Incremental progress on large ValueSet expansion with URL parameter.
This commit is contained in:
parent
c82c3a093f
commit
19676a01b7
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@ -146,12 +146,12 @@ public class DaoConfig {
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private boolean myEnableInMemorySubscriptionMatching = true;
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private boolean myEnforceReferenceTargetTypes = true;
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private ClientIdStrategyEnum myResourceClientIdStrategy = ClientIdStrategyEnum.ALPHANUMERIC;
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private boolean myFilterParameterEnabled = false;
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private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
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/**
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* EXPERIMENTAL - Do not use in production! Do not change default of {@code false}!
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*/
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private boolean myPreExpandValueSetsExperimental = true; // FIXME: DM 2019-09-03 - Return to false before merging into master.
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private boolean myFilterParameterEnabled = false;
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private StoreMetaSourceInformationEnum myStoreMetaSourceInformation = StoreMetaSourceInformationEnum.SOURCE_URI_AND_REQUEST_ID;
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private boolean myPreExpandValueSetsExperimental = false;
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/**
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* EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
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*/
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@ -121,7 +121,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
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}
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@Override
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public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
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public List<VersionIndependentConcept> expandValueSet(String theValueSet) {//FIXME: DM COWABUNGA
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ValueSet vs = myValidationSupport.fetchResource(myContext, ValueSet.class, theValueSet);
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if (vs == null) {
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return Collections.emptyList();
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@ -156,7 +156,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
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for (Long conceptId : conceptIds) {
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myValueSetConceptDao.updateOrderById(conceptId, order++);
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}
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ourLog.info("Have remove gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSet.getUrl());
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ourLog.info("Have removed gaps from concept order for {} concepts in ValueSet[{}]", conceptIds.size(), myTermValueSet.getUrl());
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return true;
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}
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@ -1,5 +1,6 @@
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package ca.uhn.fhir.jpa.provider.r4;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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@ -24,10 +25,13 @@ import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
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import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
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import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
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import org.hl7.fhir.r4.model.ValueSet.FilterOperator;
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import org.hl7.fhir.r4.model.codesystems.HttpVerb;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Before;
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import org.junit.Test;
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import org.springframework.transaction.annotation.Transactional;
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import org.springframework.transaction.TransactionStatus;
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import org.springframework.transaction.support.TransactionCallbackWithoutResult;
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import org.springframework.transaction.support.TransactionTemplate;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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@ -40,18 +44,86 @@ import static org.junit.Assert.*;
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public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderR4ValueSetTest.class);
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private IIdType myExtensionalCsId;
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private IIdType myExtensionalVsId;
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private IIdType myLocalValueSetId;
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private Long myExtensionalCsIdOnResourceTable;
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private Long myExtensionalVsIdOnResourceTable;
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private ValueSet myLocalVs;
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@Before
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@Transactional
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public void before02() throws IOException {
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CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
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myCodeSystemDao.create(cs, mySrd);
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// @Before
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// @Transactional
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// public void before02() throws IOException {
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// CodeSystem cs = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
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// myCodeSystemDao.create(cs, mySrd);
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//
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// ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
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// myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
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// }
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ValueSet upload = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
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myExtensionalVsId = myValueSetDao.create(upload, mySrd).getId().toUnqualifiedVersionless();
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private void loadAndPersistCodeSystemAndValueSet(HttpVerb theVerb) throws IOException {
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loadAndPersistCodeSystem(theVerb);
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loadAndPersistValueSet(theVerb);
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}
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private void loadAndPersistCodeSystem(HttpVerb theVerb) throws IOException {
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CodeSystem codeSystem = loadResourceFromClasspath(CodeSystem.class, "/extensional-case-3-cs.xml");
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codeSystem.setId("CodeSystem/cs");
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persistCodeSystem(codeSystem, theVerb);
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}
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private void persistCodeSystem(CodeSystem theCodeSystem, HttpVerb theVerb) {
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switch (theVerb) {
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case POST:
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new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
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@Override
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protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
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myExtensionalCsId = myCodeSystemDao.create(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
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}
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});
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break;
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case PUT:
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new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
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@Override
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protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
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myExtensionalCsId = myCodeSystemDao.update(theCodeSystem, mySrd).getId().toUnqualifiedVersionless();
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}
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});
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break;
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default:
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throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
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}
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myExtensionalCsIdOnResourceTable = myCodeSystemDao.readEntity(myExtensionalCsId, null).getId();
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}
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private void loadAndPersistValueSet(HttpVerb theVerb) throws IOException {
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ValueSet valueSet = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
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valueSet.setId("ValueSet/vs");
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persistValueSet(valueSet, theVerb);
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}
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private void persistValueSet(ValueSet theValueSet, HttpVerb theVerb) {
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switch (theVerb) {
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case POST:
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new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
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@Override
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protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
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myExtensionalVsId = myValueSetDao.create(theValueSet, mySrd).getId().toUnqualifiedVersionless();
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}
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});
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break;
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case PUT:
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new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
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@Override
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protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
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myExtensionalVsId = myValueSetDao.update(theValueSet, mySrd).getId().toUnqualifiedVersionless();
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}
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});
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break;
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default:
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throw new IllegalArgumentException("HTTP verb is not supported: " + theVerb);
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}
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myExtensionalVsIdOnResourceTable = myValueSetDao.readEntity(myExtensionalVsId, null).getId();
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}
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private CodeSystem createExternalCs() {
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@ -128,8 +200,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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}
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@Test
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public void testExpandById() {
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//@formatter:off
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public void testExpandById() throws Exception {
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loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
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Parameters respParam = ourClient
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.operation()
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.onInstance(myExtensionalVsId)
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@ -137,7 +210,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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.withNoParameters(Parameters.class)
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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//@formatter:on
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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@ -158,9 +230,42 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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}
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@Test
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public void testExpandByIdWithFilter() {
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public void testExpandByIdWithPreExpansion() throws Exception {
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myDaoConfig.setPreExpandValueSetsExperimental(true);
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loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
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myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
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Parameters respParam = ourClient
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.operation()
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.onInstance(myExtensionalVsId)
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.named("expand")
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.withNoParameters(Parameters.class)
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
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assertThat(resp, containsString("<expansion>"));
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assertThat(resp, containsString("<contains>"));
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assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
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assertThat(resp, containsString("<code value=\"8450-9\"/>"));
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assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
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assertThat(resp, containsString("</contains>"));
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assertThat(resp, containsString("<contains>"));
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assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
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assertThat(resp, containsString("<code value=\"11378-7\"/>"));
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assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
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assertThat(resp, containsString("</contains>"));
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assertThat(resp, containsString("</expansion>"));
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}
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@Test
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public void testExpandByIdWithFilter() throws Exception {
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loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
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//@formatter:off
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Parameters respParam = ourClient
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.operation()
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.onInstance(myExtensionalVsId)
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@ -168,7 +273,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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.withParameter(Parameters.class, "filter", new StringType("first"))
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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//@formatter:on
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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@ -178,12 +282,64 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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}
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@Test
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public void testExpandByUrl() {
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public void testExpandByIdWithFilterWithPreExpansion() throws Exception {
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myDaoConfig.setPreExpandValueSetsExperimental(true);
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loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
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myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
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Parameters respParam = ourClient
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.operation()
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.onInstance(myExtensionalVsId)
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.named("expand")
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.withParameter(Parameters.class, "filter", new StringType("first"))
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
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assertThat(resp, not(containsString("<display value=\"Systolic blood pressure--expiration\"/>")));
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}
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@Test
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public void testExpandByUrl() throws Exception {
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loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
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Parameters respParam = ourClient
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.operation()
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.onType(ValueSet.class)
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.named("expand")
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.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2"))
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// .withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2")) //FIXME: DM
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.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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assertThat(resp, stringContainsInOrder(
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"<code value=\"11378-7\"/>",
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"<display value=\"Systolic blood pressure at First encounter\"/>"));
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}
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@Test
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public void testExpandByUrlWithPreExpansion() throws Exception {//FIXME: DM
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myDaoConfig.setPreExpandValueSetsExperimental(true);
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ourLog.info("DIEDERIK - before loading CD and VS");
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loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
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ourLog.info("DIEDERIK - after loading CD and VS; before pre-expansion");
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myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
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ourLog.info("DIEDERIK - after pre-expansion");
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Parameters respParam = ourClient
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.operation()
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.onType(ValueSet.class)
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.named("expand")
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// .withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2")) //FIXME: DM
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.withParameter(Parameters.class, "url", new UriType("http://www.healthintersections.com.au/fhir/ValueSet/bogus"))
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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@ -197,6 +353,8 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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@Test
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public void testExpandByValueSet() throws IOException {
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loadAndPersistCodeSystem(HttpVerb.POST);
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ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
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Parameters respParam = ourClient
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@ -215,13 +373,36 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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}
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@Test
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public void testExpandByValueSetWithPreExpansion() throws IOException {
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myDaoConfig.setPreExpandValueSetsExperimental(true);
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loadAndPersistCodeSystem(HttpVerb.POST);
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myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
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ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
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Parameters respParam = ourClient
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.operation()
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.onType(ValueSet.class)
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.named("expand")
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.withParameter(Parameters.class, "valueSet", toExpand)
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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assertThat(resp, stringContainsInOrder(
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"<code value=\"11378-7\"/>",
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"<display value=\"Systolic blood pressure at First encounter\"/>"));
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}
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@Test
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public void testExpandInlineVsAgainstBuiltInCs() {
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createLocalVsPointingAtBuiltInCodeSystem();
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assertNotNull(myLocalValueSetId);
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//@formatter:off
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Parameters respParam = ourClient
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.operation()
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.onType(ValueSet.class)
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@ -229,7 +410,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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.withParameter(Parameters.class, "valueSet", myLocalVs)
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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//@formatter:on
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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@ -243,7 +423,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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assertNotNull(myLocalVs);
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myLocalVs.setId("");
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//@formatter:off
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Parameters respParam = ourClient
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.operation()
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.onType(ValueSet.class)
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@ -251,7 +430,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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.withParameter(Parameters.class, "valueSet", myLocalVs)
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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//@formatter:on
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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@ -263,7 +441,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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}
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@Test
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public void testExpandInvalidParams() throws IOException {
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public void testExpandInvalidParams() throws Exception {
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loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
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try {
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ourClient
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.operation()
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@ -334,7 +514,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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createLocalVsPointingAtBuiltInCodeSystem();
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assertNotNull(myLocalValueSetId);
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//@formatter:off
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Parameters respParam = ourClient
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.operation()
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.onInstance(myLocalValueSetId)
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@ -342,7 +521,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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.withNoParameters(Parameters.class)
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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//@formatter:on
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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@ -355,7 +533,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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createExternalCsAndLocalVs();
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assertNotNull(myLocalValueSetId);
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//@formatter:off
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Parameters respParam = ourClient
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.operation()
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.onInstance(myLocalValueSetId)
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@ -363,7 +540,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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.withNoParameters(Parameters.class)
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.execute();
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ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
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//@formatter:on
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
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ourLog.info(resp);
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@ -401,7 +577,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
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createExternalCsAndLocalVsWithUnknownCode();
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assertNotNull(myLocalValueSetId);
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//@formatter:off
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try {
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ourClient
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.operation()
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||||
|
@ -412,7 +587,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
}
|
||||
//@formatter:on
|
||||
}
|
||||
|
||||
/**
|
||||
|
@ -438,8 +612,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() {
|
||||
//@formatter:off
|
||||
public void testValidateCodeOperationByCodeAndSystemInstance() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onInstance(myExtensionalVsId)
|
||||
|
@ -498,8 +673,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationByCodeAndSystemType() {
|
||||
//@formatter:off
|
||||
public void testValidateCodeOperationByCodeAndSystemType() throws Exception {
|
||||
loadAndPersistCodeSystemAndValueSet(HttpVerb.POST);
|
||||
|
||||
Parameters respParam = ourClient
|
||||
.operation()
|
||||
.onType(ValueSet.class)
|
||||
|
@ -585,6 +761,11 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
|
|||
|
||||
}
|
||||
|
||||
@After
|
||||
public void afterResetPreExpansionDefault() {
|
||||
myDaoConfig.setPreExpandValueSetsExperimental(new DaoConfig().isPreExpandValueSetsExperimental());
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
|
|
Loading…
Reference in New Issue