Attempt to correct build issues
This commit is contained in:
James Agnew
parent
3922ff026e
commit
c8173810f4
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@ -65,14 +65,6 @@ public class BaseDstu3Config extends BaseConfig {
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return retVal;
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}
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@Bean(name="myQuestionnaireResponseValidatorDstu3")
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@Lazy
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public IValidatorModule questionnaireResponseValidatorDstu3() {
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FhirQuestionnaireResponseValidator module = new FhirQuestionnaireResponseValidator();
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module.setValidationSupport(validationSupportChainDstu3());
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return module;
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}
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@Bean(autowire = Autowire.BY_TYPE)
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public IFulltextSearchSvc searchDaoDstu3() {
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FulltextSearchSvcImpl searchDao = new FulltextSearchSvcImpl();
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@ -1,124 +1,65 @@
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package ca.uhn.fhir.jpa.dao.dstu3;
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/*
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2016 University Health Network
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* %%
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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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* http://www.apache.org/licenses/LICENSE-2.0
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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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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import javax.annotation.PostConstruct;
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import org.hl7.fhir.dstu3.model.OperationOutcome;
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import org.hl7.fhir.dstu3.model.Questionnaire;
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import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
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import org.hl7.fhir.dstu3.model.ValueSet;
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import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.entity.ResourceTable;
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import ca.uhn.fhir.rest.method.RequestDetails;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.IResourceLoader;
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import ca.uhn.fhir.validation.IValidatorModule;
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import ca.uhn.fhir.validation.ValidationResult;
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public class FhirResourceDaoQuestionnaireResponseDstu3 extends FhirResourceDaoDstu3<QuestionnaireResponse> {
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private Boolean myValidateResponses;
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@Autowired
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@Qualifier("myQuestionnaireResponseValidatorDstu3")
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private IValidatorModule myQuestionnaireResponseValidatorDstu3;
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/**
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* Initialize the bean
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*/
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@PostConstruct
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public void initialize() {
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try {
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Class.forName("org.hl7.fhir.instance.model.QuestionnaireResponse");
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myValidateResponses = true;
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} catch (ClassNotFoundException e) {
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myValidateResponses = Boolean.FALSE;
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}
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}
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@Override
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protected void validateResourceForStorage(QuestionnaireResponse theResource, ResourceTable theEntityToSave, RequestDetails theRequestDetails) {
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super.validateResourceForStorage(theResource, theEntityToSave, theRequestDetails);
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if (!myValidateResponses) {
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return;
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}
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if (theResource == null || theResource.getQuestionnaire() == null || theResource.getQuestionnaire().getReference() == null || theResource.getQuestionnaire().getReference().isEmpty()) {
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return;
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}
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FhirValidator val = getContext().newValidator();
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val.setValidateAgainstStandardSchema(false);
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val.setValidateAgainstStandardSchematron(false);
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val.registerValidatorModule(myQuestionnaireResponseValidatorDstu3);
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ValidationResult result = val.validateWithResult(getContext().newJsonParser().parseResource(getContext().newJsonParser().encodeResourceToString(theResource)));
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if (!result.isSuccessful()) {
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IBaseOperationOutcome oo = getContext().newJsonParser().parseResource(OperationOutcome.class, getContext().newJsonParser().encodeResourceToString(result.toOperationOutcome()));
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throw new UnprocessableEntityException(getContext(), oo);
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}
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}
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public class JpaResourceLoader implements IResourceLoader {
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private RequestDetails myRequestDetails;
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public JpaResourceLoader(RequestDetails theRequestDetails) {
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super();
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myRequestDetails = theRequestDetails;
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}
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@Override
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public <T extends IBaseResource> T load(Class<T> theType, IIdType theId) throws ResourceNotFoundException {
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/*
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* The QuestionnaireResponse validator uses RI structures, so for now we need to convert between that and HAPI
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* structures. This is a bit hackish, but hopefully it will go away at some point.
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*/
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if ("ValueSet".equals(theType.getSimpleName())) {
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IFhirResourceDao<ValueSet> dao = getDao(ValueSet.class);
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ValueSet in = dao.read(theId, myRequestDetails);
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return (T) in;
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} else if ("Questionnaire".equals(theType.getSimpleName())) {
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IFhirResourceDao<Questionnaire> dao = getDao(Questionnaire.class);
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Questionnaire vs = dao.read(theId, myRequestDetails);
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return (T) vs;
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} else {
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// Should not happen, validator will only ask for these two
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throw new IllegalStateException("Unexpected request to load resource of type " + theType);
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}
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}
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}
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// @Override
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// protected void validateResourceForStorage(QuestionnaireResponse theResource, ResourceTable theEntityToSave, RequestDetails theRequestDetails) {
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// super.validateResourceForStorage(theResource, theEntityToSave, theRequestDetails);
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// if (!myValidateResponses) {
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// return;
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// }
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//
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// if (theResource == null || theResource.getQuestionnaire() == null || theResource.getQuestionnaire().getReference() == null || theResource.getQuestionnaire().getReference().isEmpty()) {
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// return;
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// }
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//
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// FhirValidator val = getContext().newValidator();
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// val.setValidateAgainstStandardSchema(false);
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// val.setValidateAgainstStandardSchematron(false);
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//
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// val.registerValidatorModule(myQuestionnaireResponseValidatorDstu3);
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//
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// ValidationResult result = val.validateWithResult(getContext().newJsonParser().parseResource(getContext().newJsonParser().encodeResourceToString(theResource)));
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// if (!result.isSuccessful()) {
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// IBaseOperationOutcome oo = getContext().newJsonParser().parseResource(OperationOutcome.class, getContext().newJsonParser().encodeResourceToString(result.toOperationOutcome()));
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// throw new UnprocessableEntityException(getContext(), oo);
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// }
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// }
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//
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// public class JpaResourceLoader implements IResourceLoader {
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//
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// private RequestDetails myRequestDetails;
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//
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// public JpaResourceLoader(RequestDetails theRequestDetails) {
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// super();
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// myRequestDetails = theRequestDetails;
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// }
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//
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// @Override
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// public <T extends IBaseResource> T load(Class<T> theType, IIdType theId) throws ResourceNotFoundException {
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//
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// /*
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// * The QuestionnaireResponse validator uses RI structures, so for now we need to convert between that and HAPI
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// * structures. This is a bit hackish, but hopefully it will go away at some point.
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// */
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// if ("ValueSet".equals(theType.getSimpleName())) {
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// IFhirResourceDao<ValueSet> dao = getDao(ValueSet.class);
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// ValueSet in = dao.read(theId, myRequestDetails);
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// return (T) in;
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// } else if ("Questionnaire".equals(theType.getSimpleName())) {
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// IFhirResourceDao<Questionnaire> dao = getDao(Questionnaire.class);
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// Questionnaire vs = dao.read(theId, myRequestDetails);
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// return (T) vs;
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// } else {
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// // Should not happen, validator will only ask for these two
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// throw new IllegalStateException("Unexpected request to load resource of type " + theType);
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// }
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//
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// }
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//
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// }
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}
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@ -1,5 +1,8 @@
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package ca.uhn.fhir.jpa.term;
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import static java.util.stream.Collectors.collectingAndThen;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.IdentityHashMap;
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import java.util.Set;
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@ -73,13 +76,16 @@ public class TerminologySvcImpl implements ITerminologySvc {
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Stopwatch stopwatch = Stopwatch.createStarted();
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TermConcept concept = fetchLoadedCode(theCodeSystemResourcePid, theCodeSystemVersionPid, theCode);
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if (concept == null) {
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return Collections.emptySet();
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}
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Set<TermConcept> retVal = new HashSet<TermConcept>();
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retVal.add(concept);
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fetchParents(concept, retVal);
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ourLog.info("Fetched {} codes above code {} in {}ms", retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS));
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ourLog.info("Fetched {} codes above code {} in {}ms", new Object[] { retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS) });
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return retVal;
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}
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@ -89,13 +95,16 @@ public class TerminologySvcImpl implements ITerminologySvc {
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Stopwatch stopwatch = Stopwatch.createStarted();
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TermConcept concept = fetchLoadedCode(theCodeSystemResourcePid, theCodeSystemVersionPid, theCode);
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if (concept == null) {
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return Collections.emptySet();
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}
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Set<TermConcept> retVal = new HashSet<TermConcept>();
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retVal.add(concept);
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fetchChildren(concept, retVal);
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ourLog.info("Fetched {} codes below code {} in {}ms", retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS));
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ourLog.info("Fetched {} codes below code {} in {}ms", new Object[] { retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS) });
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return retVal;
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}
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@ -131,7 +140,8 @@ public class TerminologySvcImpl implements ITerminologySvc {
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myCodeSystemDao.save(newCodeSystem);
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} else {
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if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystem.getResource().getId())) {
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throw new InvalidRequestException(myContext.getLocalizer().getMessage(TerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri, codeSystem.getResource().getIdDt().getValue()));
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throw new InvalidRequestException(
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myContext.getLocalizer().getMessage(TerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri, codeSystem.getResource().getIdDt().getValue()));
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}
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}
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@ -9,11 +9,14 @@ import org.apache.commons.dbcp2.BasicDataSource;
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import org.hibernate.jpa.HibernatePersistenceProvider;
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import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Configuration;
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import org.springframework.context.annotation.Lazy;
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import org.springframework.orm.jpa.JpaTransactionManager;
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import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
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import org.springframework.transaction.annotation.EnableTransactionManagement;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
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import ca.uhn.fhir.validation.ResultSeverityEnum;
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@Configuration
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@EnableTransactionManagement()
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@ -65,4 +68,19 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
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return extraProperties;
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}
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/**
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* Bean which validates incoming requests
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*/
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@Bean
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@Lazy
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public RequestValidatingInterceptor requestValidatingInterceptor() {
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RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
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requestValidator.setFailOnSeverity(ResultSeverityEnum.ERROR);
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requestValidator.setAddResponseHeaderOnSeverity(null);
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requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
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requestValidator.addValidatorModule(instanceValidatorDstu3());
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return requestValidator;
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}
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}
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
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import static org.hamcrest.Matchers.containsInAnyOrder;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.empty;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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@ -100,9 +101,15 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
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concepts = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "childAA");
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codes = toCodes(concepts);
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assertThat(codes, containsInAnyOrder("childAA", "childAAA", "childAAB"));
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// Try an unknown code
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concepts = myTermSvc.findCodesBelow(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "FOO_BAD_CODE");
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codes = toCodes(concepts);
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assertThat(codes, empty());
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}
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@Test@Ignore
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@Test
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public void testFindCodesAbove() {
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CodeSystem codeSystem = new CodeSystem();
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codeSystem.setUrl("http://example.com/my_code_system");
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@ -145,6 +152,11 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
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concepts = myTermSvc.findCodesAbove(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "childAAB");
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codes = toCodes(concepts);
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assertThat(codes, containsInAnyOrder("ParentA", "childAA", "childAAB"));
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// Try an unknown code
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concepts = myTermSvc.findCodesAbove(id.getIdPartAsLong(), id.getVersionIdPartAsLong(), "FOO_BAD_CODE");
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codes = toCodes(concepts);
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assertThat(codes, empty());
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}
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@Test
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@ -157,14 +157,12 @@
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-dbcp2</artifactId>
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<version>2.0.1</version>
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</dependency>
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<!-- Only required for CORS support -->
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<dependency>
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<groupId>org.ebaysf.web</groupId>
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<artifactId>cors-filter</artifactId>
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<version>${ebay_cors_filter_version}</version>
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</dependency>
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</dependencies>
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@ -14,6 +14,7 @@ import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Configuration;
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import org.springframework.context.annotation.DependsOn;
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import org.springframework.context.annotation.Import;
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import org.springframework.context.annotation.Lazy;
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import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
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import org.springframework.orm.jpa.JpaTransactionManager;
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import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
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@ -93,12 +94,12 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
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* Bean which validates incoming requests
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*/
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@Bean
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@Lazy
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public RequestValidatingInterceptor requestValidatingInterceptor() {
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RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
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requestValidator.setFailOnSeverity(ResultSeverityEnum.ERROR);
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requestValidator.setAddResponseHeaderOnSeverity(null);
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requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
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requestValidator.addValidatorModule(questionnaireResponseValidatorDstu3());
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requestValidator.addValidatorModule(instanceValidatorDstu3());
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return requestValidator;
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@ -108,6 +109,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
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* Bean which validates outgoing responses
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*/
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@Bean
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@Lazy
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public ResponseValidatingInterceptor responseValidatingInterceptor() {
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ResponseValidatingInterceptor responseValidator = new ResponseValidatingInterceptor();
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responseValidator.setResponseHeaderValueNoIssues("Validation did not detect any issues");
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@ -124,7 +126,6 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
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responseValidator.addExcludeOperationType(RestOperationTypeEnum.HISTORY_TYPE);
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responseValidator.addExcludeOperationType(RestOperationTypeEnum.SEARCH_SYSTEM);
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responseValidator.addExcludeOperationType(RestOperationTypeEnum.SEARCH_TYPE);
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responseValidator.addValidatorModule(questionnaireResponseValidatorDstu3());
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responseValidator.addValidatorModule(instanceValidatorDstu3());
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return responseValidator;
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}
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@ -2,16 +2,14 @@ package ca.uhn.fhirtest;
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import org.eclipse.jetty.server.Server;
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import org.eclipse.jetty.webapp.WebAppContext;
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import org.hl7.fhir.dstu3.model.Organization;
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import org.hl7.fhir.dstu3.model.Patient;
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import org.hl7.fhir.dstu3.model.Subscription;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
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import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
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import org.hl7.fhir.instance.model.api.IIdType;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.api.TagList;
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import ca.uhn.fhir.model.dstu.resource.Organization;
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import ca.uhn.fhir.model.dstu.resource.Patient;
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import ca.uhn.fhir.model.dstu2.resource.Subscription;
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import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
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import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.client.IGenericClient;
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@ -20,7 +18,7 @@ public class UhnFhirTestApp {
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public static void main(String[] args) throws Exception {
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int myPort = 8888;
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String base = "http://localhost:" + myPort + "/baseDstu2";
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String base = "http://localhost:" + myPort + "/baseDstu3";
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// new File("target/testdb").mkdirs();
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||||
System.setProperty("fhir.db.location", "./target/testdb");
|
||||
|
|
@ -50,28 +48,24 @@ public class UhnFhirTestApp {
|
|||
// base = "http://spark.furore.com/fhir";
|
||||
|
||||
if (true) {
|
||||
FhirContext ctx = FhirContext.forDstu2();
|
||||
FhirContext ctx = FhirContext.forDstu3();
|
||||
IGenericClient client = ctx.newRestfulGenericClient(base);
|
||||
// client.setLogRequestAndResponse(true);
|
||||
|
||||
Organization o1 = new Organization();
|
||||
o1.getName().setValue("Some Org");
|
||||
o1.getNameElement().setValue("Some Org");
|
||||
MethodOutcome create = client.create().resource(o1).execute();
|
||||
IdDt orgId = (IdDt) create.getId();
|
||||
IIdType orgId = (IIdType) create.getId();
|
||||
|
||||
Patient p1 = new Patient();
|
||||
p1.addIdentifier("foo:bar", "12345");
|
||||
p1.getMeta().addTag("http://hl7.org/fhir/tag", "urn:happytag", "This is a happy resource");
|
||||
p1.addIdentifier().setSystem("foo:bar").setValue("12345");
|
||||
p1.addName().addFamily("Smith").addGiven("John");
|
||||
p1.getManagingOrganization().setReference(orgId);
|
||||
|
||||
TagList list = new TagList();
|
||||
list.addTag("http://hl7.org/fhir/tag", "urn:happytag", "This is a happy resource");
|
||||
ResourceMetadataKeyEnum.TAG_LIST.put(p1, list);
|
||||
client.create().resource(p1).execute();
|
||||
p1.getManagingOrganization().setReferenceElement(orgId);
|
||||
|
||||
Subscription subs = new Subscription();
|
||||
subs.setStatus(SubscriptionStatusEnum.ACTIVE);
|
||||
subs.getChannel().setType(SubscriptionChannelTypeEnum.WEBSOCKET);
|
||||
subs.setStatus(SubscriptionStatus.ACTIVE);
|
||||
subs.getChannel().setType(SubscriptionChannelType.WEBSOCKET);
|
||||
subs.setCriteria("Observation?");
|
||||
client.create().resource(subs).execute();
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue