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Add repository validating interceptor, and update for EMPI->MDM rename

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This commit is contained in:
jamesagnew
2021-01-01 16:06:18 -05:00
parent 695ef2583f
commit 803f713be6
14 changed files with 233 additions and 169 deletions
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45
src/main/java/ca/uhn/fhir/jpa/empi/EmpiConfig.java
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@@ -1,45 +0,0 @@
package ca.uhn.fhir.jpa.empi;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.empi.api.IEmpiSettings;
import ca.uhn.fhir.empi.rules.config.EmpiRuleValidator;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import java.io.IOException;
/**
* TODO: Move this to package "ca.uhn.fhir.jpa.starter" in HAPI FHIR 5.2.0+. The lousy component scan
* in 5.1.0 picks this up even if EMPI is disabled currently.
*/
@Configuration
@Conditional(EmpiConfigCondition.class)
@Import({EmpiConsumerConfig.class, EmpiSubmitterConfig.class})
public class EmpiConfig {
@Bean
EmpiRuleValidator empiRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
return new EmpiRuleValidator(theFhirContext, theSearchParamRetriever);
}
@Bean
IEmpiSettings empiSettings(@Autowired EmpiRuleValidator theEmpiRuleValidator, AppProperties appProperties) throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("empi-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new EmpiSettings(theEmpiRuleValidator).setEnabled(appProperties.getEmpi_enabled()).setScriptText(json);
}
}

45
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfig.java Normal file
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@@ -0,0 +1,45 @@
package ca.uhn.fhir.jpa.mdm;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.mdm.config.MdmConsumerConfig;
import ca.uhn.fhir.jpa.mdm.config.MdmSubmitterConfig;
import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import java.io.IOException;
/**
* TODO: Move this to package "ca.uhn.fhir.jpa.starter" in HAPI FHIR 5.2.0+. The lousy component scan
* in 5.1.0 picks this up even if MDM is disabled currently.
*/
@Configuration
@Conditional(MdmConfigCondition.class)
@Import({MdmConsumerConfig.class, MdmSubmitterConfig.class})
public class MdmConfig {
@Bean
MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
return new MdmRuleValidator(theFhirContext, theSearchParamRetriever);
}
@Bean
IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("mdm-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
}
}

6
src/main/java/ca/uhn/fhir/jpa/empi/EmpiConfigCondition.java → src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfigCondition.java
View File

@@ -1,13 +1,13 @@
package ca.uhn.fhir.jpa.empi;
package ca.uhn.fhir.jpa.mdm;
import org.springframework.context.annotation.Condition;
import org.springframework.context.annotation.ConditionContext;
import org.springframework.core.type.AnnotatedTypeMetadata;
public class EmpiConfigCondition implements Condition {
public class MdmConfigCondition implements Condition {
@Override
public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
String property = conditionContext.getEnvironment().getProperty("hapi.fhir.empi_enabled");
String property = conditionContext.getEnvironment().getProperty("hapi.fhir.mdm_enabled");
return Boolean.parseBoolean(property);
}
}

21
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -23,7 +23,7 @@ import org.springframework.context.annotation.Configuration;
@EnableConfigurationProperties
public class AppProperties {
private Boolean empi_enabled = false;
private Boolean mdm_enabled = false;
private Boolean allow_cascading_deletes = false;
private Boolean allow_contains_searches = true;
private Boolean allow_external_references = false;
@@ -32,6 +32,7 @@ public class AppProperties {
private Boolean allow_placeholder_references = true;
private Boolean auto_create_placeholder_reference_targets = true;
private Boolean enable_index_missing_fields = false;
private Boolean enable_repository_validating_interceptor = false;
private Boolean enforce_referential_integrity_on_delete = true;
private Boolean enforce_referential_integrity_on_write = true;
private Boolean etag_support_enabled = true;
@@ -90,12 +91,12 @@ public class AppProperties {
this.partitioning = partitioning;
}
public Boolean getEmpi_enabled() {
return empi_enabled;
public Boolean getMdm_enabled() {
return mdm_enabled;
}
public void setEmpi_enabled(Boolean empi_enabled) {
this.empi_enabled = empi_enabled;
public void setMdm_enabled(Boolean mdm_enabled) {
this.mdm_enabled = mdm_enabled;
}
@@ -246,7 +247,15 @@ public class AppProperties {
this.enable_index_missing_fields = enable_index_missing_fields;
}
public Boolean getEnforce_referential_integrity_on_delete() {
public Boolean getEnable_repository_validating_interceptor() {
return enable_repository_validating_interceptor;
}
public void setEnable_repository_validating_interceptor(Boolean theEnable_repository_validating_interceptor) {
enable_repository_validating_interceptor = theEnable_repository_validating_interceptor;
}
public Boolean getEnforce_referential_integrity_on_delete() {
return enforce_referential_integrity_on_delete;
}

4
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -1,6 +1,6 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.jpa.empi.EmpiConfig;
import ca.uhn.fhir.jpa.mdm.MdmConfig;
import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
@@ -24,7 +24,7 @@ import org.springframework.web.servlet.DispatcherServlet;
@ServletComponentScan(basePackageClasses = {
JpaRestfulServer.class})
@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class})
@Import({SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class, WebsocketDispatcherConfig.class, EmpiConfig.class})
@Import({SubscriptionSubmitterConfig.class, SubscriptionProcessorConfig.class, SubscriptionChannelConfig.class, WebsocketDispatcherConfig.class, MdmConfig.class})
public class Application extends SpringBootServletInitializer {
public static void main(String[] args) {

7
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
@@ -362,6 +363,12 @@ public class BaseJpaRestfulServer extends RestfulServer {
daoConfig.setLastNEnabled(true);
}
// Repository Validating Interceptor
if (Boolean.TRUE.equals(appProperties.getEnable_repository_validating_interceptor())) {
RepositoryValidationInterceptorFactory repositoryValidationInterceptorFactory = myApplicationContext.getBean(RepositoryValidationInterceptorFactory.class);
RepositoryValidatingInterceptor interceptor = repositoryValidationInterceptorFactory.build();
interceptorService.registerInterceptor(interceptor);
}
}

7
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -132,6 +132,13 @@ public class FhirServerConfigCommon {
}
@Bean
@Lazy
public RepositoryValidationInterceptorFactory repositoryValidationInterceptorFactory() {
return new RepositoryValidationInterceptorFactory();
}
@Primary
@Bean
public HibernateDialectProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {

38
src/main/java/ca/uhn/fhir/jpa/starter/RepositoryValidationInterceptorFactory.java Normal file
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@@ -0,0 +1,38 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.interceptor.validation.IRepositoryValidatingRule;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor;
import ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingRuleBuilder;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import java.util.List;
/**
* This class can be customized to enable the {@link ca.uhn.fhir.jpa.interceptor.validation.RepositoryValidatingInterceptor}
* on this server.
*
* The <code>enable_repository_validating_interceptor</code> property must be enabled in <code>application.yaml</code>
* in order to use this class.
*/
public class RepositoryValidationInterceptorFactory {
@Autowired
private ApplicationContext myApplicationContext;
@Autowired
private FhirContext myFhirContext;
public RepositoryValidatingInterceptor build() {
RepositoryValidatingRuleBuilder ruleBuilder = myApplicationContext.getBean(RepositoryValidatingRuleBuilder.class);
// Customize the ruleBuilder here to have the rules you want! We will give a simple example
// of enabling validation for all Patient resources
ruleBuilder.forResourcesOfType("Patient").requireValidationToDeclaredProfiles();
// Do not customize below this line
List<IRepositoryValidatingRule> rules = ruleBuilder.build();
return new RepositoryValidatingInterceptor(myFhirContext, rules);
}
}

1
src/main/resources/application.yaml
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@@ -57,6 +57,7 @@ hapi:
# default_encoding: JSON
# default_pretty_print: true
# default_page_size: 20
# enable_repository_validating_interceptor: false
# enable_index_missing_fields: false
# enforce_referential_integrity_on_delete: false
# enforce_referential_integrity_on_write: false

1
src/main/resources/empi-rules.json → src/main/resources/mdm-rules.json
View File

@@ -1,5 +1,6 @@
{
"version": "1",
"mdmTypes": ["Patient", "Practitioner"],
"candidateSearchParams": [
{
"resourceType": "Patient",

213
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -12,8 +12,12 @@ import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Subscription;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.boot.test.context.SpringBootTest;
@@ -21,146 +25,145 @@ import org.springframework.boot.web.server.LocalServerPort;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.net.URI;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static java.util.Comparator.comparing;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.Matchers.equalTo;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@ExtendWith(SpringExtension.class)
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
{
"spring.batch.job.enabled=false",
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.fhir_version=r4",
"hapi.fhir.subscription.websocket_enabled=true",
"hapi.fhir.empi_enabled=true",
//Override is currently required when using Empi as the construction of the Empi beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment
"spring.main.allow-bean-definition-overriding=true"
})
{
"spring.batch.job.enabled=false",
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4",
"hapi.fhir.subscription.websocket_enabled=true",
"hapi.fhir.mdm_enabled=true",
//Override is currently required when using MDM as the construction of the MDM beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment
"spring.main.allow-bean-definition-overriding=true"
})
public class ExampleServerR4IT {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
private IGenericClient ourClient;
private FhirContext ourCtx;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu2IT.class);
private IGenericClient ourClient;
private FhirContext ourCtx;
@LocalServerPort
private int port;
@LocalServerPort
private int port;
@Test
void testCreateAndRead() {
@Test
@Order(0)
void testCreateAndRead() {
String methodName = "testCreateResourceConditional";
String methodName = "testCreateResourceConditional";
Patient pt = new Patient();
pt.setActive(true);
pt.getBirthDateElement().setValueAsString("2020-01-01");
pt.addIdentifier().setSystem("http://foo").setValue("12345");
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt = new Patient();
pt.setActive(true);
pt.getBirthDateElement().setValueAsString("2020-01-01");
pt.addIdentifier().setSystem("http://foo").setValue("12345");
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
// Test EMPI
// Test MDM
// Wait until the EMPI message has been processed
await().until(() -> getPeople().size() > 0);
List<Person> persons = getPeople();
// Wait until the MDM message has been processed
await().until(() -> getPatients().size(), equalTo(2));
List<Patient> persons = getPatients();
Patient goldenRecord = persons.get(0);
// Verify a Person was created that links to our Patient
Optional<String> personLinkToCreatedPatient = persons.stream()
.map(Person::getLink)
.flatMap(Collection::stream)
.map(Person.PersonLinkComponent::getTarget)
.map(Reference::getReference)
.filter(pid -> id.toUnqualifiedVersionless().getValue().equals(pid))
.findAny();
assertTrue(personLinkToCreatedPatient.isPresent());
}
// Verify that a golden record Patient was created
assertNotNull(goldenRecord.getMeta().getTag("http://hapifhir.io/fhir/NamingSystem/mdm-record-status", "GOLDEN_RECORD"));
}
private List<Person> getPeople() {
Bundle bundle = ourClient.search().forResource(Person.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
return BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Person.class);
}
private List<Patient> getPatients() {
Bundle bundle = ourClient.search().forResource(Patient.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
List<Patient> retVal = BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Patient.class);
retVal.sort(comparing(o -> ((Patient) o).getMeta().getLastUpdated()).reversed());
return retVal;
}
@Test
public void testWebsocketSubscription() throws Exception {
/*
* Create subscription
*/
Subscription subscription = new Subscription();
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
subscription.setCriteria("Observation?status=final");
@Test
@Order(1)
public void testWebsocketSubscription() throws Exception {
/*
* Create subscription
*/
Subscription subscription = new Subscription();
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
subscription.setCriteria("Observation?status=final");
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
channel.setPayload("application/json");
subscription.setChannel(channel);
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
channel.setPayload("application/json");
subscription.setChannel(channel);
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();
// Wait for the subscription to be activated
await().until(() -> activeSubscriptionCount() == 3);
// Wait for the subscription to be activated
await().until(() -> activeSubscriptionCount() == 3);
/*
* Attach websocket
*/
/*
* Attach websocket
*/
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + port + "/websocket");
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
Session session = connection.get(2, TimeUnit.SECONDS);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + port + "/websocket");
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
Session session = connection.get(2, TimeUnit.SECONDS);
ourLog.info("Connected to WS: {}", session.isOpen());
ourLog.info("Connected to WS: {}", session.isOpen());
/*
* Create a matching resource
*/
Observation obs = new Observation();
obs.setStatus(Observation.ObservationStatus.FINAL);
ourClient.create().resource(obs).execute();
/*
* Create a matching resource
*/
Observation obs = new Observation();
obs.setStatus(Observation.ObservationStatus.FINAL);
ourClient.create().resource(obs).execute();
// Give some time for the subscription to deliver
Thread.sleep(2000);
// Give some time for the subscription to deliver
Thread.sleep(2000);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
/*
* Clean up
*/
ourClient.delete().resourceById(mySubscriptionId).execute();
}
/*
* Clean up
*/
ourClient.delete().resourceById(mySubscriptionId).execute();
}
private int activeSubscriptionCount() {
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
}
private int activeSubscriptionCount() {
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
}
@BeforeEach
void beforeEach() {
@BeforeEach
void beforeEach() {
ourCtx = FhirContext.forR4();
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
ourCtx = FhirContext.forR4();
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + port + "/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
}