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hapi-fhir
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Merge latest changes

This commit is contained in:
James Agnew 2019-10-18 13:36:26 -04:00
parent a1bf50685d
commit 50af4bfb19
66 changed files with 200 additions and 429 deletions
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12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
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@ -7,11 +7,11 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu2;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu2;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu2;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.TermReadSvcDstu2;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.hapi.validation.CachingValidationSupport;
import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
@ -83,7 +83,7 @@ public class BaseDstu2Config extends BaseConfig {
@Bean(name = "myInstanceValidatorDstu2")
@Lazy
public IValidatorModule instanceValidatorDstu2() {
public IInstanceValidatorModule instanceValidatorDstu2() {
FhirInstanceValidator retVal = new FhirInstanceValidator();
retVal.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
retVal.setValidationSupport(new CachingValidationSupport(new ValidationSupportChain(new DefaultProfileValidationSupport(), jpaValidationSupportDstu2())));
@ -134,8 +134,8 @@ public class BaseDstu2Config extends BaseConfig {
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvc terminologyService() {
return new HapiTerminologySvcDstu2();
public ITermReadSvc terminologyService() {
return new TermReadSvcDstu2();
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
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@ -18,6 +18,7 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
@ -92,7 +93,7 @@ public class BaseDstu3Config extends BaseConfig {
@Bean(name = "myInstanceValidatorDstu3")
@Lazy
public IValidatorModule instanceValidatorDstu3() {
public IInstanceValidatorModule instanceValidatorDstu3() {
FhirInstanceValidator val = new FhirInstanceValidator();
val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
val.setValidationSupport(validationSupportChainDstu3());

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
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@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.config.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@ -12,13 +12,15 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR4;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcR4;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.TermReadSvcR4;
import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcR4;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
@ -55,13 +57,19 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
public class BaseR4Config extends BaseConfig {
public class BaseR4Config extends BaseConfigDstu3Plus {
@Override
public FhirContext fhirContext() {
return fhirContextR4();
}
@Bean
@Override
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcR4();
}
@Bean
@Primary
public FhirContext fhirContextR4() {
@ -92,7 +100,7 @@ public class BaseR4Config extends BaseConfig {
@Bean(name = "myInstanceValidatorR4")
@Lazy
public IValidatorModule instanceValidatorR4() {
public IInstanceValidatorModule instanceValidatorR4() {
FhirInstanceValidator val = new FhirInstanceValidator();
IResourceValidator.BestPracticeWarningLevel level = IResourceValidator.BestPracticeWarningLevel.Warning;
val.setBestPracticeWarningLevel(level);
@ -154,13 +162,13 @@ public class BaseR4Config extends BaseConfig {
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologyLoaderSvc terminologyLoaderService() {
return new TerminologyLoaderSvcImpl();
public ITermLoaderSvc termLoaderService() {
return new TermLoaderSvcImpl();
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvcR4 terminologyService() {
return new HapiTerminologySvcR4();
public ITermReadSvcR4 terminologyService() {
return new TermReadSvcR4();
}
@Primary

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
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@ -18,6 +18,7 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR5;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR5;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
@ -92,7 +93,7 @@ public class BaseR5Config extends BaseConfig {
@Bean(name = "myInstanceValidatorR5")
@Lazy
public IValidatorModule instanceValidatorR5() {
public IInstanceValidatorModule instanceValidatorR5() {
FhirInstanceValidator val = new FhirInstanceValidator();
IResourceValidator.BestPracticeWarningLevel level = IResourceValidator.BestPracticeWarningLevel.Warning;
val.setBestPracticeWarningLevel(level);

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -94,6 +94,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
private MatchResourceUrlService myMatchResourceUrlService;
@Autowired
private IResourceReindexingSvc myResourceReindexingSvc;
@Autowired
private IInstanceValidatorModule myInstanceValidator;
private String myResourceName;
private Class<T> myResourceType;
@ -182,9 +184,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return createOperationOutcome(OO_SEVERITY_INFO, theMessage, "informational");
}
protected abstract IValidatorModule getInstanceValidator();
protected final IInstanceValidatorModule getInstanceValidator() {
return myInstanceValidator;
}
protected abstract IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode);
protected final IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
OperationOutcomeUtil.addIssue(getContext(), oo, theSeverity, theMessage, null, theCode);
return oo;
}
@Override
public DaoMethodOutcome delete(IIdType theId) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoBundleDstu2.java
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@ -28,7 +28,7 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.defaultString;
public class FhirResourceDaoBundleDstu2 extends FhirResourceDaoDstu2<Bundle> {
public class FhirResourceDaoBundleDstu2 extends BaseHapiFhirResourceDao<Bundle> {
@Override
protected void preProcessResourceForStorage(Bundle theResource) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoCompositionDstu2.java
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@ -32,7 +32,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest;
public class FhirResourceDaoCompositionDstu2 extends FhirResourceDaoDstu2<Composition>implements IFhirResourceDaoComposition<Composition> {
public class FhirResourceDaoCompositionDstu2 extends BaseHapiFhirResourceDao<Composition>implements IFhirResourceDaoComposition<Composition> {
@Override
public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java
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@ -1,51 +0,0 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.validation.IValidatorModule;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResourceDao<T> {
@Autowired
@Qualifier("myInstanceValidatorDstu2")
private IValidatorModule myInstanceValidator;
@Override
protected IValidatorModule getInstanceValidator() {
return myInstanceValidator;
}
@Override
protected IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
OperationOutcome oo = new OperationOutcome();
oo.getIssueFirstRep().getSeverityElement().setValue(theSeverity);
oo.getIssueFirstRep().getDiagnosticsElement().setValue(theMessage);
oo.getIssueFirstRep().getCodeElement().setValue(theCode);
return oo;
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoEncounterDstu2.java
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@ -36,7 +36,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
public class FhirResourceDaoEncounterDstu2 extends FhirResourceDaoDstu2<Encounter>implements IFhirResourceDaoEncounter<Encounter> {
public class FhirResourceDaoEncounterDstu2 extends BaseHapiFhirResourceDao<Encounter>implements IFhirResourceDaoEncounter<Encounter> {
@Override
public IBundleProvider encounterInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoMessageHeaderDstu2.java
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@ -25,7 +25,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
import org.hl7.fhir.instance.model.api.IBaseBundle;
public class FhirResourceDaoMessageHeaderDstu2 extends FhirResourceDaoDstu2<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
public class FhirResourceDaoMessageHeaderDstu2 extends BaseHapiFhirResourceDao<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
public static IBaseBundle throwProcessMessageNotImplemented() {
throw new NotImplementedOperationException("This operation is not yet implemented on this server");

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java
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@ -37,7 +37,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
public class FhirResourceDaoPatientDstu2 extends BaseHapiFhirResourceDao<Patient>implements IFhirResourceDaoPatient<Patient> {
public FhirResourceDaoPatientDstu2() {
super();

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoQuestionnaireResponseDstu2.java
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@ -43,7 +43,7 @@ import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IResourceLoader;
import ca.uhn.fhir.validation.ValidationResult;
public class FhirResourceDaoQuestionnaireResponseDstu2 extends FhirResourceDaoDstu2<QuestionnaireResponse> {
public class FhirResourceDaoQuestionnaireResponseDstu2 extends BaseHapiFhirResourceDao<QuestionnaireResponse> {
@Autowired
@Qualifier("myFhirContextDstu2Hl7Org")

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSearchParameterDstu2.java
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@ -35,7 +35,7 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.List;
public class FhirResourceDaoSearchParameterDstu2 extends FhirResourceDaoDstu2<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
public class FhirResourceDaoSearchParameterDstu2 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
@Autowired
private IFhirSystemDao<Bundle, MetaDt> mySystemDao;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoStructureDefinitionDstu2.java
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@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.model.dstu2.resource.StructureDefinition;
public class FhirResourceDaoStructureDefinitionDstu2 extends FhirResourceDaoDstu2<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
public class FhirResourceDaoStructureDefinitionDstu2 extends BaseHapiFhirResourceDao<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
@Override
public StructureDefinition generateSnapshot(StructureDefinition theInput, String theUrl, String theWebUrl, String theName) {
// FIXME: implement

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java
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@ -38,7 +38,7 @@ import java.util.Date;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FhirResourceDaoSubscriptionDstu2 extends FhirResourceDaoDstu2<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
public class FhirResourceDaoSubscriptionDstu2 extends BaseHapiFhirResourceDao<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
@Autowired
private ISubscriptionTableDao mySubscriptionTableDao;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
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@ -57,7 +57,7 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueSet>
implements IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>, IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt> {
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoBundleDstu3.java
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@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
@ -29,7 +30,7 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.defaultString;
public class FhirResourceDaoBundleDstu3 extends FhirResourceDaoDstu3<Bundle> {
public class FhirResourceDaoBundleDstu3 extends BaseHapiFhirResourceDao<Bundle> {
@Override
protected void preProcessResourceForStorage(Bundle theResource) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
*/
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
@ -48,7 +49,7 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemDstu3.class);

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCompositionDstu3.java
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@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoComposition;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IResource;
@ -35,7 +36,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import javax.servlet.http.HttpServletRequest;
import java.util.Collections;
public class FhirResourceDaoCompositionDstu3 extends FhirResourceDaoDstu3<Composition> implements IFhirResourceDaoComposition<Composition> {
public class FhirResourceDaoCompositionDstu3 extends BaseHapiFhirResourceDao<Composition> implements IFhirResourceDaoComposition<Composition> {
@Override
public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.term.TranslationMatch;
import ca.uhn.fhir.jpa.term.TranslationRequest;
@ -27,7 +28,7 @@ import ca.uhn.fhir.jpa.term.TranslationResult;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
@ -42,11 +43,9 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoConceptMapDstu3 extends FhirResourceDaoDstu3<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Override
public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

65
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3.java
View File

@ -1,65 +0,0 @@
package ca.uhn.fhir.jpa.dao.dstu3;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
public class FhirResourceDaoDstu3<T extends IAnyResource> extends BaseHapiFhirResourceDao<T> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3.class);
@Autowired()
@Qualifier("myInstanceValidatorDstu3")
private IValidatorModule myInstanceValidator;
@Override
protected IValidatorModule getInstanceValidator() {
return myInstanceValidator;
}
@Override
protected IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
OperationOutcome oo = new OperationOutcome();
OperationOutcomeIssueComponent issue = oo.addIssue();
issue.getSeverityElement().setValueAsString(theSeverity);
issue.setDiagnostics(theMessage);
try {
issue.setCode(org.hl7.fhir.dstu3.model.OperationOutcome.IssueType.fromCode(theCode));
} catch (FHIRException e) {
ourLog.error("Unknown code: {}", theCode);
}
return oo;
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoEncounterDstu3.java
View File

@ -24,6 +24,7 @@ import java.util.Collections;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -37,7 +38,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
public class FhirResourceDaoEncounterDstu3 extends FhirResourceDaoDstu3<Encounter>implements IFhirResourceDaoEncounter<Encounter> {
public class FhirResourceDaoEncounterDstu3 extends BaseHapiFhirResourceDao<Encounter> implements IFhirResourceDaoEncounter<Encounter> {
@Override
public IBundleProvider encounterInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoMessageHeaderDstu3.java
View File

@ -20,9 +20,10 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoMessageHeader;
import org.hl7.fhir.dstu3.model.MessageHeader;
public class FhirResourceDaoMessageHeaderDstu3 extends FhirResourceDaoDstu3<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
public class FhirResourceDaoMessageHeaderDstu3 extends BaseHapiFhirResourceDao<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
// nothing right now
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoPatientDstu3.java
View File

@ -39,7 +39,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.*;
public class FhirResourceDaoPatientDstu3 extends FhirResourceDaoDstu3<Patient>implements IFhirResourceDaoPatient<Patient> {
public class FhirResourceDaoPatientDstu3 extends BaseHapiFhirResourceDao<Patient>implements IFhirResourceDaoPatient<Patient> {
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, StringAndListParam theFilter, RequestDetails theRequest) {
SearchParameterMap paramMap = new SearchParameterMap();

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoQuestionnaireResponseDstu3.java
View File

@ -20,9 +20,10 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
public class FhirResourceDaoQuestionnaireResponseDstu3 extends FhirResourceDaoDstu3<QuestionnaireResponse> {
public class FhirResourceDaoQuestionnaireResponseDstu3 extends BaseHapiFhirResourceDao<QuestionnaireResponse> {
// @Override

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
@ -31,7 +32,7 @@ import java.util.List;
* #L%
*/
public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
public class FhirResourceDaoSearchParameterDstu3 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
protected void markAffectedResources(SearchParameter theResource) {
Boolean reindex = theResource != null ? CURRENTLY_REINDEXING.get(theResource) : null;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoStructureDefinitionDstu3.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoStructureDefinition;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
@ -26,7 +27,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* #L%
*/
public class FhirResourceDaoStructureDefinitionDstu3 extends FhirResourceDaoDstu3<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
public class FhirResourceDaoStructureDefinitionDstu3 extends BaseHapiFhirResourceDao<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
@Autowired
private IValidationSupport myValidationSupport;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
*/
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
@ -43,7 +44,7 @@ import java.util.Date;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FhirResourceDaoSubscriptionDstu3 extends FhirResourceDaoDstu3<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
public class FhirResourceDaoSubscriptionDstu3 extends BaseHapiFhirResourceDao<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoSubscriptionDstu3.class);

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
*/
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -58,7 +59,7 @@ import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@Autowired

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoBundleR4.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleType;
@ -30,7 +31,7 @@ import java.util.TreeSet;
import static org.apache.commons.lang3.StringUtils.defaultString;
public class FhirResourceDaoBundleR4 extends FhirResourceDaoR4<Bundle> {
public class FhirResourceDaoBundleR4 extends BaseHapiFhirResourceDao<Bundle> {
@Override
protected void preProcessResourceForStorage(Bundle theResource) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.r4;
*/
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
@ -48,7 +49,7 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemR4.class);

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCompositionR4.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoComposition;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IResource;
@ -35,7 +36,7 @@ import org.hl7.fhir.r4.model.Composition;
import javax.servlet.http.HttpServletRequest;
import java.util.Collections;
public class FhirResourceDaoCompositionR4 extends FhirResourceDaoR4<Composition>implements IFhirResourceDaoComposition<Composition> {
public class FhirResourceDaoCompositionR4 extends BaseHapiFhirResourceDao<Composition> implements IFhirResourceDaoComposition<Composition> {
@Override
public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -20,11 +20,12 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.TranslationMatch;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.TranslationResult;
@ -38,11 +39,9 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
public class FhirResourceDaoConceptMapR4 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Override
public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoEncounterR4.java
View File

@ -24,6 +24,7 @@ import java.util.Collections;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -37,7 +38,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
public class FhirResourceDaoEncounterR4 extends FhirResourceDaoR4<Encounter>implements IFhirResourceDaoEncounter<Encounter> {
public class FhirResourceDaoEncounterR4 extends BaseHapiFhirResourceDao<Encounter> implements IFhirResourceDaoEncounter<Encounter> {
@Override
public IBundleProvider encounterInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoMessageHeaderR4.java
View File

@ -20,9 +20,10 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoMessageHeader;
import org.hl7.fhir.r4.model.MessageHeader;
public class FhirResourceDaoMessageHeaderR4 extends FhirResourceDaoR4<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
public class FhirResourceDaoMessageHeaderR4 extends BaseHapiFhirResourceDao<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
// nothing right now
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoPatientR4.java
View File

@ -39,7 +39,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.*;
public class FhirResourceDaoPatientR4 extends FhirResourceDaoR4<Patient>implements IFhirResourceDaoPatient<Patient> {
public class FhirResourceDaoPatientR4 extends BaseHapiFhirResourceDao<Patient>implements IFhirResourceDaoPatient<Patient> {
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, StringAndListParam theFilter, RequestDetails theRequest) {
SearchParameterMap paramMap = new SearchParameterMap();

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoQuestionnaireResponseR4.java
View File

@ -20,9 +20,10 @@ package ca.uhn.fhir.jpa.dao.r4;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import org.hl7.fhir.r4.model.QuestionnaireResponse;
public class FhirResourceDaoQuestionnaireResponseR4 extends FhirResourceDaoR4<QuestionnaireResponse> {
public class FhirResourceDaoQuestionnaireResponseR4 extends BaseHapiFhirResourceDao<QuestionnaireResponse> {
// @Override

83
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4.java
View File

@ -1,83 +0,0 @@
package ca.uhn.fhir.jpa.dao.r4;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.delete.DeleteConflictList;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoR4<T extends IAnyResource> extends BaseHapiFhirResourceDao<T> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4.class);
@Autowired()
@Qualifier("myInstanceValidatorR4")
private IValidatorModule myInstanceValidator;
@Override
protected IValidatorModule getInstanceValidator() {
return myInstanceValidator;
}
@Override
protected IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
OperationOutcome oo = new OperationOutcome();
OperationOutcomeIssueComponent issue = oo.addIssue();
issue.getSeverityElement().setValueAsString(theSeverity);
issue.setDiagnostics(theMessage);
try {
issue.setCode(org.hl7.fhir.r4.model.OperationOutcome.IssueType.fromCode(theCode));
} catch (FHIRException e) {
ourLog.error("Unknown code: {}", theCode);
}
return oo;
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
@ -44,7 +45,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
* #L%
*/
public class FhirResourceDaoSearchParameterR4 extends FhirResourceDaoR4<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
public static final DefaultProfileValidationSupport VALIDATION_SUPPORT = new DefaultProfileValidationSupport();
@Autowired

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoStructureDefinitionR4.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoStructureDefinition;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
@ -26,7 +27,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* #L%
*/
public class FhirResourceDaoStructureDefinitionR4 extends FhirResourceDaoR4<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
public class FhirResourceDaoStructureDefinitionR4 extends BaseHapiFhirResourceDao<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
@Autowired
private IValidationSupport myValidationSupport;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSubscriptionR4.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.r4;
*/
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
@ -43,7 +44,7 @@ import java.util.Date;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FhirResourceDaoSubscriptionR4 extends FhirResourceDaoR4<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
public class FhirResourceDaoSubscriptionR4 extends BaseHapiFhirResourceDao<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
@Autowired
private ISubscriptionTableDao mySubscriptionTableDao;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.r4;
*/
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -53,7 +54,7 @@ import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
public class FhirResourceDaoValueSetR4 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoBundleR5.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.hl7.fhir.r5.model.Bundle;
@ -27,7 +28,7 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
* #L%
*/
public class FhirResourceDaoBundleR5 extends FhirResourceDaoR5<Bundle> {
public class FhirResourceDaoBundleR5 extends BaseHapiFhirResourceDao<Bundle> {
@Override
protected void preProcessResourceForStorage(Bundle theResource) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.r5;
*/
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
@ -48,7 +49,7 @@ import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCodeSystemR5.class);

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCompositionR5.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoComposition;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.SortSpec;
@ -35,7 +36,7 @@ import org.hl7.fhir.r5.model.Composition;
import javax.servlet.http.HttpServletRequest;
import java.util.Collections;
public class FhirResourceDaoCompositionR5 extends FhirResourceDaoR5<Composition> implements IFhirResourceDaoComposition<Composition> {
public class FhirResourceDaoCompositionR5 extends BaseHapiFhirResourceDao<Composition> implements IFhirResourceDaoComposition<Composition> {
@Override
public IBundleProvider getDocumentForComposition(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdate, SortSpec theSort, RequestDetails theRequestDetails) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
@ -39,7 +40,7 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
public class FhirResourceDaoConceptMapR5 extends FhirResourceDaoR5<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoEncounterR5.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoEncounter;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@ -35,7 +36,7 @@ import org.hl7.fhir.r5.model.Encounter;
import javax.servlet.http.HttpServletRequest;
import java.util.Collections;
public class FhirResourceDaoEncounterR5 extends FhirResourceDaoR5<Encounter> implements IFhirResourceDaoEncounter<Encounter> {
public class FhirResourceDaoEncounterR5 extends BaseHapiFhirResourceDao<Encounter> implements IFhirResourceDaoEncounter<Encounter> {
@Override
public IBundleProvider encounterInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoMessageHeaderR5.java
View File

@ -20,9 +20,10 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoMessageHeader;
import org.hl7.fhir.r5.model.MessageHeader;
public class FhirResourceDaoMessageHeaderR5 extends FhirResourceDaoR5<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
public class FhirResourceDaoMessageHeaderR5 extends BaseHapiFhirResourceDao<MessageHeader> implements IFhirResourceDaoMessageHeader<MessageHeader> {
// nothing right now
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoPatientR5.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@ -39,7 +40,7 @@ import org.hl7.fhir.r5.model.Patient;
import javax.servlet.http.HttpServletRequest;
import java.util.Collections;
public class FhirResourceDaoPatientR5 extends FhirResourceDaoR5<Patient> implements IFhirResourceDaoPatient<Patient> {
public class FhirResourceDaoPatientR5 extends BaseHapiFhirResourceDao<Patient> implements IFhirResourceDaoPatient<Patient> {
private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, RequestDetails theRequest) {
SearchParameterMap paramMap = new SearchParameterMap();

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoQuestionnaireResponseR5.java
View File

@ -20,9 +20,10 @@ package ca.uhn.fhir.jpa.dao.r5;
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import org.hl7.fhir.r5.model.QuestionnaireResponse;
public class FhirResourceDaoQuestionnaireResponseR5 extends FhirResourceDaoR5<QuestionnaireResponse> {
public class FhirResourceDaoQuestionnaireResponseR5 extends BaseHapiFhirResourceDao<QuestionnaireResponse> {
// @Override

61
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5.java
View File

@ -1,61 +0,0 @@
package ca.uhn.fhir.jpa.dao.r5;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.validation.IValidatorModule;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
public class FhirResourceDaoR5<T extends IAnyResource> extends BaseHapiFhirResourceDao<T> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR5.class);
@Autowired()
@Qualifier("myInstanceValidatorR5")
private IValidatorModule myInstanceValidator;
@Override
protected IValidatorModule getInstanceValidator() {
return myInstanceValidator;
}
@Override
protected IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
OperationOutcome oo = new OperationOutcome();
OperationOutcomeIssueComponent issue = oo.addIssue();
issue.getSeverityElement().setValueAsString(theSeverity);
issue.setDiagnostics(theMessage);
try {
issue.setCode(OperationOutcome.IssueType.fromCode(theCode));
} catch (FHIRException e) {
ourLog.error("Unknown code: {}", theCode);
}
return oo;
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSearchParameterR5.java
View File

@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
@ -44,7 +45,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
* #L%
*/
public class FhirResourceDaoSearchParameterR5 extends FhirResourceDaoR5<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
public class FhirResourceDaoSearchParameterR5 extends BaseHapiFhirResourceDao<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
public static final DefaultProfileValidationSupport VALIDATION_SUPPORT = new DefaultProfileValidationSupport();
@Autowired

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoStructureDefinitionR5.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoStructureDefinition;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
@ -26,7 +27,7 @@ import org.springframework.beans.factory.annotation.Autowired;
* #L%
*/
public class FhirResourceDaoStructureDefinitionR5 extends FhirResourceDaoR5<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
public class FhirResourceDaoStructureDefinitionR5 extends BaseHapiFhirResourceDao<StructureDefinition> implements IFhirResourceDaoStructureDefinition<StructureDefinition> {
@Autowired
private IValidationSupport myValidationSupport;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoSubscriptionR5.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.r5;
*/
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSubscription;
import ca.uhn.fhir.jpa.dao.data.ISubscriptionTableDao;
@ -41,7 +42,7 @@ import java.util.Date;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FhirResourceDaoSubscriptionR5 extends FhirResourceDaoR5<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
public class FhirResourceDaoSubscriptionR5 extends BaseHapiFhirResourceDao<Subscription> implements IFhirResourceDaoSubscription<Subscription> {
@Autowired
private ISubscriptionTableDao mySubscriptionTableDao;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.dao.r5;
*/
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -53,7 +54,7 @@ import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
View File

@ -3,7 +3,7 @@ package ca.uhn.fhir.jpa.dao.dstu2;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.FhirResourceDaoDstu2;
import ca.uhn.fhir.jpa.dao.JpaResourceDao;
import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3Test;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
@ -359,23 +359,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
assertEquals(ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum.WARNING.getCode(), BaseHapiFhirResourceDao.OO_SEVERITY_WARN);
}
@Test
public void testCreateOperationOutcomeError() {
FhirResourceDaoDstu2<Bundle> dao = new FhirResourceDaoDstu2<Bundle>();
OperationOutcome oo = (OperationOutcome) dao.createErrorOperationOutcome("my message", "incomplete");
assertEquals(IssueSeverityEnum.ERROR.getCode(), oo.getIssue().get(0).getSeverity());
assertEquals("my message", oo.getIssue().get(0).getDiagnostics());
assertEquals(IssueTypeEnum.INCOMPLETE_RESULTS, oo.getIssue().get(0).getCodeElement().getValueAsEnum());
}
@Test
public void testCreateOperationOutcomeInfo() {
FhirResourceDaoDstu2<Bundle> dao = new FhirResourceDaoDstu2<Bundle>();
OperationOutcome oo = (OperationOutcome) dao.createInfoOperationOutcome("my message");
assertEquals(IssueSeverityEnum.INFORMATION.getCode(), oo.getIssue().get(0).getSeverity());
assertEquals("my message", oo.getIssue().get(0).getDiagnostics());
}
@Test
public void testCreateSummaryFails() {
Patient p = new Patient();

0
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/CustomObservationDstu3.java → hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/CustomObservationDstu3.java
View File

18
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -613,24 +613,6 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirDao.OO_SEVERITY_WARN);
}
@Test
public void testCreateOperationOutcomeError() {
FhirResourceDaoDstu3<Bundle> dao = new FhirResourceDaoDstu3<Bundle>();
OperationOutcome oo = (OperationOutcome) dao.createErrorOperationOutcome("my message", "incomplete");
assertEquals(IssueSeverity.ERROR.toCode(), oo.getIssue().get(0).getSeverity().toCode());
assertEquals("my message", oo.getIssue().get(0).getDiagnostics());
assertEquals(IssueType.INCOMPLETE, oo.getIssue().get(0).getCode());
}
@Test
public void testCreateOperationOutcomeInfo() {
FhirResourceDaoDstu3<Bundle> dao = new FhirResourceDaoDstu3<Bundle>();
OperationOutcome oo = (OperationOutcome) dao.createInfoOperationOutcome("my message");
assertEquals(IssueSeverity.INFORMATION.toCode(), oo.getIssue().get(0).getSeverity().toCode());
assertEquals("my message", oo.getIssue().get(0).getDiagnostics());
assertEquals(IssueType.INFORMATIONAL, oo.getIssue().get(0).getCode());
}
@Test
public void testCreateReferenceToDeletedResource() {
Organization org = new Organization();

11
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
View File

@ -1,9 +1,6 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
@ -769,7 +766,8 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
@Test
public void testCreateOperationOutcomeError() {
FhirResourceDaoR4<Bundle> dao = new FhirResourceDaoR4<Bundle>();
JpaResourceDao<Bundle> dao = new JpaResourceDao<Bundle>();
dao.setContext(myFhirCtx);
OperationOutcome oo = (OperationOutcome) dao.createErrorOperationOutcome("my message", "incomplete");
assertEquals(IssueSeverity.ERROR.toCode(), oo.getIssue().get(0).getSeverity().toCode());
assertEquals("my message", oo.getIssue().get(0).getDiagnostics());
@ -778,7 +776,8 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
@Test
public void testCreateOperationOutcomeInfo() {
FhirResourceDaoR4<Bundle> dao = new FhirResourceDaoR4<Bundle>();
JpaResourceDao<Bundle> dao = new JpaResourceDao<Bundle>();
dao.setContext(myFhirCtx);
OperationOutcome oo = (OperationOutcome) dao.createInfoOperationOutcome("my message");
assertEquals(IssueSeverity.INFORMATION.toCode(), oo.getIssue().get(0).getSeverity().toCode());
assertEquals("my message", oo.getIssue().get(0).getDiagnostics());

45
hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/FhirInstanceValidator.java
View File

@ -1,34 +1,33 @@
package org.hl7.fhir.dstu2016may.hapi.validation;
import java.io.StringReader;
import java.util.*;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu2016may.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu2016may.model.StructureDefinition;
import org.hl7.fhir.dstu2016may.validation.*;
import org.hl7.fhir.dstu2016may.validation.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.w3c.dom.*;
import org.xml.sax.InputSource;
import com.google.gson.*;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.XmlUtil;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonObject;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu2016may.model.StructureDefinition;
import org.hl7.fhir.dstu2016may.validation.IResourceValidator;
import org.hl7.fhir.dstu2016may.validation.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.dstu2016may.validation.InstanceValidator;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
public class FhirInstanceValidator extends BaseValidatorBridge implements IValidatorModule {
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class FhirInstanceValidator extends BaseValidatorBridge implements IInstanceValidatorModule {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidator.class);
private BestPracticeWarningLevel myBestPracticeWarningLevel;
private DocumentBuilderFactory myDocBuilderFactory;
private StructureDefinition myStructureDefintion;
private IValidationSupport myValidationSupport;
@ -48,8 +47,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
* The validation support
*/
public FhirInstanceValidator(IValidationSupport theValidationSupport) {
myDocBuilderFactory = DocumentBuilderFactory.newInstance();
myDocBuilderFactory.setNamespaceAware(true);
myValidationSupport = theValidationSupport;
}
@ -139,9 +136,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
if (theEncoding == EncodingEnum.XML) {
Document document;
try {
DocumentBuilder builder = myDocBuilderFactory.newDocumentBuilder();
InputSource src = new InputSource(new StringReader(theInput));
document = builder.parse(src);
document = XmlUtil.parseDocument(theInput);
} catch (Exception e2) {
ourLog.error("Failure to parse XML input", e2);
ValidationMessage m = new ValidationMessage();

3
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidator.java
View File

@ -3,6 +3,7 @@ package org.hl7.fhir.dstu3.hapi.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import com.github.benmanes.caffeine.cache.Caffeine;
@ -44,7 +45,7 @@ import java.util.*;
import java.util.concurrent.TimeUnit;
@SuppressWarnings({"PackageAccessibility", "Duplicates"})
public class FhirInstanceValidator extends BaseValidatorBridge implements IValidatorModule {
public class FhirInstanceValidator extends BaseValidatorBridge implements IInstanceValidatorModule {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidator.class);

16
hapi-fhir-validation/src/main/java/org/hl7/fhir/instance/hapi/validation/FhirInstanceValidator.java
View File

@ -3,8 +3,9 @@ package org.hl7.fhir.instance.hapi.validation;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.XmlUtil;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import com.github.benmanes.caffeine.cache.CacheLoader;
import com.github.benmanes.caffeine.cache.Caffeine;
import com.github.benmanes.caffeine.cache.LoadingCache;
@ -40,13 +41,9 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringReader;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.*;
@ -54,7 +51,7 @@ import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FhirInstanceValidator extends BaseValidatorBridge implements IValidatorModule {
public class FhirInstanceValidator extends BaseValidatorBridge implements IInstanceValidatorModule {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidator.class);
private static final FhirContext FHIR_CONTEXT = FhirContext.forDstu2();
@ -62,7 +59,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
private boolean myAnyExtensionsAllowed = true;
private BestPracticeWarningLevel myBestPracticeWarningLevel;
private DocumentBuilderFactory myDocBuilderFactory;
private StructureDefinition myStructureDefintion;
private IValidationSupport myValidationSupport;
private boolean noTerminologyChecks = false;
@ -84,8 +80,6 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
* @param theValidationSupport The validation support
*/
public FhirInstanceValidator(IValidationSupport theValidationSupport) {
myDocBuilderFactory = DocumentBuilderFactory.newInstance();
myDocBuilderFactory.setNamespaceAware(true);
myValidationSupport = theValidationSupport;
}
@ -280,9 +274,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
if (theEncoding == EncodingEnum.XML) {
Document document;
try {
DocumentBuilder builder = myDocBuilderFactory.newDocumentBuilder();
InputSource src = new InputSource(new StringReader(theInput));
document = builder.parse(src);
document = XmlUtil.parseDocument(theInput);
} catch (Exception e2) {
ourLog.error("Failure to parse XML input", e2);
ValidationMessage m = new ValidationMessage();

4
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/FhirInstanceValidator.java
View File

@ -2,8 +2,8 @@ package org.hl7.fhir.r4.hapi.validation;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import com.github.benmanes.caffeine.cache.Caffeine;
import com.github.benmanes.caffeine.cache.LoadingCache;
import org.apache.commons.lang3.Validate;
@ -37,7 +37,7 @@ import java.util.*;
import java.util.concurrent.TimeUnit;
@SuppressWarnings({"PackageAccessibility", "Duplicates"})
public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseValidatorBridge implements IValidatorModule {
public class FhirInstanceValidator extends org.hl7.fhir.r4.hapi.validation.BaseValidatorBridge implements IInstanceValidatorModule {
private boolean myAnyExtensionsAllowed = true;
private BestPracticeWarningLevel myBestPracticeWarningLevel;

4
hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/FhirInstanceValidator.java
View File

@ -2,8 +2,8 @@ package org.hl7.fhir.r5.hapi.validation;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import com.github.benmanes.caffeine.cache.CacheLoader;
import com.github.benmanes.caffeine.cache.Caffeine;
import com.github.benmanes.caffeine.cache.LoadingCache;
@ -40,7 +40,7 @@ import java.util.*;
import java.util.concurrent.TimeUnit;
@SuppressWarnings({"PackageAccessibility", "Duplicates"})
public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseValidatorBridge implements IValidatorModule {
public class FhirInstanceValidator extends org.hl7.fhir.r5.hapi.validation.BaseValidatorBridge implements IInstanceValidatorModule {
private boolean myAnyExtensionsAllowed = true;
private BestPracticeWarningLevel myBestPracticeWarningLevel;

34
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -803,7 +803,6 @@ public class FhirInstanceValidatorR4Test {
@Test
public void testValidateRawXmlResourceWithPrimitiveContainingOnlyAnExtension() {
// @formatter:off
String input = "<ActivityDefinition xmlns=\"http://hl7.org/fhir\">\n" +
" <id value=\"referralToMentalHealthCare\"/>\n" +
" <text>\n" +
@ -829,7 +828,6 @@ public class FhirInstanceValidatorR4Test {
" </event>\n" +
" </timingTiming>\n" +
" </ActivityDefinition>";
// @formatter:on
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> res = logResultsAndReturnNonInformationalOnes(output);
@ -838,7 +836,6 @@ public class FhirInstanceValidatorR4Test {
@Test
public void testValidateRawXmlWithMissingRootNamespace() {
//@formatter:off
String input = ""
+ "<Patient>"
+ " <text>"
@ -853,7 +850,6 @@ public class FhirInstanceValidatorR4Test {
+ " <gender value=\"male\"/>"
+ " <birthDate value=\"1974-12-25\"/>"
+ "</Patient>";
//@formatter:on
ValidationResult output = myVal.validateWithResult(input);
assertEquals(output.toString(), 1, output.getMessages().size());
@ -1031,6 +1027,36 @@ public class FhirInstanceValidatorR4Test {
output.getMessages().get(0).getMessage());
}
@Test
@Ignore
public void testValidateDecimalWithTrailingDot() {
String input = "{" +
" \"resourceType\": \"Observation\"," +
" \"status\": \"final\"," +
" \"subject\": {\"reference\":\"Patient/123\"}," +
" \"code\": { \"coding\": [{ \"system\":\"http://foo\", \"code\":\"123\" }] }," +
" \"referenceRange\": [\n" +
" {\n" +
" \"low\": {\n" +
" \"value\": 210.0,\n" +
" \"unit\": \"pg/mL\"\n" +
" },\n" +
" \"high\": {\n" +
" \"value\": 925.,\n" +
" \"unit\": \"pg/mL\"\n" +
" },\n" +
" \"text\": \"210.0-925.\"\n" +
" }\n" +
" ]"+
"}";
ourLog.info(input);
ValidationResult output = myVal.validateWithResult(input);
logResultsAndReturnAll(output);
assertEquals(
"",
output.getMessages().get(0).getMessage());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
Observation input = new Observation();

15
hapi-tinder-plugin/src/main/resources/vm/jpa_spring_beans_java.vm
View File

@ -71,15 +71,20 @@ public abstract class BaseJavaConfig${versionCapitalized} extends ca.uhn.fhir.jp
#else
IFhirResourceDao<${resourcePackage}.${res.declaringClassNameComplete}>
#end
dao${res.declaringClassNameComplete}${versionCapitalized}() {
dao${res.declaringClassNameComplete}${versionCapitalized}() {
#if ( ${versionCapitalized} == 'Dstu3' && ${res.name} == 'ConceptMap' )
ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized} retVal = new ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized}();
ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized} retVal;
retVal = new ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized}();
#elseif ( ${versionCapitalized.startsWith('R')} && ${res.name} == 'ConceptMap' )
ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized} retVal = new ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized}();
ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized} retVal;
retVal = new ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized}();
#elseif ( ${res.name} == 'Bundle' || ${res.name} == 'Encounter' || ${res.name} == 'Everything' || ${res.name} == 'Patient' || ${res.name} == 'Subscription' || ${res.name} == 'ValueSet' || ${res.name} == 'QuestionnaireResponse' || ${res.name} == 'SearchParameter' || ${res.name} == 'CodeSystem' || ${res.name} == 'MessageHeader' || ${res.name} == 'Composition' || ${res.name} == 'StructureDefinition')
ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized} retVal = new ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized}();
ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized} retVal;
retVal = new ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${res.name}${versionCapitalized}();
#else
ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${versionCapitalized}<${resourcePackage}.${res.declaringClassNameComplete}> retVal = new ca.uhn.fhir.jpa.dao${package_suffix}.FhirResourceDao${versionCapitalized}<${resourcePackage}.${res.declaringClassNameComplete}>();
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao<${resourcePackage}.${res.declaringClassNameComplete}> retVal;
retVal = new ca.uhn.fhir.jpa.dao.JpaResourceDao<${resourcePackage}.${res.declaringClassNameComplete}>();
#end
retVal.setResourceType(${resourcePackage}.${res.declaringClassNameComplete}.class);
retVal.setContext(fhirContext${versionCapitalized}());