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Merging master into working branch.

This commit is contained in:
Diederik Muylwyk 2019-09-30 09:41:43 -04:00
parent 0386448b3f 1b2892f475
commit 7eaa5d5574
24 changed files with 706 additions and 437 deletions
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4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
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@ -237,6 +237,10 @@ public class Constants {
public static final int STATUS_HTTP_202_ACCEPTED = 202;
public static final String HEADER_X_PROGRESS = "X-Progress";
public static final String HEADER_RETRY_AFTER = "Retry-After";
/**
* Operation name for the $lastn operation
*/
public static final String OPERATION_LASTN = "$lastn";
static {
CHARSET_UTF8 = StandardCharsets.UTF_8;

11
hapi-fhir-jpaserver-base/pom.xml
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@ -483,6 +483,8 @@
<groupId>org.glassfish</groupId>
<artifactId>javax.el</artifactId>
</dependency>
<!-- Hibernate Search -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-search-orm</artifactId>
@ -495,6 +497,10 @@
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-phonetic</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-search-elasticsearch</artifactId>
</dependency>
<!-- Misc -->
<dependency>
@ -568,6 +574,11 @@
<artifactId>greenmail-spring</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>pl.allegro.tech</groupId>
<artifactId>embedded-elasticsearch</artifactId>
<version>2.10.0</version>
</dependency>
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceSearchView.java
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@ -62,17 +62,13 @@ public class ResourceSearchView implements IBaseResourceEntity, Serializable {
@Id
@Column(name = "PID")
private Long myId;
@Column(name = "RES_ID")
private Long myResourceId;
@Column(name = "RES_TYPE", length = Constants.MAX_RESOURCE_NAME_LENGTH)
private String myResourceType;
@Column(name = "RES_VERSION")
@Enumerated(EnumType.STRING)
private FhirVersionEnum myFhirVersion;
@Column(name = "RES_VER")
private Long myResourceVersion;
@Column(name = "PROV_REQUEST_ID", length = Constants.REQUEST_ID_LENGTH)

90
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchHibernatePropertiesBuilder.java Normal file
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@ -0,0 +1,90 @@
package ca.uhn.fhir.jpa.search.elastic;
import org.hibernate.search.cfg.Environment;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchEnvironment;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
import java.util.Properties;
/**
* This class is used to inject appropriate properties into a hibernate
* Properties object being used to create an entitymanager for a HAPI
* FHIR JPA server.
*/
public class ElasticsearchHibernatePropertiesBuilder {
private ElasticsearchIndexStatus myRequiredIndexStatus = ElasticsearchIndexStatus.YELLOW;
private String myRestUrl;
private String myUsername;
private String myPassword;
private IndexSchemaManagementStrategy myIndexSchemaManagementStrategy = IndexSchemaManagementStrategy.CREATE;
private long myIndexManagementWaitTimeoutMillis = 10000L;
private boolean myDebugRefreshAfterWrite = false;
private boolean myDebugPrettyPrintJsonLog = false;
public ElasticsearchHibernatePropertiesBuilder setUsername(String theUsername) {
myUsername = theUsername;
return this;
}
public ElasticsearchHibernatePropertiesBuilder setPassword(String thePassword) {
myPassword = thePassword;
return this;
}
public void apply(Properties theProperties) {
// Don't use the Lucene properties as they conflict
theProperties.remove("hibernate.search.model_mapping");
// the below properties are used for ElasticSearch integration
theProperties.put("hibernate.search.default." + Environment.INDEX_MANAGER_IMPL_NAME, "elasticsearch");
theProperties.put("hibernate.search." + ElasticsearchEnvironment.ANALYSIS_DEFINITION_PROVIDER, ElasticsearchMappingProvider.class.getName());
theProperties.put("hibernate.search.default.elasticsearch.host", myRestUrl);
theProperties.put("hibernate.search.default.elasticsearch.username", myUsername);
theProperties.put("hibernate.search.default.elasticsearch.password", myPassword);
theProperties.put("hibernate.search.default." + ElasticsearchEnvironment.INDEX_SCHEMA_MANAGEMENT_STRATEGY, myIndexSchemaManagementStrategy.getExternalName());
theProperties.put("hibernate.search.default." + ElasticsearchEnvironment.INDEX_MANAGEMENT_WAIT_TIMEOUT, Long.toString(myIndexManagementWaitTimeoutMillis));
theProperties.put("hibernate.search.default." + ElasticsearchEnvironment.REQUIRED_INDEX_STATUS, myRequiredIndexStatus.getElasticsearchString());
// Only for unit tests
theProperties.put("hibernate.search.default." + ElasticsearchEnvironment.REFRESH_AFTER_WRITE, Boolean.toString(myDebugRefreshAfterWrite));
theProperties.put("hibernate.search." + ElasticsearchEnvironment.LOG_JSON_PRETTY_PRINTING, Boolean.toString(myDebugPrettyPrintJsonLog));
}
public ElasticsearchHibernatePropertiesBuilder setRequiredIndexStatus(ElasticsearchIndexStatus theRequiredIndexStatus) {
myRequiredIndexStatus = theRequiredIndexStatus;
return this;
}
public ElasticsearchHibernatePropertiesBuilder setRestUrl(String theRestUrl) {
myRestUrl = theRestUrl;
return this;
}
public ElasticsearchHibernatePropertiesBuilder setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy theIndexSchemaManagementStrategy) {
myIndexSchemaManagementStrategy = theIndexSchemaManagementStrategy;
return this;
}
public ElasticsearchHibernatePropertiesBuilder setIndexManagementWaitTimeoutMillis(long theIndexManagementWaitTimeoutMillis) {
myIndexManagementWaitTimeoutMillis = theIndexManagementWaitTimeoutMillis;
return this;
}
public ElasticsearchHibernatePropertiesBuilder setDebugRefreshAfterWrite(boolean theDebugRefreshAfterWrite) {
myDebugRefreshAfterWrite = theDebugRefreshAfterWrite;
return this;
}
public ElasticsearchHibernatePropertiesBuilder setDebugPrettyPrintJsonLog(boolean theDebugPrettyPrintJsonLog) {
myDebugPrettyPrintJsonLog = theDebugPrettyPrintJsonLog;
return this;
}
}

10
hapi-fhir-jpaserver-elasticsearch/src/main/java/ca/uhn/fhir/jpa/search/ElasticsearchMappingProvider.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchMappingProvider.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.search;
package ca.uhn.fhir.jpa.search.elastic;
/*-
* #%L
@ -20,9 +20,8 @@ package ca.uhn.fhir.jpa.search;
* #L%
*/
import org.apache.lucene.analysis.core.WhitespaceTokenizerFactory;
import org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionRegistryBuilder;
import org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionProvider;
import org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionRegistryBuilder;
public class ElasticsearchMappingProvider implements ElasticsearchAnalysisDefinitionProvider {
@ -39,10 +38,7 @@ public class ElasticsearchMappingProvider implements ElasticsearchAnalysisDefini
builder.analyzer("autocompletePhoneticAnalyzer")
.withTokenizer("standard")
.withTokenFilters("standard", "stop", "snowball_english", "phonetic_doublemetaphone");
builder.tokenFilter("phonetic_doublemetaphone")
.type("phonetic")
.param("encoder", "double_metaphone");
.withTokenFilters("standard", "stop", "snowball_english");
builder.tokenFilter("snowball_english").type("snowball").param("language", "English");
builder.analyzer("autocompleteNGramAnalyzer")

46
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3WithoutLuceneConfig.java
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@ -1,46 +0,0 @@
package ca.uhn.fhir.jpa.config;
import java.util.Properties;
import org.hibernate.dialect.H2Dialect;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@Configuration
@EnableTransactionManagement()
public class TestDstu3WithoutLuceneConfig extends TestDstu3Config {
/**
* Disable fulltext searching
*/
@Override
public IFulltextSearchSvc searchDaoDstu3() {
return null;
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
retVal.setJpaProperties(jpaProperties());
return retVal;
}
private Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.dialect", H2Dialect.class.getName());
extraProperties.put("hibernate.search.autoregister_listeners", "false");
return extraProperties;
}
}

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
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@ -138,7 +138,8 @@ public class TestR4Config extends BaseJavaConfigR4 {
return retVal;
}
private Properties jpaProperties() {
@Bean
public Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");

74
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticSearch.java Normal file
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@ -0,0 +1,74 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import pl.allegro.tech.embeddedelasticsearch.EmbeddedElastic;
import pl.allegro.tech.embeddedelasticsearch.PopularProperties;
import javax.annotation.PreDestroy;
import java.io.IOException;
import java.util.Properties;
import java.util.UUID;
import java.util.concurrent.TimeUnit;
@Configuration
public class TestR4ConfigWithElasticSearch extends TestR4Config {
private static final Logger ourLog = LoggerFactory.getLogger(TestR4ConfigWithElasticSearch.class);
private static final String ELASTIC_VERSION = "6.5.4";
@Override
@Bean
public Properties jpaProperties() {
Properties retVal = super.jpaProperties();
// Force elasticsearch to start first
int httpPort = embeddedElasticSearch().getHttpPort();
ourLog.info("ElasticSearch started on port: {}", httpPort);
new ElasticsearchHibernatePropertiesBuilder()
.setDebugRefreshAfterWrite(true)
.setDebugPrettyPrintJsonLog(true)
.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE)
.setIndexManagementWaitTimeoutMillis(10000)
.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW)
.setRestUrl("http://localhost:" + httpPort)
.setUsername("")
.setPassword("")
.apply(retVal);
return retVal;
}
@Bean
public EmbeddedElastic embeddedElasticSearch() {
EmbeddedElastic embeddedElastic = null;
try {
embeddedElastic = EmbeddedElastic.builder()
.withElasticVersion(ELASTIC_VERSION)
.withSetting(PopularProperties.TRANSPORT_TCP_PORT, 0)
.withSetting(PopularProperties.HTTP_PORT, 0)
.withSetting(PopularProperties.CLUSTER_NAME, UUID.randomUUID())
.withStartTimeout(60, TimeUnit.SECONDS)
.build()
.start();
} catch (IOException | InterruptedException e) {
throw new ConfigurationException(e);
}
return embeddedElastic;
}
@PreDestroy
public void stop() {
embeddedElasticSearch().stop();
}
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4WithoutLuceneConfig.java → hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4WithLuceneDisabledConfig.java
View File

@ -15,7 +15,7 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@Configuration
@EnableTransactionManagement()
public class TestR4WithoutLuceneConfig extends TestR4Config {
public class TestR4WithLuceneDisabledConfig extends TestR4Config {
/**
* Disable fulltext searching
@ -34,7 +34,8 @@ public class TestR4WithoutLuceneConfig extends TestR4Config {
return retVal;
}
private Properties jpaProperties() {
@Override
public Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");

234
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java
View File

@ -1,234 +0,0 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.config.TestDstu3WithoutLuceneConfig;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.PlatformTransactionManager;
import javax.persistence.EntityManager;
import static org.junit.Assert.*;
// @RunWith(SpringJUnit4ClassRunner.class)
// @ContextConfiguration(classes= {TestDstu3WithoutLuceneConfig.class})
// @SuppressWarnings("unchecked")
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = {TestDstu3WithoutLuceneConfig.class})
public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3SearchWithLuceneDisabledTest.class);
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
protected PlatformTransactionManager myTxManager;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
@Autowired
@Qualifier("myAllergyIntoleranceDaoDstu3")
private IFhirResourceDao<AllergyIntolerance> myAllergyIntoleranceDao;
@Autowired
@Qualifier("myAppointmentDaoDstu3")
private IFhirResourceDao<Appointment> myAppointmentDao;
@Autowired
@Qualifier("myAuditEventDaoDstu3")
private IFhirResourceDao<AuditEvent> myAuditEventDao;
@Autowired
@Qualifier("myBundleDaoDstu3")
private IFhirResourceDao<Bundle> myBundleDao;
@Autowired
@Qualifier("myCarePlanDaoDstu3")
private IFhirResourceDao<CarePlan> myCarePlanDao;
@Autowired
@Qualifier("myCodeSystemDaoDstu3")
private IFhirResourceDao<CodeSystem> myCodeSystemDao;
@Autowired
@Qualifier("myCompartmentDefinitionDaoDstu3")
private IFhirResourceDao<CompartmentDefinition> myCompartmentDefinitionDao;
@Autowired
@Qualifier("myConceptMapDaoDstu3")
private IFhirResourceDao<ConceptMap> myConceptMapDao;
@Autowired
@Qualifier("myConditionDaoDstu3")
private IFhirResourceDao<Condition> myConditionDao;
@Autowired
@Qualifier("myDeviceDaoDstu3")
private IFhirResourceDao<Device> myDeviceDao;
@Autowired
@Qualifier("myDiagnosticReportDaoDstu3")
private IFhirResourceDao<DiagnosticReport> myDiagnosticReportDao;
@Autowired
@Qualifier("myEncounterDaoDstu3")
private IFhirResourceDao<Encounter> myEncounterDao;
// @PersistenceContext()
@Autowired
private EntityManager myEntityManager;
@Autowired
private FhirContext myFhirCtx;
@Autowired
@Qualifier("myImmunizationDaoDstu3")
private IFhirResourceDao<Immunization> myImmunizationDao;
@Autowired
@Qualifier("myLocationDaoDstu3")
private IFhirResourceDao<Location> myLocationDao;
@Autowired
@Qualifier("myMediaDaoDstu3")
private IFhirResourceDao<Media> myMediaDao;
@Autowired
@Qualifier("myMedicationDaoDstu3")
private IFhirResourceDao<Medication> myMedicationDao;
@Autowired
@Qualifier("myMedicationRequestDaoDstu3")
private IFhirResourceDao<MedicationRequest> myMedicationRequestDao;
@Autowired
@Qualifier("myNamingSystemDaoDstu3")
private IFhirResourceDao<NamingSystem> myNamingSystemDao;
@Autowired
@Qualifier("myObservationDaoDstu3")
private IFhirResourceDao<Observation> myObservationDao;
@Autowired
@Qualifier("myOperationDefinitionDaoDstu3")
private IFhirResourceDao<OperationDefinition> myOperationDefinitionDao;
@Autowired
@Qualifier("myOrganizationDaoDstu3")
private IFhirResourceDao<Organization> myOrganizationDao;
@Autowired
@Qualifier("myPatientDaoDstu3")
private IFhirResourceDaoPatient<Patient> myPatientDao;
@Autowired
@Qualifier("myPractitionerDaoDstu3")
private IFhirResourceDao<Practitioner> myPractitionerDao;
@Autowired
@Qualifier("myQuestionnaireDaoDstu3")
private IFhirResourceDao<Questionnaire> myQuestionnaireDao;
@Autowired
@Qualifier("myQuestionnaireResponseDaoDstu3")
private IFhirResourceDao<QuestionnaireResponse> myQuestionnaireResponseDao;
@Autowired
@Qualifier("myResourceProvidersDstu3")
private Object myResourceProviders;
@Autowired
@Qualifier("myStructureDefinitionDaoDstu3")
private IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
@Autowired
@Qualifier("mySubscriptionDaoDstu3")
private IFhirResourceDaoSubscription<Subscription> mySubscriptionDao;
@Autowired
@Qualifier("mySubstanceDaoDstu3")
private IFhirResourceDao<Substance> mySubstanceDao;
@Autowired
@Qualifier("mySystemDaoDstu3")
private IFhirSystemDao<Bundle, Meta> mySystemDao;
@Autowired
@Qualifier("mySystemProviderDstu3")
private JpaSystemProviderDstu3 mySystemProvider;
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
private IValidationSupport myValidationSupport;
@Autowired
private IResourceReindexingSvc myResourceReindexingSvc;
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
@Before
public void beforePurgeDatabase() {
purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
}
@Before
public void beforeResetConfig() {
myDaoConfig.setHardSearchLimit(1000);
myDaoConfig.setHardTagListLimit(1000);
myDaoConfig.setIncludeLimit(2000);
}
@Override
protected FhirContext getContext() {
return myFhirCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
@Test
public void testSearchWithContent() throws Exception {
String methodName = "testEverythingIncludesBackReferences";
Organization org = new Organization();
org.setName(methodName);
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, new StringParam(methodName));
try {
myOrganizationDao.search(map).size();
fail();
} catch (InvalidRequestException e) {
assertEquals("Fulltext search is not enabled on this service, can not process parameter: _content", e.getMessage());
}
}
@Test
public void testSearchWithRegularParam() throws Exception {
String methodName = "testEverythingIncludesBackReferences";
Organization org = new Organization();
org.setName(methodName);
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add(Organization.SP_NAME, new StringParam(methodName));
myOrganizationDao.search(map);
}
@Test
public void testSearchWithText() throws Exception {
String methodName = "testEverythingIncludesBackReferences";
Organization org = new Organization();
org.setName(methodName);
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add(ca.uhn.fhir.rest.api.Constants.PARAM_TEXT, new StringParam(methodName));
try {
myOrganizationDao.search(map).size();
fail();
} catch (InvalidRequestException e) {
assertEquals("Fulltext search is not enabled on this service, can not process parameter: _text", e.getMessage());
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

96
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchFtTest.java
View File

@ -1,28 +1,29 @@
package ca.uhn.fhir.jpa.dao.r4;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Mockito.mock;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import javax.servlet.http.HttpServletRequest;
import java.util.List;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Mockito.mock;
public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4SearchFtTest.class);
@Before
@ -30,12 +31,6 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test
public void testCodeTextSearch() {
Observation obs1 = new Observation();
@ -52,7 +47,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map;
map = new SearchParameterMap();
map.add(Observation.SP_CODE, new TokenParam(null, "systolic").setModifier(TokenParamModifier.TEXT));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
@ -72,7 +67,6 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
}
@Test
public void testResourceTextSearch() {
Observation obs1 = new Observation();
@ -81,15 +75,15 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
obs1.setValue(new Quantity(123));
obs1.getNoteFirstRep().setText("obs1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs2.getCode().setText("Diastolic Blood Pressure");
obs2.setStatus(ObservationStatus.FINAL);
obs2.setValue(new Quantity(81));
IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map;
map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, new StringParam("systolic"));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
@ -112,22 +106,21 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
obs1.setValue(new StringType("Systolic Blood Pressure"));
obs1.setStatus(ObservationStatus.FINAL);
IIdType id1 = myObservationDao.create(obs1, mockSrd()).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs1.getCode().setText("AAAAA");
obs1.setValue(new StringType("Diastolic Blood Pressure"));
obs2.setStatus(ObservationStatus.FINAL);
IIdType id2 = myObservationDao.create(obs2, mockSrd()).getId().toUnqualifiedVersionless();
SearchParameterMap map;
map = new SearchParameterMap();
map.add(Observation.SP_VALUE_STRING, new StringParam("sure").setContains(true));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1, id2)));
}
@Test
public void testSuggestIgnoresBase64Content() {
Patient patient = new Patient();
@ -153,11 +146,11 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
Media med = new Media();
med.getSubject().setReferenceElement(ptId);
med.getContent().setContentType("LCws");
med.getContent().setDataElement(new Base64BinaryType(new byte[] {44,44,44,44,44,44,44,44}));
med.getContent().setDataElement(new Base64BinaryType(new byte[]{44, 44, 44, 44, 44, 44, 44, 44}));
med.getContent().setTitle("bbbb syst");
myMediaDao.create(med, mockSrd());
ourLog.info(myFhirCtx.newJsonParser().encodeResourceToString(med));
List<Suggestion> output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "press", null);
ourLog.info("Found: " + output);
assertEquals(2, output.size());
@ -177,12 +170,12 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
assertEquals("bbbb syst", output.get(1).getTerm());
assertEquals("Systolic", output.get(2).getTerm());
assertEquals("Systolic Blood Pressure", output.get(3).getTerm());
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "LCws", null);
ourLog.info("Found: " + output);
assertEquals(0, output.size());
}
@Test
public void testSuggest() {
Patient patient = new Patient();
@ -238,7 +231,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
assertEquals(2, output.size());
assertEquals("HELLO", output.get(0).getTerm());
assertEquals("ZXC HELLO", output.get(1).getTerm());
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "Z", null);
ourLog.info("Found: " + output);
assertEquals(0, output.size());
@ -250,8 +243,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
assertEquals("ZXC HELLO", output.get(1).getTerm());
}
@Test
public void testSearchAndReindex() {
Patient patient;
@ -311,7 +303,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
Device dev1 = new Device();
dev1.setManufacturer("Some Manufacturer");
IIdType devId1 = myDeviceDao.create(dev1, mockSrd()).getId().toUnqualifiedVersionless();
Device dev2 = new Device();
dev2.setManufacturer("Some Manufacturer 2");
myDeviceDao.create(dev2, mockSrd()).getId().toUnqualifiedVersionless();
@ -335,14 +327,14 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
obs3.getCode().addCoding().setCode("CODE3");
obs3.setValue(new StringType("obsvalue3"));
IIdType obsId3 = myObservationDao.create(obs3, mockSrd()).getId().toUnqualifiedVersionless();
HttpServletRequest request;
List<String> actual;
request = mock(HttpServletRequest.class);
StringAndListParam param;
ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart());
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, null, mockSrd()));
@ -360,7 +352,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
/*
* Add another match
*/
Observation obs4 = new Observation();
obs4.getSubject().setReferenceElement(ptId1);
obs4.getCode().addCoding().setCode("CODE1");
@ -376,7 +368,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
/*
* Make one previous match no longer match
*/
obs1 = new Observation();
obs1.setId(obsId1);
obs1.getSubject().setReferenceElement(ptId1);
@ -390,7 +382,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId4)));
}
@Test
public void testEverythingTypeWithContentFilter() {
Patient pt1 = new Patient();
@ -404,7 +396,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
Device dev1 = new Device();
dev1.setManufacturer("Some Manufacturer");
IIdType devId1 = myDeviceDao.create(dev1, mockSrd()).getId().toUnqualifiedVersionless();
Device dev2 = new Device();
dev2.setManufacturer("Some Manufacturer 2");
myDeviceDao.create(dev2, mockSrd()).getId().toUnqualifiedVersionless();
@ -427,14 +419,14 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
obs3.getCode().addCoding().setCode("CODE3");
obs3.setValue(new StringType("obsvalue3"));
IIdType obsId3 = myObservationDao.create(obs3, mockSrd()).getId().toUnqualifiedVersionless();
HttpServletRequest request;
List<String> actual;
request = mock(HttpServletRequest.class);
StringAndListParam param;
ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart());
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, param, null, null, mockSrd()));
@ -447,7 +439,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
/*
* Add another match
*/
Observation obs4 = new Observation();
obs4.getSubject().setReferenceElement(ptId1);
obs4.getCode().addCoding().setCode("CODE1");
@ -463,7 +455,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
/*
* Make one previous match no longer match
*/
obs1 = new Observation();
obs1.setId(obsId1);
obs1.getSubject().setReferenceElement(ptId1);
@ -478,7 +470,6 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
}
/**
* When processing transactions, we do two passes. Make sure we don't update the lucene index twice since that would
* be inefficient
@ -576,4 +567,9 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
View File

@ -527,7 +527,12 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
/*
* 20 should be prefetched since that's the initial page size
*/
await().until(()->{
return runInTransaction(()->{
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
return search.getNumFound() == 20;
});
});
runInTransaction(() -> {
Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
assertEquals(20, search.getNumFound());

230
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchTest.java Normal file
View File

@ -0,0 +1,230 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticSearch;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.PlatformTransactionManager;
import javax.persistence.EntityManager;
import java.util.ArrayList;
import java.util.List;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = {TestR4ConfigWithElasticSearch.class})
public class FhirResourceDaoR4SearchWithElasticSearchTest extends BaseJpaTest {
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4SearchWithElasticSearchTest.class);
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
protected PlatformTransactionManager myTxManager;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
@Autowired
@Qualifier("myValueSetDaoR4")
protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
@Autowired
protected IHapiTerminologySvcR4 myTermSvc;
@Autowired
protected IResourceTableDao myResourceTableDao;
@Autowired
@Qualifier("myCodeSystemDaoR4")
private IFhirResourceDao<CodeSystem> myCodeSystemDao;
@Autowired
private FhirContext myFhirCtx;
@Autowired
@Qualifier("myObservationDaoR4")
private IFhirResourceDao<Observation> myObservationDao;
@Autowired
@Qualifier("mySystemDaoR4")
private IFhirSystemDao<Bundle, Meta> mySystemDao;
@Autowired
private IResourceReindexingSvc myResourceReindexingSvc;
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
@Before
public void beforePurgeDatabase() {
purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
}
@Override
protected FhirContext getContext() {
return myFhirCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
@Test
public void testResourceTextSearch() throws InterruptedException {
Observation obs1 = new Observation();
obs1.getCode().setText("Systolic Blood Pressure");
obs1.setStatus(Observation.ObservationStatus.FINAL);
obs1.setValue(new Quantity(123));
obs1.getNoteFirstRep().setText("obs1");
IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
Observation obs2 = new Observation();
obs2.getCode().setText("Diastolic Blood Pressure");
obs2.setStatus(Observation.ObservationStatus.FINAL);
obs2.setValue(new Quantity(81));
IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map;
map = new SearchParameterMap();
map.add(ca.uhn.fhir.rest.api.Constants.PARAM_CONTENT, new StringParam("systolic"));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, new StringParam("blood"));
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1, id2)));
}
@Test
public void testExpandWithIsAInExternalValueSet() {
createExternalCsAndLocalVs();
ValueSet vs = new ValueSet();
ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(URL_MY_CODE_SYSTEM);
include.addFilter().setOp(ValueSet.FilterOperator.ISA).setValue("childAA").setProperty("concept");
ValueSet result = myValueSetDao.expand(vs, null);
logAndValidateValueSet(result);
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
}
private CodeSystem createExternalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
TermConcept childAA = new TermConcept(cs, "childAA").setDisplay("Child AA");
parentA.addChild(childAA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
TermConcept childAAA = new TermConcept(cs, "childAAA").setDisplay("Child AAA");
childAA.addChild(childAAA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
TermConcept childAAB = new TermConcept(cs, "childAAB").setDisplay("Child AAB");
childAA.addChild(childAAB, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
TermConcept childAB = new TermConcept(cs, "childAB").setDisplay("Child AB");
parentA.addChild(childAB, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
cs.getConcepts().add(parentB);
TermConcept childBA = new TermConcept(cs, "childBA").setDisplay("Child BA");
childBA.addChild(childAAB, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
parentB.addChild(childBA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
TermConcept parentC = new TermConcept(cs, "ParentC").setDisplay("Parent C");
cs.getConcepts().add(parentC);
TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
parentC.addChild(childCA, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
return codeSystem;
}
private void createExternalCsAndLocalVs() {
CodeSystem codeSystem = createExternalCs();
createLocalVs(codeSystem);
}
private void createLocalVs(CodeSystem codeSystem) {
ValueSet valueSet = new ValueSet();
valueSet.setUrl(URL_MY_VALUE_SET);
valueSet.getCompose().addInclude().setSystem(codeSystem.getUrl());
myValueSetDao.create(valueSet, mySrd);
}
private ArrayList<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
ArrayList<String> retVal = new ArrayList<String>();
for (ValueSet.ValueSetExpansionContainsComponent next : theContains) {
retVal.add(next.getCode());
}
return retVal;
}
private void logAndValidateValueSet(ValueSet theResult) {
IParser parser = myFhirCtx.newXmlParser().setPrettyPrint(true);
String encoded = parser.encodeResourceToString(theResult);
ourLog.info(encoded);
FhirValidator validator = myFhirCtx.newValidator();
validator.setValidateAgainstStandardSchema(true);
validator.setValidateAgainstStandardSchematron(true);
ValidationResult result = validator.validateWithResult(theResult);
assertEquals(0, result.getMessages().size());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java
View File

@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.TestR4Config;
import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.config.TestR4WithoutLuceneConfig;
import ca.uhn.fhir.jpa.config.TestR4WithLuceneDisabledConfig;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
@ -27,7 +26,6 @@ import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Transactional;
@ -40,7 +38,7 @@ import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = {TestR4WithoutLuceneConfig.class})
@ContextConfiguration(classes = {TestR4WithLuceneDisabledConfig.class})
public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4SearchWithLuceneDisabledTest.class);
@Autowired

7
hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml
View File

@ -1,7 +1,7 @@
<configuration>
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level>
<level>TRACE</level>
</filter>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
@ -40,6 +40,11 @@
<appender-ref ref="STDOUT" />
</logger>
<logger name="org.hibernate.search.elasticsearch.request" additivity="false" level="trace">
<appender-ref ref="STDOUT" />
</logger>
<root level="info">
<appender-ref ref="STDOUT" />
</root>

23
hapi-fhir-jpaserver-elasticsearch/pom.xml
View File

@ -1,23 +0,0 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.1.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jpaserver-elasticsearch</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR JPA Server - ElasticSearch Integration</name>
<dependencies>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-search-elasticsearch</artifactId>
</dependency>
</dependencies>
</project>

2
hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/elasticsearch/FhirServerConfig.java
View File

@ -6,7 +6,7 @@ import javax.sql.DataSource;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.search.ElasticsearchMappingProvider;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchMappingProvider;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;

70
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/OperationParameter.java
View File

@ -14,6 +14,7 @@ import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.BaseAndListParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.binder.CollectionBinder;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -21,14 +22,12 @@ import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ReflectionUtil;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.instance.model.api.*;
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import java.util.*;
import java.util.function.Consumer;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -163,7 +162,10 @@ public class OperationParameter implements IParameter {
*/
isSearchParam &= typeIsConcrete && !IBase.class.isAssignableFrom(myParameterType);
myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType) || String.class.equals(myParameterType) || isSearchParam || ValidationModeEnum.class.equals(myParameterType);
myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType)
|| String.class.equals(myParameterType)
|| isSearchParam
|| ValidationModeEnum.class.equals(myParameterType);
/*
* The parameter can be of type string for validation methods - This is a bit weird. See ValidateDstu2Test. We
@ -172,6 +174,12 @@ public class OperationParameter implements IParameter {
if (!myParameterType.equals(IBase.class) && !myParameterType.equals(String.class)) {
if (IBaseResource.class.isAssignableFrom(myParameterType) && myParameterType.isInterface()) {
myParamType = "Resource";
} else if (IBaseReference.class.isAssignableFrom(myParameterType)) {
myParamType = "Reference";
myAllowGet = true;
} else if (IBaseCoding.class.isAssignableFrom(myParameterType)) {
myParamType = "Coding";
myAllowGet = true;
} else if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
myParamType = "date";
myMax = 2;
@ -266,7 +274,7 @@ public class OperationParameter implements IParameter {
if (myAllowGet) {
if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
List<QualifiedParamList> parameters = new ArrayList<>();
parameters.add(QualifiedParamList.singleton(paramValues[0]));
if (paramValues.length > 1) {
parameters.add(QualifiedParamList.singleton(paramValues[1]));
@ -275,11 +283,31 @@ public class OperationParameter implements IParameter {
FhirContext ctx = theRequest.getServer().getFhirContext();
dateRangeParam.setValuesAsQueryTokens(ctx, myName, parameters);
matchingParamValues.add(dateRangeParam);
} else if (IBaseReference.class.isAssignableFrom(myParameterType)) {
processAllCommaSeparatedValues(paramValues, t -> {
IBaseReference param = (IBaseReference) ReflectionUtil.newInstance(myParameterType);
param.setReference(t);
matchingParamValues.add(param);
});
} else if (IBaseCoding.class.isAssignableFrom(myParameterType)) {
processAllCommaSeparatedValues(paramValues, t -> {
TokenParam tokenParam = new TokenParam();
tokenParam.setValueAsQueryToken(myContext, myName, null, t);
IBaseCoding param = (IBaseCoding) ReflectionUtil.newInstance(myParameterType);
param.setSystem(tokenParam.getSystem());
param.setCode(tokenParam.getValue());
matchingParamValues.add(param);
});
} else if (String.class.isAssignableFrom(myParameterType)) {
for (String next : paramValues) {
matchingParamValues.add(next);
}
matchingParamValues.addAll(Arrays.asList(paramValues));
} else if (ValidationModeEnum.class.equals(myParameterType)) {
if (isNotBlank(paramValues[0])) {
@ -309,6 +337,22 @@ public class OperationParameter implements IParameter {
}
}
/**
* This method is here to mediate between the POST form of operation parameters (i.e. elements within a <code>Parameters</code>
* resource) and the GET form (i.e. URL parameters).
* <p>
* Essentially we want to allow comma-separated values as is done with searches on URLs.
* </p>
*/
private void processAllCommaSeparatedValues(String[] theParamValues, Consumer<String> theHandler) {
for (String nextValue : theParamValues) {
QualifiedParamList qualifiedParamList = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(null, nextValue);
for (String nextSplitValue : qualifiedParamList) {
theHandler.accept(nextSplitValue);
}
}
}
private void translateQueryParametersIntoServerArgumentForPost(RequestDetails theRequest, List<Object> matchingParamValues) {
IBaseResource requestContents = (IBaseResource) theRequest.getUserData().get(REQUEST_CONTENTS_USERDATA_KEY);
if (requestContents != null) {
@ -394,10 +438,6 @@ public class OperationParameter implements IParameter {
}
}
public static void throwInvalidMode(String paramValues) {
throw new InvalidRequestException("Invalid mode value: \"" + paramValues + "\"");
}
interface IOperationParamConverter {
Object incomingServer(Object theObject);
@ -429,5 +469,9 @@ public class OperationParameter implements IParameter {
}
public static void throwInvalidMode(String paramValues) {
throw new InvalidRequestException("Invalid mode value: \"" + paramValues + "\"");
}
}

43
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/provider/BaseLastNProvider.java Normal file
View File

@ -0,0 +1,43 @@
package ca.uhn.fhir.rest.server.provider;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.util.List;
/**
* This class implements the Observation
* <a href="http://hl7.org/fhir/observation-operation-lastn.html">$lastn</a> operation.
* <p>
* It is does not implement the actual storage logic for this operation, but can be
* subclassed to provide this functionality.
* </p>
*
* @since 4.1.0
*/
public abstract class BaseLastNProvider {
@Operation(name = Constants.OPERATION_LASTN, typeName = "Observation", idempotent = true)
public IBaseBundle lastN(
ServletRequestDetails theRequestDetails,
@OperationParam(name = "subject", typeName = "reference", min = 0, max = 1) IBaseReference theSubject,
@OperationParam(name = "category", typeName = "coding", min = 0, max = OperationParam.MAX_UNLIMITED) List<IBaseCoding> theCategories,
@OperationParam(name = "code", typeName = "coding", min = 0, max = OperationParam.MAX_UNLIMITED) List<IBaseCoding> theCodes,
@OperationParam(name = "max", typeName = "integer", min = 0, max = 1) IPrimitiveType<Integer> theMax
) {
return processLastN(theSubject, theCategories, theCodes, theMax);
}
/**
* Subclasses should implement this method
*/
protected abstract IBaseBundle processLastN(IBaseReference theSubject, List<IBaseCoding> theCategories, List<IBaseCoding> theCodes, IPrimitiveType<Integer> theMax);
}

44
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/BaseR4ServerTest.java Normal file
View File

@ -0,0 +1,44 @@
package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.api.BundleInclusionRule;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.test.utilities.JettyUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.junit.After;
public class BaseR4ServerTest {
private FhirContext myCtx = FhirContext.forR4();
private Server myServer;
protected IGenericClient myClient;
protected String myBaseUrl;
@After
public void after() throws Exception {
JettyUtil.closeServer(myServer);
}
protected void startServer(Object theProvider) throws Exception {
RestfulServer servlet = new RestfulServer(myCtx);
servlet.registerProvider(theProvider);
ServletHandler proxyHandler = new ServletHandler();
servlet.setDefaultResponseEncoding(EncodingEnum.XML);
servlet.setBundleInclusionRule(BundleInclusionRule.BASED_ON_RESOURCE_PRESENCE);
ServletHolder servletHolder = new ServletHolder(servlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
myServer = new Server(0);
myServer.setHandler(proxyHandler);
JettyUtil.startServer(myServer);
int port = JettyUtil.getPortForStartedServer(myServer);
myBaseUrl = "http://localhost:" + port;
myCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
myClient = myCtx.newRestfulGenericClient(myBaseUrl);
}
}

64
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/LastNProviderTest.java Normal file
View File

@ -0,0 +1,64 @@
package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.rest.server.provider.BaseLastNProvider;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.Bundle;
import org.junit.Test;
import java.util.List;
import static org.junit.Assert.assertEquals;
public class LastNProviderTest extends BaseR4ServerTest {
private IBaseReference myLastSubject;
private List<IBaseCoding> myLastCategories;
private List<IBaseCoding> myLastCodes;
private IPrimitiveType<Integer> myLastMax;
@Test
public void testAllParamsPopulated() throws Exception {
class MyProvider extends BaseLastNProvider {
@Override
protected IBaseBundle processLastN(IBaseReference theSubject, List<IBaseCoding> theCategories, List<IBaseCoding> theCodes, IPrimitiveType<Integer> theMax) {
myLastSubject = theSubject;
myLastCategories = theCategories;
myLastCodes = theCodes;
myLastMax = theMax;
Bundle retVal = new Bundle();
retVal.setId("abc123");
retVal.setType(Bundle.BundleType.SEARCHSET);
return retVal;
}
}
MyProvider provider = new MyProvider();
startServer(provider);
Bundle response = myClient
.search()
.byUrl(myBaseUrl + "/Observation/$lastn?subject=Patient/123&category=http://terminology.hl7.org/CodeSystem/observation-category|laboratory,http://terminology.hl7.org/CodeSystem/observation-category|vital-signs&code=http://loinc.org|1111-1,http://loinc.org|2222-2&max=15")
.returnBundle(Bundle.class)
.execute();
assertEquals("abc123", response.getIdElement().getIdPart());
assertEquals("Patient/123", myLastSubject.getReferenceElement().getValue());
assertEquals(2, myLastCategories.size());
assertEquals("http://terminology.hl7.org/CodeSystem/observation-category", myLastCategories.get(0).getSystem());
assertEquals("laboratory", myLastCategories.get(0).getCode());
assertEquals("http://terminology.hl7.org/CodeSystem/observation-category", myLastCategories.get(1).getSystem());
assertEquals("vital-signs", myLastCategories.get(1).getCode());
assertEquals(2, myLastCodes.size());
assertEquals("http://loinc.org", myLastCodes.get(0).getSystem());
assertEquals("1111-1", myLastCodes.get(0).getCode());
assertEquals("http://loinc.org", myLastCodes.get(1).getSystem());
assertEquals("2222-2", myLastCodes.get(1).getCode());
assertEquals(15, myLastMax.getValue().intValue());
}
}

37
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerMethodSelectionR4Test.java
View File

@ -1,24 +1,15 @@
package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.api.BundleInclusionRule;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.annotation.IncludeParam;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.test.utilities.JettyUtil;
import com.google.common.collect.Lists;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.After;
import org.junit.Test;
import java.util.List;
@ -27,18 +18,9 @@ import java.util.Set;
import static org.hamcrest.CoreMatchers.containsString;
import static org.junit.Assert.*;
public class ServerMethodSelectionR4Test {
public class ServerMethodSelectionR4Test extends BaseR4ServerTest {
private FhirContext myCtx = FhirContext.forR4();
private Server myServer;
private IGenericClient myClient;
@After
public void after() throws Exception {
JettyUtil.closeServer(myServer);
}
/**
* Server method with no _include
* Client request with _include
@ -161,22 +143,6 @@ public class ServerMethodSelectionR4Test {
assertEquals(1, results.getEntry().size());
}
private void startServer(Object theProvider) throws Exception {
RestfulServer servlet = new RestfulServer(myCtx);
servlet.registerProvider(theProvider);
ServletHandler proxyHandler = new ServletHandler();
servlet.setDefaultResponseEncoding(EncodingEnum.XML);
servlet.setBundleInclusionRule(BundleInclusionRule.BASED_ON_RESOURCE_PRESENCE);
ServletHolder servletHolder = new ServletHolder(servlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
myServer = new Server(0);
myServer.setHandler(proxyHandler);
JettyUtil.startServer(myServer);
int port = JettyUtil.getPortForStartedServer(myServer);
myClient = myCtx.newRestfulGenericClient("http://localhost:" + port);
}
public static class MyBaseProvider implements IResourceProvider {
@ -185,6 +151,7 @@ public class ServerMethodSelectionR4Test {
public Class<? extends IBaseResource> getResourceType() {
return Patient.class;
}
}
}

25
pom.xml
View File

@ -601,7 +601,7 @@
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.4.4.Final</hibernate_version>
<!-- Update lucene version when you update hibernate-search version -->
<hibernate_search_version>5.11.1.Final</hibernate_search_version>
<hibernate_search_version>5.11.3.Final</hibernate_search_version>
<lucene_version>5.5.5</lucene_version>
<hibernate_validator_version>5.4.2.Final</hibernate_validator_version>
<httpcore_version>4.4.11</httpcore_version>
@ -857,18 +857,6 @@
<!--<version>6.2.2.jre8</version>-->
<version>7.0.0.jre8</version>
</dependency>
<!--
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>${jaxb_core_version}</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>${jaxb_core_version}</version>
</dependency>
-->
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
@ -1405,6 +1393,11 @@
<artifactId>xmlunit-core</artifactId>
<version>2.4.0</version>
</dependency>
<dependency>
<groupId>pl.allegro.tech</groupId>
<artifactId>embedded-elasticsearch</artifactId>
<version>2.10.0</version>
</dependency>
<dependency>
<groupId>xpp3</groupId>
<artifactId>xpp3</artifactId>
@ -1669,6 +1662,11 @@
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.4</version>
<configuration>
<excludes>
<exclude>ca/uhn/fhir/model/dstu2/**/*.class</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@ -2391,7 +2389,6 @@
<module>hapi-fhir-jaxrsserver-base</module>
<module>hapi-fhir-jaxrsserver-example</module>
<module>hapi-fhir-jpaserver-base</module>
<module>hapi-fhir-jpaserver-elasticsearch</module>
<module>hapi-fhir-jpaserver-migrate</module>
<module>restful-server-example</module>
<module>hapi-fhir-testpage-overlay</module>

8
src/changes/changes.xml
View File

@ -12,7 +12,8 @@
latest versions (dependent HAPI modules listed in brackets):
<![CDATA[
<ul>
<li>Hibernate Core (Core): 5.4.2.Final -&gt; 5.4.4.Final</li>
<li>Hibernate Core (JPA): 5.4.2.Final -&gt; 5.4.4.Final</li>
<li>Hibernate Search (JPA): 5.11.1.Final -&gt; 5.11.3.Final</li>
<li>Jackson Databind (JPA): 2.9.9 -&gt; 2.9.10 (CVE-2019-16335, CVE-2019-14540)</li>
</ul>
]]>
@ -252,6 +253,11 @@
The JPA server failed to find codes defined in not-present codesystems in some cases, and reported
that the CodeSystem did not exist. This has been corrected.
</action>
<action type="add">
Support for ElasticSearch has been added to the JPA server directly (i.e. without needing a separate
module) and a new class called "ElasticsearchHibernatePropertiesBuilder" has been added to facilitate
the creation of relevant properties.
</action>
</release>
<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix">