystem)) {
|
||||
for (Iterator<TermConceptMapGroupElementTarget> iter = nextElement.getConceptMapGroupElementTargets().iterator(); iter.hasNext(); ) {
|
||||
TermConceptMapGroupElementTarget next = iter.next();
|
||||
if (targetCodeSystem.equals(next.getSystem())) {
|
||||
if (targetCode.equals(next.getCode())) {
|
||||
continue;
|
||||
}
|
||||
}
|
||||
|
||||
iter.remove();
|
||||
}
|
||||
}
|
||||
|
||||
elements.add(nextElement);
|
||||
}
|
||||
|
||||
ourLastResultsFromTranslationWithReverseCache = false; // For testing.
|
||||
|
|
|
|||
|
|
@ -395,6 +395,12 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
|
|||
target.setDisplay("Target Code 45678");
|
||||
target.setEquivalence(ConceptMapEquivalence.WIDER);
|
||||
|
||||
// Add a duplicate
|
||||
target = element.addTarget();
|
||||
target.setCode("45678");
|
||||
target.setDisplay("Target Code 45678");
|
||||
target.setEquivalence(ConceptMapEquivalence.WIDER);
|
||||
|
||||
group = conceptMap.addGroup();
|
||||
group.setSource(CS_URL);
|
||||
group.setSourceVersion("Version 3");
|
||||
|
|
|
|||
|
|
@ -613,7 +613,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("narrower", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
|
|
@ -625,6 +625,49 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseHavingEquivalence() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
||||
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
|
||||
|
||||
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
|
||||
@Override
|
||||
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
|
||||
/*
|
||||
* Provided:
|
||||
* source code
|
||||
* source code system
|
||||
* target code system
|
||||
* reverse = true
|
||||
*/
|
||||
TranslationRequest translationRequest = new TranslationRequest();
|
||||
translationRequest.getCodeableConcept().addCoding()
|
||||
.setSystem(CS_URL_3)
|
||||
.setCode("67890");
|
||||
translationRequest.setTargetSystem(new UriType(CS_URL));
|
||||
translationRequest.setReverse(true);
|
||||
|
||||
TranslationResult translationResult = myConceptMapDao.translate(translationRequest, null);
|
||||
|
||||
assertTrue(translationResult.getResult().booleanValue());
|
||||
assertEquals("Matches found!", translationResult.getMessage().getValueAsString());
|
||||
|
||||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
assertEquals(CS_URL, concept.getSystem());
|
||||
assertEquals("Version 3", concept.getVersion());
|
||||
assertFalse(concept.getUserSelected());
|
||||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
assertEquals("wider", translationMatch.getEquivalence().getCode());
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTranslateWithReverseByCodeSystemsAndSourceCodeUnmapped() {
|
||||
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
|
||||
|
|
@ -680,7 +723,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(2, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("equal", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
|
|
@ -690,7 +733,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
|
||||
translationMatch = translationResult.getMatches().get(1);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("narrower", translationMatch.getEquivalence().getCode());
|
||||
concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
|
|
@ -733,7 +776,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("equal", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
|
|
@ -776,7 +819,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(1, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("narrower", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
|
|
@ -817,7 +860,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(2, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("equal", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
|
|
@ -827,7 +870,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
|
||||
translationMatch = translationResult.getMatches().get(1);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("narrower", translationMatch.getEquivalence().getCode());
|
||||
concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
|
|
@ -870,7 +913,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(2, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("equal", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
|
|
@ -880,7 +923,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
|
||||
translationMatch = translationResult.getMatches().get(1);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("narrower", translationMatch.getEquivalence().getCode());
|
||||
concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
|
|
@ -921,7 +964,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(2, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("equal", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
|
|
@ -931,7 +974,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
|
||||
translationMatch = translationResult.getMatches().get(1);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("narrower", translationMatch.getEquivalence().getCode());
|
||||
concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
|
|
@ -972,7 +1015,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(2, translationResult.getMatches().size());
|
||||
|
||||
TranslationMatch translationMatch = translationResult.getMatches().get(0);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("equal", translationMatch.getEquivalence().getCode());
|
||||
Coding concept = translationMatch.getConcept();
|
||||
assertEquals("12345", concept.getCode());
|
||||
assertEquals("Source Code 12345", concept.getDisplay());
|
||||
|
|
@ -982,7 +1025,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
|
|||
assertEquals(CM_URL, translationMatch.getSource().getValueAsString());
|
||||
|
||||
translationMatch = translationResult.getMatches().get(1);
|
||||
assertNull(translationMatch.getEquivalence());
|
||||
assertEquals("narrower", translationMatch.getEquivalence().getCode());
|
||||
concept = translationMatch.getConcept();
|
||||
assertEquals("78901", concept.getCode());
|
||||
assertEquals("Source Code 78901", concept.getDisplay());
|
||||
|
|
|
|||
|
|
@ -16,6 +16,7 @@ import ca.uhn.fhir.rest.server.exceptions.*;
|
|||
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hamcrest.Matchers;
|
||||
import org.hl7.fhir.instance.model.api.IAnyResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
|
|
@ -50,6 +51,11 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoR4Test.class);
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
|
||||
@After
|
||||
public void after() {
|
||||
myDaoConfig.setAllowInlineMatchUrlReferences(false);
|
||||
|
|
@ -187,7 +193,6 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testBatchCreateWithBadRead() {
|
||||
Bundle request = new Bundle();
|
||||
|
|
@ -1520,26 +1525,6 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTransactionDoesNotAllowDanglingTemporaryIds() throws Exception {
|
||||
String input = IOUtils.toString(getClass().getResourceAsStream("/cdr-bundle.json"), StandardCharsets.UTF_8);
|
||||
Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
|
||||
|
||||
BundleEntryComponent entry = bundle.addEntry();
|
||||
Patient p = new Patient();
|
||||
p.getManagingOrganization().setReference("urn:uuid:30ce60cf-f7cb-4196-961f-cadafa8b7ff5");
|
||||
entry.setResource(p);
|
||||
entry.getRequest().setMethod(HTTPVerb.POST);
|
||||
entry.getRequest().setUrl("Patient");
|
||||
|
||||
try {
|
||||
mySystemDao.transaction(mySrd, bundle);
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Unable to satisfy placeholder ID: urn:uuid:30ce60cf-f7cb-4196-961f-cadafa8b7ff5", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTransactionDoesNotLeavePlaceholderIds() {
|
||||
String input;
|
||||
|
|
@ -1624,7 +1609,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
map.add(Patient.SP_IDENTIFIER, new TokenParam("foo", "bar"));
|
||||
search = myPatientDao.search(map);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(search), contains(createdPatientId.toUnqualifiedVersionless().getValue()));
|
||||
pat = (Patient) search.getResources(0,1).get(0);
|
||||
pat = (Patient) search.getResources(0, 1).get(0);
|
||||
assertEquals("foo", pat.getIdentifierFirstRep().getSystem());
|
||||
// Observation
|
||||
map = new SearchParameterMap();
|
||||
|
|
@ -1632,7 +1617,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
map.add(Observation.SP_IDENTIFIER, new TokenParam("foo", "dog"));
|
||||
search = myObservationDao.search(map);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(search), contains(createdObservationId.toUnqualifiedVersionless().getValue()));
|
||||
obs = (Observation) search.getResources(0,1).get(0);
|
||||
obs = (Observation) search.getResources(0, 1).get(0);
|
||||
assertEquals("foo", obs.getIdentifierFirstRep().getSystem());
|
||||
assertEquals(createdPatientId.toUnqualifiedVersionless().getValue(), obs.getSubject().getReference());
|
||||
|
||||
|
|
@ -1689,7 +1674,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
map.add(Patient.SP_IDENTIFIER, new TokenParam("foo", "bar"));
|
||||
search = myPatientDao.search(map);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(search), contains(createdPatientId.toUnqualifiedVersionless().getValue()));
|
||||
pat = (Patient) search.getResources(0,1).get(0);
|
||||
pat = (Patient) search.getResources(0, 1).get(0);
|
||||
assertEquals("foo", pat.getIdentifierFirstRep().getSystem());
|
||||
// Observation
|
||||
map = new SearchParameterMap();
|
||||
|
|
@ -1697,7 +1682,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
map.add(Observation.SP_IDENTIFIER, new TokenParam("foo", "dog"));
|
||||
search = myObservationDao.search(map);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(search), contains(createdObservationId.toUnqualifiedVersionless().getValue()));
|
||||
obs = (Observation) search.getResources(0,1).get(0);
|
||||
obs = (Observation) search.getResources(0, 1).get(0);
|
||||
assertEquals("foo", obs.getIdentifierFirstRep().getSystem());
|
||||
assertEquals(createdPatientId.toUnqualifiedVersionless().getValue(), obs.getSubject().getReference());
|
||||
|
||||
|
|
@ -1755,7 +1740,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
map.add(Patient.SP_IDENTIFIER, new TokenParam("foo", "bar"));
|
||||
search = myPatientDao.search(map);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(search), contains(createdPatientId.toUnqualifiedVersionless().getValue()));
|
||||
pat = (Patient) search.getResources(0,1).get(0);
|
||||
pat = (Patient) search.getResources(0, 1).get(0);
|
||||
assertEquals("foo", pat.getIdentifierFirstRep().getSystem());
|
||||
// Observation
|
||||
map = new SearchParameterMap();
|
||||
|
|
@ -1763,7 +1748,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
map.add(Observation.SP_IDENTIFIER, new TokenParam("foo", "dog"));
|
||||
search = myObservationDao.search(map);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(search), contains(createdObservationId.toUnqualifiedVersionless().getValue()));
|
||||
obs = (Observation) search.getResources(0,1).get(0);
|
||||
obs = (Observation) search.getResources(0, 1).get(0);
|
||||
assertEquals("foo", obs.getIdentifierFirstRep().getSystem());
|
||||
assertEquals(createdPatientId.toUnqualifiedVersionless().getValue(), obs.getSubject().getReference());
|
||||
assertEquals(ObservationStatus.FINAL, obs.getStatus());
|
||||
|
|
@ -2132,6 +2117,29 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
assertNull(nextEntry.getResource());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTransactionWithUnknownTemnporaryIdReference() {
|
||||
String methodName = "testTransactionWithUnknownTemnporaryIdReference";
|
||||
|
||||
Bundle request = new Bundle();
|
||||
|
||||
Patient p = new Patient();
|
||||
p.addIdentifier().setSystem("urn:system").setValue(methodName);
|
||||
request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
|
||||
|
||||
p = new Patient();
|
||||
p.addIdentifier().setSystem("urn:system").setValue(methodName);
|
||||
p.getManagingOrganization().setReference(IdType.newRandomUuid().getValue());
|
||||
request.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
|
||||
|
||||
try {
|
||||
mySystemDao.transaction(mySrd, request);
|
||||
fail();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertThat(e.getMessage(), Matchers.matchesPattern("Unable to satisfy placeholder ID urn:uuid:[0-9a-z-]+ found in element named 'managingOrganization' within resource of type: Patient"));
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTransactionSearchWithCount() {
|
||||
String methodName = "testTransactionSearchWithCount";
|
||||
|
|
@ -3047,44 +3055,6 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
assertEquals(1, found.size().intValue());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testTransactionWithRelativeOidIds() {
|
||||
Bundle res = new Bundle();
|
||||
res.setType(BundleType.TRANSACTION);
|
||||
|
||||
Patient p1 = new Patient();
|
||||
p1.setId("urn:oid:0.1.2.3");
|
||||
p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
|
||||
res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
|
||||
|
||||
Observation o1 = new Observation();
|
||||
o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
|
||||
o1.setSubject(new Reference("urn:oid:0.1.2.3"));
|
||||
res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
|
||||
|
||||
Observation o2 = new Observation();
|
||||
o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
|
||||
o2.setSubject(new Reference("urn:oid:0.1.2.3"));
|
||||
res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
|
||||
|
||||
Bundle resp = mySystemDao.transaction(mySrd, res);
|
||||
|
||||
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
|
||||
|
||||
assertEquals(BundleType.TRANSACTIONRESPONSE, resp.getTypeElement().getValue());
|
||||
assertEquals(3, resp.getEntry().size());
|
||||
|
||||
assertTrue(resp.getEntry().get(0).getResponse().getLocation(), new IdType(resp.getEntry().get(0).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
|
||||
assertTrue(resp.getEntry().get(1).getResponse().getLocation(), new IdType(resp.getEntry().get(1).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
|
||||
assertTrue(resp.getEntry().get(2).getResponse().getLocation(), new IdType(resp.getEntry().get(2).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
|
||||
|
||||
o1 = myObservationDao.read(new IdType(resp.getEntry().get(1).getResponse().getLocation()), mySrd);
|
||||
o2 = myObservationDao.read(new IdType(resp.getEntry().get(2).getResponse().getLocation()), mySrd);
|
||||
assertThat(o1.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart()));
|
||||
assertThat(o2.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart()));
|
||||
|
||||
}
|
||||
|
||||
//
|
||||
//
|
||||
// /**
|
||||
|
|
@ -3187,6 +3157,44 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
//
|
||||
// }
|
||||
|
||||
@Test
|
||||
public void testTransactionWithRelativeOidIds() {
|
||||
Bundle res = new Bundle();
|
||||
res.setType(BundleType.TRANSACTION);
|
||||
|
||||
Patient p1 = new Patient();
|
||||
p1.setId("urn:oid:0.1.2.3");
|
||||
p1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds01");
|
||||
res.addEntry().setResource(p1).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
|
||||
|
||||
Observation o1 = new Observation();
|
||||
o1.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds02");
|
||||
o1.setSubject(new Reference("urn:oid:0.1.2.3"));
|
||||
res.addEntry().setResource(o1).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
|
||||
|
||||
Observation o2 = new Observation();
|
||||
o2.addIdentifier().setSystem("system").setValue("testTransactionWithRelativeOidIds03");
|
||||
o2.setSubject(new Reference("urn:oid:0.1.2.3"));
|
||||
res.addEntry().setResource(o2).getRequest().setMethod(HTTPVerb.POST).setUrl("Observation");
|
||||
|
||||
Bundle resp = mySystemDao.transaction(mySrd, res);
|
||||
|
||||
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
|
||||
|
||||
assertEquals(BundleType.TRANSACTIONRESPONSE, resp.getTypeElement().getValue());
|
||||
assertEquals(3, resp.getEntry().size());
|
||||
|
||||
assertTrue(resp.getEntry().get(0).getResponse().getLocation(), new IdType(resp.getEntry().get(0).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
|
||||
assertTrue(resp.getEntry().get(1).getResponse().getLocation(), new IdType(resp.getEntry().get(1).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
|
||||
assertTrue(resp.getEntry().get(2).getResponse().getLocation(), new IdType(resp.getEntry().get(2).getResponse().getLocation()).getIdPart().matches("^[0-9]+$"));
|
||||
|
||||
o1 = myObservationDao.read(new IdType(resp.getEntry().get(1).getResponse().getLocation()), mySrd);
|
||||
o2 = myObservationDao.read(new IdType(resp.getEntry().get(2).getResponse().getLocation()), mySrd);
|
||||
assertThat(o1.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart()));
|
||||
assertThat(o2.getSubject().getReferenceElement().getValue(), endsWith("Patient/" + p1.getIdElement().getIdPart()));
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* This is not the correct way to do it, but we'll allow it to be lenient
|
||||
*/
|
||||
|
|
@ -3230,7 +3238,7 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
|
||||
@Test
|
||||
public void testTransactionWithReplacement() {
|
||||
byte[] bytes = new byte[] {0, 1, 2, 3, 4};
|
||||
byte[] bytes = new byte[]{0, 1, 2, 3, 4};
|
||||
|
||||
Binary binary = new Binary();
|
||||
binary.setId(IdType.newRandomUuid());
|
||||
|
|
@ -3399,9 +3407,4 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
|
|||
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -988,9 +988,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1069,9 +1069,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(2, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1083,9 +1083,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1135,9 +1135,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(2, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1149,9 +1149,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1205,9 +1205,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(4, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1219,9 +1219,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1247,9 +1247,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(3);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1298,9 +1298,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(2, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1312,9 +1312,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1365,9 +1365,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(2, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1379,9 +1379,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1432,9 +1432,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1485,9 +1485,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(1, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1536,9 +1536,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(2, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1550,9 +1550,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1601,9 +1601,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(2, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1615,9 +1615,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
@ -1659,9 +1659,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(2, getNumberOfParametersByName(respParams, "match"));
|
||||
|
||||
param = getParametersByName(respParams, "match").get(0);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
ParametersParameterComponent part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("equal", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
Coding coding = (Coding) part.getValue();
|
||||
assertEquals("12345", coding.getCode());
|
||||
|
|
@ -1673,9 +1673,9 @@ public class ResourceProviderR4ConceptMapTest extends BaseResourceProviderR4Test
|
|||
assertEquals(CM_URL, ((UriType) part.getValue()).getValueAsString());
|
||||
|
||||
param = getParametersByName(respParams, "match").get(1);
|
||||
assertEquals(2, param.getPart().size());
|
||||
assertEquals(3, param.getPart().size());
|
||||
part = getPartByName(param, "equivalence");
|
||||
assertFalse(part.hasValue());
|
||||
assertEquals("narrower", ((CodeType)part.getValue()).getCode());
|
||||
part = getPartByName(param, "concept");
|
||||
coding = (Coding) part.getValue();
|
||||
assertEquals("78901", coding.getCode());
|
||||
|
|
|
|||
|
|
@ -190,12 +190,22 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
|
|||
assertEquals("Version 1", element.getSystemVersion());
|
||||
assertEquals(VS_URL, element.getValueSet());
|
||||
assertEquals(CM_URL, element.getConceptMapUrl());
|
||||
assertEquals(1, element.getConceptMapGroupElementTargets().size());
|
||||
|
||||
assertEquals(2, element.getConceptMapGroupElementTargets().size());
|
||||
|
||||
target = element.getConceptMapGroupElementTargets().get(0);
|
||||
|
||||
ourLog.info("ConceptMap.group(0).element(1).target(0):\n" + target.toString());
|
||||
assertEquals("45678", target.getCode());
|
||||
assertEquals("Target Code 45678", target.getDisplay());
|
||||
assertEquals(CS_URL_2, target.getSystem());
|
||||
assertEquals("Version 2", target.getSystemVersion());
|
||||
assertEquals(ConceptMapEquivalence.WIDER, target.getEquivalence());
|
||||
assertEquals(VS_URL_2, target.getValueSet());
|
||||
assertEquals(CM_URL, target.getConceptMapUrl());
|
||||
|
||||
// We had deliberately added a duplicate, and here it is...
|
||||
target = element.getConceptMapGroupElementTargets().get(1);
|
||||
ourLog.info("ConceptMap.group(0).element(1).target(1):\n" + target.toString());
|
||||
assertEquals("45678", target.getCode());
|
||||
assertEquals("Target Code 45678", target.getDisplay());
|
||||
assertEquals(CS_URL_2, target.getSystem());
|
||||
|
|
|
|||
|
|
@ -195,3 +195,38 @@ drop column SP_ID from table HFJ_RES_PARAM_PRESENT;
|
|||
drop index IDX_SEARCHPARM_RESTYPE_SPNAME;
|
||||
drop index IDX_RESPARMPRESENT_SPID_RESID;
|
||||
drop table HFJ_SEARCH_PARM;
|
||||
|
||||
|
||||
|
||||
# Delete everything
|
||||
update hfj_res_ver set forced_id_pid = null where res_id in (select res_id from hfj_resource);
|
||||
update hfj_resource set forced_id_pid = null where res_id in (select res_id from hfj_resource);
|
||||
delete from hfj_history_tag where res_id in (select res_id from hfj_resource);
|
||||
delete from hfj_res_ver where res_id in (select res_id from hfj_resource);
|
||||
delete from hfj_forced_id where resource_pid in (select res_id from hfj_resource);
|
||||
delete from hfj_res_link where src_resource_id in (select res_id from hfj_resource);
|
||||
delete from hfj_res_link where target_resource_id in (select res_id from hfj_resource);
|
||||
delete from hfj_spidx_coords;
|
||||
delete from hfj_spidx_date;
|
||||
delete from hfj_spidx_number;
|
||||
delete from hfj_spidx_quantity;
|
||||
delete from hfj_spidx_string;
|
||||
delete from hfj_spidx_token;
|
||||
delete from hfj_spidx_uri;
|
||||
delete from hfj_res_tag;
|
||||
delete from hfj_search_result;
|
||||
delete from hfj_res_param_present;
|
||||
delete from hfj_idx_cmp_string_uniq;
|
||||
delete from hfj_subscription_stats;
|
||||
DELETE FROM TRM_CONCEPT_MAP_GRP_ELM_TGT;
|
||||
DELETE FROM TRM_CONCEPT_MAP_GRP_ELEMENT;
|
||||
DELETE FROM TRM_CONCEPT_MAP_GROUP;
|
||||
DELETE FROM TRM_CONCEPT_MAP;
|
||||
DELETE FROM TRM_CONCEPT_DESIG;
|
||||
DELETE FROM TRM_CONCEPT_PC_LINK;
|
||||
DELETE FROM TRM_CONCEPT_PROPERTY;
|
||||
DELETE FROM TRM_CONCEPT;
|
||||
DELETE FROM TRM_CODESYSTEM_VER;
|
||||
DELETE FROM TRM_CODESYSTEM;
|
||||
delete from hfj_resource;
|
||||
|
||||
|
|
|
|||
|
|
@ -249,6 +249,19 @@
|
|||
queue (only the ID), which should reduce the memory/disk footprint of the queue
|
||||
when it grows long.
|
||||
</action>
|
||||
<action type="add">
|
||||
When performing a ConceptMap/$translate operation with reverse="true" in the arguments,
|
||||
the equivalency flag is now set on the response just as it is for a non-reverse lookup.
|
||||
</action>
|
||||
<action type="add">
|
||||
When executing a FHIR transaction in JPA server, if the request bundle contains
|
||||
placeholder IDs references (i.e. "urn:uuid:*" references) that can not be resolved
|
||||
anywhere else in the bundle, a user friendly error is now returned. Previously,
|
||||
a cryptic error containing only the UUID was returned. As a part of this change,
|
||||
transaction processing has now been consolidated into a single codebase for DSTU3
|
||||
/ R4 (and future) versions of FHIR. This should greatly improve maintainability
|
||||
and consistency for transaction processing.
|
||||
</action>
|
||||
<action type="add">
|
||||
ResponseHighlighterInterceptor now displays the total size of the output and
|
||||
an estimate of the transfer time at the bottom of the response.
|
||||
|
|
|
|||
Loading…
Reference in New Issue