honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Additional tests and cleanup.

This commit is contained in:
ianmarshall 2020-04-17 17:38:42 -04:00
parent d03ce6533e
commit 4a89860f9b
31 changed files with 1577 additions and 2241 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
View File

@ -20,7 +20,6 @@ package ca.uhn.fhir.cli;
* #L% * #L%
*/ */
import ca.uhn.fhir.jpa.demo.*;
import ca.uhn.fhir.jpa.api.config.DaoConfig; import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.demo.ContextHolder; import ca.uhn.fhir.jpa.demo.ContextHolder;
import ca.uhn.fhir.jpa.demo.FhirServerConfig; import ca.uhn.fhir.jpa.demo.FhirServerConfig;
@ -48,10 +47,8 @@ public class RunServerCommand extends BaseCommand {
private static final String OPTION_LOWMEM = "lowmem"; private static final String OPTION_LOWMEM = "lowmem";
private static final String OPTION_ALLOW_EXTERNAL_REFS = "allow-external-refs"; private static final String OPTION_ALLOW_EXTERNAL_REFS = "allow-external-refs";
private static final String OPTION_REUSE_SEARCH_RESULTS_MILLIS = "reuse-search-results-milliseconds"; private static final String OPTION_REUSE_SEARCH_RESULTS_MILLIS = "reuse-search-results-milliseconds";
private static final String OPTION_EXTERNAL_ELASTICSEARCH = "external-elasticsearch";
private static final int DEFAULT_PORT = 8080; private static final int DEFAULT_PORT = 8080;
private static final String OPTION_P = "p"; private static final String OPTION_P = "p";
private static final String OPTION_POSTGRES = "postgresql";
// TODO: Don't use qualified names for loggers in HAPI CLI. // TODO: Don't use qualified names for loggers in HAPI CLI.
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RunServerCommand.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RunServerCommand.class);
@ -73,8 +70,6 @@ public class RunServerCommand extends BaseCommand {
options.addOption(null, OPTION_LOWMEM, false, "If this flag is set, the server will operate in low memory mode (some features disabled)"); options.addOption(null, OPTION_LOWMEM, false, "If this flag is set, the server will operate in low memory mode (some features disabled)");
options.addOption(null, OPTION_ALLOW_EXTERNAL_REFS, false, "If this flag is set, the server will allow resources to be persisted contaning external resource references"); options.addOption(null, OPTION_ALLOW_EXTERNAL_REFS, false, "If this flag is set, the server will allow resources to be persisted contaning external resource references");
options.addOption(null, OPTION_DISABLE_REFERENTIAL_INTEGRITY, false, "If this flag is set, the server will not enforce referential integrity"); options.addOption(null, OPTION_DISABLE_REFERENTIAL_INTEGRITY, false, "If this flag is set, the server will not enforce referential integrity");
options.addOption(null, OPTION_EXTERNAL_ELASTICSEARCH, false, "If this flag is set, the server will attempt to use a local elasticsearch server listening on port 9301");
options.addOption(null, OPTION_POSTGRES, false, "If this flag is set, the server will attempt to use a local postgresql DB instance listening on port 5432");
addOptionalOption(options, "u", "url", "Url", "If this option is set, specifies the JDBC URL to use for the database connection"); addOptionalOption(options, "u", "url", "Url", "If this option is set, specifies the JDBC URL to use for the database connection");
addOptionalOption(options, "d", "default-size", "PageSize", "If this option is set, specifies the default page size for number of query results"); addOptionalOption(options, "d", "default-size", "PageSize", "If this option is set, specifies the default page size for number of query results");
@ -115,18 +110,8 @@ public class RunServerCommand extends BaseCommand {
ContextHolder.setDisableReferentialIntegrity(true); ContextHolder.setDisableReferentialIntegrity(true);
} }
if (theCommandLine.hasOption(OPTION_EXTERNAL_ELASTICSEARCH)) {
ourLog.info("Server is configured to use external elasticsearch");
ContextHolder.setExternalElasticsearch(true);
}
ContextHolder.setDatabaseUrl(theCommandLine.getOptionValue("u")); ContextHolder.setDatabaseUrl(theCommandLine.getOptionValue("u"));
if (theCommandLine.hasOption(OPTION_POSTGRES)) {
ourLog.info("Server is configured to use PostgreSQL database");
ContextHolder.setPostgreSql(true);
}
String defaultPageSize = theCommandLine.getOptionValue("d"); String defaultPageSize = theCommandLine.getOptionValue("d");
String maxPageSize = theCommandLine.getOptionValue("m"); String maxPageSize = theCommandLine.getOptionValue("m");
if (defaultPageSize != null) { if (defaultPageSize != null) {

98
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/CommonConfig.java
View File

@ -46,7 +46,6 @@ import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank;
@SuppressWarnings("Duplicates") @SuppressWarnings("Duplicates")
// TODO: Merge this with new CommonPostgreSQLConfig or find way to avoid conflicts with it.
@Configuration @Configuration
public class CommonConfig { public class CommonConfig {
@ -76,42 +75,6 @@ public class CommonConfig {
*/ */
@Bean(destroyMethod = "close") @Bean(destroyMethod = "close")
public DataSource dataSource() { public DataSource dataSource() {
if (ContextHolder.isPostGreSql()) {
return getPostgreSqlDataSource();
} else {
return getH2DataSource();
}
}
/**
* The following method creates a PostgreSQL database connection. The 'url' property value of "jdbc:postgresql://localhost:5432/hapi" indicates that the server should save resources in a
* PostgreSQL database named "hapi".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
private DataSource getPostgreSqlDataSource() {
String dbUrl = "jdbc:postgresql://localhost:5432/hapi";
String dbUsername = "hapi";
String dbPassword = "HapiFHIR";
if (isNotBlank(ContextHolder.getDatabaseUrl())) {
dbUrl = ContextHolder.getDatabaseUrl();
}
BasicDataSource retVal = new BasicDataSource();
retVal.setDriverClassName("org.postgresql.Driver");
retVal.setUrl(dbUrl);
retVal.setUsername(dbUsername);
retVal.setPassword(dbPassword);
return retVal;
}
/**
* The following method creates an H2 database connection. The 'url' property value of "jdbc:h2:file:target./jpaserver_h2_files" indicates that the server should save resources in a
* directory called "jpaserver_h2_files".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
private DataSource getH2DataSource() {
String url = "jdbc:h2:file:./target/jpaserver_h2_files"; String url = "jdbc:h2:file:./target/jpaserver_h2_files";
if (isNotBlank(ContextHolder.getDatabaseUrl())) { if (isNotBlank(ContextHolder.getDatabaseUrl())) {
url = ContextHolder.getDatabaseUrl(); url = ContextHolder.getDatabaseUrl();
@ -127,14 +90,6 @@ public class CommonConfig {
@Bean @Bean
public Properties jpaProperties() { public Properties jpaProperties() {
if (ContextHolder.isPostGreSql()) {
return getPostGreSqlJpaProperties();
} else {
return getH2JpaProperties();
}
}
private Properties getH2JpaProperties() {
Properties extraProperties = new Properties(); Properties extraProperties = new Properties();
extraProperties.put("hibernate.dialect", H2Dialect.class.getName()); extraProperties.put("hibernate.dialect", H2Dialect.class.getName());
extraProperties.put("hibernate.format_sql", "true"); extraProperties.put("hibernate.format_sql", "true");
@ -158,44 +113,12 @@ public class CommonConfig {
return configureElasticearch(extraProperties); return configureElasticearch(extraProperties);
} }
private Properties getPostGreSqlJpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.dialect", org.hibernate.dialect.PostgreSQL94Dialect.class.getName());
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");
extraProperties.put("hibernate.cache.use_structured_entries", "false");
extraProperties.put("hibernate.cache.use_minimal_puts", "false");
extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
extraProperties.put("hibernate.search.default.directory_provider", "local-heap");
extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
extraProperties.put("hibernate.search.default.worker.execution", "sync");
if (System.getProperty("lowmem") != null) {
extraProperties.put("hibernate.search.autoregister_listeners", "false");
}
return configureElasticearch(extraProperties);
}
private Properties configureElasticearch(Properties theExtraProperties) { private Properties configureElasticearch(Properties theExtraProperties) {
String elasticsearchHost = "localhost"; String elasticsearchHost = "localhost";
String elasticsearchUserId = ""; String elasticsearchUserId = "";
String elasticsearchPassword = ""; String elasticsearchPassword = "";
Integer elasticsearchPort; int elasticsearchPort = embeddedElasticSearch().getHttpPort();
if(ContextHolder.isExternalElasticsearch()) {
elasticsearchUserId = "elastic";
elasticsearchPassword = "changeme";
elasticsearchPort = 9301;
} else {
elasticsearchPort = embeddedElasticSearch().getHttpPort();
}
new ElasticsearchHibernatePropertiesBuilder() new ElasticsearchHibernatePropertiesBuilder()
.setDebugRefreshAfterWrite(true) .setDebugRefreshAfterWrite(true)
@ -212,29 +135,11 @@ public class CommonConfig {
} }
@Bean()
public ElasticsearchSvcImpl myElasticsearchSvc() throws IOException {
String elasticsearchHost = "localhost";
String elasticsearchUserId = "";
String elasticsearchPassword = "";
Integer elasticsearchPort;
if(ContextHolder.isExternalElasticsearch()) {
elasticsearchUserId = "elastic";
elasticsearchPassword = "changeme";
elasticsearchPort = 9301;
} else {
elasticsearchPort = embeddedElasticSearch().getHttpPort();
}
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
}
@Bean @Bean
public EmbeddedElastic embeddedElasticSearch() { public EmbeddedElastic embeddedElasticSearch() {
String ELASTIC_VERSION = "6.5.4"; String ELASTIC_VERSION = "6.5.4";
EmbeddedElastic embeddedElastic = null; EmbeddedElastic embeddedElastic = null;
if(!ContextHolder.isExternalElasticsearch()) {
try { try {
embeddedElastic = EmbeddedElastic.builder() embeddedElastic = EmbeddedElastic.builder()
.withElasticVersion(ELASTIC_VERSION) .withElasticVersion(ELASTIC_VERSION)
@ -247,7 +152,6 @@ public class CommonConfig {
} catch (IOException | InterruptedException e) { } catch (IOException | InterruptedException e) {
throw new ConfigurationException(e); throw new ConfigurationException(e);
} }
}
return embeddedElastic; return embeddedElastic;
} }

18
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/ContextHolder.java
View File

@ -33,8 +33,6 @@ public class ContextHolder {
private static String ourPath; private static String ourPath;
private static Long ourReuseSearchResultsMillis; private static Long ourReuseSearchResultsMillis;
private static String ourDatabaseUrl; private static String ourDatabaseUrl;
private static boolean myExternalElasticsearch = false;
private static boolean myPostGreSql = false;
private static Integer myDefaultPageSize = 10; private static Integer myDefaultPageSize = 10;
private static Integer myMaxPageSize = 50; private static Integer myMaxPageSize = 50;
@ -105,22 +103,6 @@ public class ContextHolder {
ourDatabaseUrl = theDatabaseUrl; ourDatabaseUrl = theDatabaseUrl;
} }
public static void setExternalElasticsearch(Boolean theExternalElasticsearch) {
myExternalElasticsearch = theExternalElasticsearch;
}
public static Boolean isExternalElasticsearch() {
return myExternalElasticsearch;
}
public static void setPostgreSql(boolean thePostGreSql) {
myPostGreSql = thePostGreSql;
}
public static boolean isPostGreSql() {
return myPostGreSql;
}
public static void setDefaultPageSize(Integer theDefaultPageSize) { public static void setDefaultPageSize(Integer theDefaultPageSize) {
myDefaultPageSize = theDefaultPageSize; myDefaultPageSize = theDefaultPageSize;
} }

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java
View File

@ -122,7 +122,6 @@ public class JpaServerDemo extends RestfulServer {
myAppCtx.getBean(DaoConfig.class)); myAppCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("Example Server"); confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider); setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.DSTU3) { } else if (fhirVersion == FhirVersionEnum.DSTU3) {
IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, org.hl7.fhir.dstu3.model.Meta> systemDao = myAppCtx IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, org.hl7.fhir.dstu3.model.Meta> systemDao = myAppCtx
.getBean("mySystemDaoDstu3", IFhirSystemDao.class); .getBean("mySystemDaoDstu3", IFhirSystemDao.class);
@ -161,7 +160,6 @@ public class JpaServerDemo extends RestfulServer {
/* /*
* This is a simple paging strategy that keeps the last 10 searches in memory * This is a simple paging strategy that keeps the last 10 searches in memory
*/ */
// TODO: Make this configurable via the ContextHolder
setPagingProvider(new FifoMemoryPagingProvider(10).setDefaultPageSize(ContextHolder.getDefaultPageSize()).setMaximumPageSize(ContextHolder.getMaxPageSize())); setPagingProvider(new FifoMemoryPagingProvider(10).setDefaultPageSize(ContextHolder.getDefaultPageSize()).setMaximumPageSize(ContextHolder.getMaxPageSize()));
// Register a CORS filter // Register a CORS filter

5
hapi-fhir-jpaserver-base/pom.xml
View File

@ -618,11 +618,6 @@
<version>1.0-SNAPSHOT</version> <version>1.0-SNAPSHOT</version>
<classifier>shaded6</classifier> <classifier>shaded6</classifier>
</dependency> </dependency>
<!-- <dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>elasticsearch-rest-high-level-client</artifactId>
<version>5.6.16</version>
</dependency> -->
</dependencies> </dependencies>

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -270,7 +270,7 @@ public abstract class BaseConfig {
public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) { public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer())); theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
// TODO: Looking at moving the lastn entities into jpa.model.entity package. // TODO: Looking at moving the lastn entities into jpa.model.entity package. Note that moving the lastn entities may require re-building elasticsearch indexes.
theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity", "ca.uhn.fhir.jpa.dao.lastn.entity"); theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity", "ca.uhn.fhir.jpa.dao.lastn.entity");
theFactory.setPersistenceProvider(new HibernatePersistenceProvider()); theFactory.setPersistenceProvider(new HibernatePersistenceProvider());
} }

45
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDaoObservation.java Normal file
View File

@ -0,0 +1,45 @@
package ca.uhn.fhir.jpa.dao;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2020 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.search.lastn.IndexConstants;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.*;
import org.hl7.fhir.instance.model.api.*;
public abstract class BaseHapiFhirResourceDaoObservation<T extends IBaseResource> extends BaseHapiFhirResourceDao<T> implements IFhirResourceDaoObservation<T> {
protected void updateSearchParamsForLastn(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails) {
if (!isPagingProviderDatabaseBacked(theRequestDetails)) {
theSearchParameterMap.setLoadSynchronous(true);
}
theSearchParameterMap.setLastN(true);
if (theSearchParameterMap.getSort() == null) {
SortSpec effectiveDtm = new SortSpec("date").setOrder(SortOrderEnum.DESC);
SortSpec observationCode = new SortSpec(IndexConstants.CODE_SEARCH_PARAM).setOrder(SortOrderEnum.ASC).setChain(effectiveDtm);
theSearchParameterMap.setSort(new SortSpec(IndexConstants.SUBJECT_SEARCH_PARAM).setChain(observationCode));
}
}
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -348,7 +348,17 @@ public class SearchBuilder implements ISearchBuilder {
} }
if (myParams.isLastN()) { if (myParams.isLastN()) {
lastnPids = myIElasticsearchSvc.executeLastN(myParams, theRequest, myIdHelperService); Integer myMaxObservationsPerCode = null;
String[] maxCountParams = theRequest.getParameters().get("max");
if (maxCountParams != null && maxCountParams.length > 0) {
myMaxObservationsPerCode = Integer.valueOf(maxCountParams[0]);
} else {
throw new InvalidRequestException("Max parameter is required for $lastn operation");
}
List<String> lastnResourceIds = myIElasticsearchSvc.executeLastN(myParams, myMaxObservationsPerCode);
for (String lastnResourceId : lastnResourceIds) {
lastnPids.add(myIdHelperService.resolveResourcePersistentIds(myResourceName, lastnResourceId));
}
} }
} }

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/lastn/ObservationLastNIndexPersistDstu3Svc.java
View File

@ -70,6 +70,7 @@ public class ObservationLastNIndexPersistDstu3Svc {
codeableConceptField.addCoding(new ObservationIndexedCodeCodingEntity(codeCoding.getSystem(), codeCoding.getCode(), codeCoding.getDisplay(), observationCodeNormalizedId)); codeableConceptField.addCoding(new ObservationIndexedCodeCodingEntity(codeCoding.getSystem(), codeCoding.getCode(), codeCoding.getDisplay(), observationCodeNormalizedId));
} }
myObservationIndexedCodeableConceptSearchParamDao.save(codeableConceptField); myObservationIndexedCodeableConceptSearchParamDao.save(codeableConceptField);
codeableConceptField = myObservationIndexedCodeableConceptSearchParamDao.findByCodeableConceptId(observationCodeNormalizedId);
indexedObservation.setObservationCode(codeableConceptField); indexedObservation.setObservationCode(codeableConceptField);
indexedObservation.setCodeNormalizedId(observationCodeNormalizedId); indexedObservation.setCodeNormalizedId(observationCodeNormalizedId);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/lastn/ObservationLastNIndexPersistR5Svc.java
View File

@ -70,6 +70,7 @@ public class ObservationLastNIndexPersistR5Svc {
codeableConceptField.addCoding(new ObservationIndexedCodeCodingEntity(codeCoding.getSystem(), codeCoding.getCode(), codeCoding.getDisplay(), observationCodeNormalizedId)); codeableConceptField.addCoding(new ObservationIndexedCodeCodingEntity(codeCoding.getSystem(), codeCoding.getCode(), codeCoding.getDisplay(), observationCodeNormalizedId));
} }
myObservationIndexedCodeableConceptSearchParamDao.save(codeableConceptField); myObservationIndexedCodeableConceptSearchParamDao.save(codeableConceptField);
codeableConceptField = myObservationIndexedCodeableConceptSearchParamDao.findByCodeableConceptId(observationCodeNormalizedId);
indexedObservation.setObservationCode(codeableConceptField); indexedObservation.setObservationCode(codeableConceptField);
indexedObservation.setCodeNormalizedId(observationCodeNormalizedId); indexedObservation.setCodeNormalizedId(observationCodeNormalizedId);

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoObservationR4.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao; import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation; import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.dao.lastn.ObservationLastNIndexPersistR4Svc; import ca.uhn.fhir.jpa.dao.lastn.ObservationLastNIndexPersistR4Svc;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource; import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable; import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -38,16 +39,15 @@ import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletResponse;
import java.util.Date; import java.util.Date;
public class FhirResourceDaoObservationR4 extends BaseHapiFhirResourceDao<Observation> implements IFhirResourceDaoObservation<Observation> { public class FhirResourceDaoObservationR4 extends BaseHapiFhirResourceDaoObservation<Observation> {
@Autowired @Autowired
ObservationLastNIndexPersistR4Svc myObservationLastNIndexPersistR4Svc; ObservationLastNIndexPersistR4Svc myObservationLastNIndexPersistR4Svc;
@Override @Override
public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) { public IBundleProvider observationsLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse) {
if (!isPagingProviderDatabaseBacked(theRequestDetails)) {
theSearchParameterMap.setLoadSynchronous(true); updateSearchParamsForLastn(theSearchParameterMap, theRequestDetails);
}
return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails); return mySearchCoordinatorSvc.registerSearch(this, theSearchParameterMap, getResourceName(), new CacheControlDirective().parse(theRequestDetails.getHeaders(Constants.HEADER_CACHE_CONTROL)), theRequestDetails);
} }

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderObservationR4.java
View File

@ -129,7 +129,7 @@ public class BaseJpaResourceProviderObservationR4 extends JpaResourceProviderR4<
paramMap.setRevIncludes(theRevIncludes); paramMap.setRevIncludes(theRevIncludes);
paramMap.setLastUpdated(theLastUpdated); paramMap.setLastUpdated(theLastUpdated);
paramMap.setIncludes(theIncludes); paramMap.setIncludes(theIncludes);
paramMap.setLastN(true); /* paramMap.setLastN(true);
if (theSort == null) { if (theSort == null) {
SortSpec effectiveDtm = new SortSpec("date").setOrder(SortOrderEnum.DESC); SortSpec effectiveDtm = new SortSpec("date").setOrder(SortOrderEnum.DESC);
SortSpec observationCode = new SortSpec("code").setOrder(SortOrderEnum.ASC).setChain(effectiveDtm); SortSpec observationCode = new SortSpec("code").setOrder(SortOrderEnum.ASC).setChain(effectiveDtm);
@ -138,7 +138,7 @@ public class BaseJpaResourceProviderObservationR4 extends JpaResourceProviderR4<
} else { } else {
theSort = new SortSpec("subject").setChain(observationCode); theSort = new SortSpec("subject").setChain(observationCode);
} }
} } */
paramMap.setSort(theSort); paramMap.setSort(theSort);
paramMap.setCount(theCount); paramMap.setCount(theCount);
paramMap.setSummaryMode(theSummaryMode); paramMap.setSummaryMode(theSummaryMode);

188
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchBulkIndexSvcImpl.java
View File

@ -1,188 +0,0 @@
package ca.uhn.fhir.jpa.search.lastn;
/*
import org.shadehapi.elasticsearch.action.DocWriteRequest;
import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexRequest;
import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexResponse;
import org.shadehapi.elasticsearch.action.admin.indices.get.GetIndexRequest;
import org.shadehapi.elasticsearch.action.bulk.BulkItemResponse;
import org.shadehapi.elasticsearch.action.bulk.BulkRequest;
import org.shadehapi.elasticsearch.action.bulk.BulkResponse;
import org.shadehapi.elasticsearch.action.index.IndexRequest;
import org.shadehapi.elasticsearch.client.RequestOptions;
import org.shadehapi.elasticsearch.client.RestHighLevelClient;
import org.shadehapi.elasticsearch.common.xcontent.XContentType;
*/
import java.io.IOException;
public class ElasticsearchBulkIndexSvcImpl {
// RestHighLevelClient myRestHighLevelClient;
// BulkRequest myBulkRequest = null;
public ElasticsearchBulkIndexSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) {
// myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theHostname, thePort, theUsername,thePassword);
try {
createObservationIndexIfMissing();
createCodeIndexIfMissing();
} catch (IOException theE) {
throw new RuntimeException("Failed to create document index", theE);
}
}
public void createObservationIndexIfMissing() throws IOException {
if(indexExists(IndexConstants.OBSERVATION_INDEX)) {
return;
}
String observationMapping = "{\n" +
" \"mappings\" : {\n" +
" \"ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedSearchParamLastNEntity\" : {\n" +
" \"properties\" : {\n" +
" \"codeconceptid\" : {\n" +
" \"type\" : \"keyword\",\n" +
" \"norms\" : true\n" +
" },\n" +
" \"codeconcepttext\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"codeconceptcodingcode\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codeconceptcodingsystem\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codeconceptcodingcode_system_hash\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codeconceptcodingdisplay\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"categoryconcepttext\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"categoryconceptcodingcode\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"categoryconceptcodingsystem\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"categoryconceptcodingcode_system_hash\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"categoryconceptcodingdisplay\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"effectivedtm\" : {\n" +
" \"type\" : \"date\"\n" +
" },\n" +
" \"identifier\" : {\n" +
" \"type\" : \"keyword\",\n" +
" \"store\" : true\n" +
" },\n" +
" \"subject\" : {\n" +
" \"type\" : \"keyword\"\n" +
" }\n" +
" }\n" +
" }\n" +
" }\n" +
"}\n";
if(!createIndex(IndexConstants.OBSERVATION_INDEX, observationMapping)) {
throw new RuntimeException("Failed to create observation index");
}
}
public void createCodeIndexIfMissing() throws IOException {
if(indexExists(IndexConstants.CODE_INDEX)) {
return;
}
String codeMapping = "{\n" +
" \"mappings\" : {\n" +
" \"ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedCodeCodeableConceptEntity\" : {\n" +
" \"properties\" : {\n" +
" \"codeable_concept_id\" : {\n" +
" \"type\" : \"keyword\",\n" +
" \"store\" : true\n" +
" },\n" +
" \"codeable_concept_text\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"codingcode\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codingcode_system_hash\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codingdisplay\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"codingsystem\" : {\n" +
" \"type\" : \"keyword\"\n" +
" }\n" +
" }\n" +
" }\n" +
" }\n" +
"}\n";
if (!createIndex(IndexConstants.CODE_INDEX, codeMapping)) {
throw new RuntimeException("Failed to create code index");
}
}
public boolean createIndex(String theIndexName, String theMapping) throws IOException {
/* CreateIndexRequest request = new CreateIndexRequest(theIndexName);
request.source(theMapping, XContentType.JSON);
CreateIndexResponse createIndexResponse = myRestHighLevelClient.indices().create(request, RequestOptions.DEFAULT);
return createIndexResponse.isAcknowledged();
*/
return false;
}
public boolean indexExists(String theIndexName) throws IOException {
/* GetIndexRequest request = new GetIndexRequest();
request.indices(theIndexName);
return myRestHighLevelClient.indices().exists(request, RequestOptions.DEFAULT);
*/
return false;
}
public void addToBulkIndexRequest(String theIndexName, String theDocumentId, String theObservationDocument, String theDocumentType) {
/* IndexRequest request = new IndexRequest(theIndexName);
request.id(theDocumentId);
request.type(theDocumentType);
request.source(theObservationDocument, XContentType.JSON);
if (myBulkRequest == null) {
myBulkRequest = new BulkRequest();
}
myBulkRequest.add(request); */
}
public void executeBulkIndex() throws IOException {
/* if (myBulkRequest == null) {
throw new RuntimeException(("No index requests have been added to the bulk request"));
}
BulkResponse bulkResponse = myRestHighLevelClient.bulk(myBulkRequest, RequestOptions.DEFAULT);
for (BulkItemResponse bulkItemResponse : bulkResponse) {
if (bulkItemResponse.getOpType() != DocWriteRequest.OpType.CREATE && bulkItemResponse.getOpType() != DocWriteRequest.OpType.INDEX) {
throw new RuntimeException("Unexpected response for bulk index request: " + bulkItemResponse.getOpType());
}
}
myBulkRequest = null; */
}
public boolean bulkRequestPending() {
// return (myBulkRequest != null);
return false;
}
public void closeClient() throws IOException {
// myRestHighLevelClient.close();
}
}

235
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchSvcImpl.java
View File

@ -1,20 +1,16 @@
package ca.uhn.fhir.jpa.search.lastn; package ca.uhn.fhir.jpa.search.lastn;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.ReferenceParam; import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.TokenParam; import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson; import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson; import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash; import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException; import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.annotations.VisibleForTesting;
import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexRequest; import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexRequest;
import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexResponse; import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexResponse;
import org.shadehapi.elasticsearch.action.admin.indices.get.GetIndexRequest; import org.shadehapi.elasticsearch.action.admin.indices.get.GetIndexRequest;
@ -55,6 +51,9 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
ObjectMapper objectMapper = new ObjectMapper(); ObjectMapper objectMapper = new ObjectMapper();
private final String GROUP_BY_SUBJECT = "group_by_subject";
private final String GROUP_BY_CODE = "group_by_code";
public ElasticsearchSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) { public ElasticsearchSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) {
myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theHostname, thePort, theUsername, thePassword); myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theHostname, thePort, theUsername, thePassword);
@ -174,6 +173,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
} }
@VisibleForTesting
boolean performIndex(String theIndexName, String theDocumentId, String theIndexDocument, String theDocumentType) throws IOException { boolean performIndex(String theIndexName, String theDocumentId, String theIndexDocument, String theDocumentType) throws IOException {
IndexResponse indexResponse = myRestHighLevelClient.index(createIndexRequest(theIndexName, theDocumentId, theIndexDocument, theDocumentType), IndexResponse indexResponse = myRestHighLevelClient.index(createIndexRequest(theIndexName, theDocumentId, theIndexDocument, theDocumentType),
RequestOptions.DEFAULT); RequestOptions.DEFAULT);
@ -197,24 +197,36 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
} }
@Override @Override
public List<ResourcePersistentId> executeLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, IdHelperService theIdHelperService) { public List<String> executeLastN(SearchParameterMap theSearchParameterMap, Integer theMaxObservationsPerCode) {
Integer myMaxObservationsPerCode = 1; String[] topHitsInclude = {"identifier"};
String[] maxCountParams = theRequestDetails.getParameters().get("max"); SearchRequest myLastNRequest = buildObservationsSearchRequest(theSearchParameterMap, createCompositeAggregationBuilder(theMaxObservationsPerCode, topHitsInclude));
if (maxCountParams != null && maxCountParams.length > 0) {
myMaxObservationsPerCode = Integer.valueOf(maxCountParams[0]);
}
SearchRequest myLastNRequest = buildObservationCompositeSearchRequest(10000, theSearchParameterMap, myMaxObservationsPerCode);
SearchResponse lastnResponse = null;
try { try {
lastnResponse = executeSearchRequest(myLastNRequest); SearchResponse lastnResponse = executeSearchRequest(myLastNRequest);
List<ResourcePersistentId> observationIds = buildObservationIdList(lastnResponse, theIdHelperService); return buildObservationIdList(lastnResponse);
return observationIds;
} catch (IOException theE) { } catch (IOException theE) {
throw new InvalidRequestException("Unable to execute LastN request", theE); throw new InvalidRequestException("Unable to execute LastN request", theE);
} }
} }
@VisibleForTesting
List<ObservationJson> executeLastNWithAllFields(SearchParameterMap theSearchParameterMap, Integer theMaxObservationsPerCode) {
SearchRequest myLastNRequest = buildObservationsSearchRequest(theSearchParameterMap, createCompositeAggregationBuilder(theMaxObservationsPerCode, null));
try {
SearchResponse lastnResponse = executeSearchRequest(myLastNRequest);
return buildObservationDocumentList(lastnResponse);
} catch (IOException theE) {
throw new InvalidRequestException("Unable to execute LastN request", theE);
}
}
@VisibleForTesting
List<CodeJson> queryAllIndexedObservationCodes(int theMaxResultSetSize) throws IOException {
SearchRequest codeSearchRequest = buildObservationCodesSearchRequest(theMaxResultSetSize);
SearchResponse codeSearchResponse = executeSearchRequest(codeSearchRequest);
return buildCodeResult(codeSearchResponse);
}
@VisibleForTesting
SearchRequest buildObservationCodesSearchRequest(int theMaxResultSetSize) { SearchRequest buildObservationCodesSearchRequest(int theMaxResultSetSize) {
SearchRequest searchRequest = new SearchRequest(IndexConstants.CODE_INDEX); SearchRequest searchRequest = new SearchRequest(IndexConstants.CODE_INDEX);
SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder(); SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
@ -225,110 +237,75 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
return searchRequest; return searchRequest;
} }
private CompositeAggregationBuilder createCompositeAggregationBuilder(int theMaximumResultSetSize, int theMaxNumberObservationsPerCode, String[] theTopHitsInclude) { private CompositeAggregationBuilder createCompositeAggregationBuilder(int theMaxNumberObservationsPerCode, String[] theTopHitsInclude) {
TermsAggregationBuilder observationCodeAggregationBuilder = new TermsAggregationBuilder("group_by_code", ValueType.STRING).field("codeconceptid"); TermsAggregationBuilder observationCodeAggregationBuilder = new TermsAggregationBuilder(GROUP_BY_CODE, ValueType.STRING).field("codeconceptid");
// Top Hits Aggregation // Top Hits Aggregation
observationCodeAggregationBuilder.subAggregation(AggregationBuilders.topHits("most_recent_effective") observationCodeAggregationBuilder.subAggregation(AggregationBuilders.topHits("most_recent_effective")
.sort("effectivedtm", SortOrder.DESC) .sort("effectivedtm", SortOrder.DESC)
.fetchSource(theTopHitsInclude, null).size(theMaxNumberObservationsPerCode)); .fetchSource(theTopHitsInclude, null).size(theMaxNumberObservationsPerCode));
observationCodeAggregationBuilder.size(theMaximumResultSetSize); observationCodeAggregationBuilder.size(10000);
CompositeValuesSourceBuilder<?> subjectValuesBuilder = new TermsValuesSourceBuilder("subject").field("subject"); CompositeValuesSourceBuilder<?> subjectValuesBuilder = new TermsValuesSourceBuilder("subject").field("subject");
List<CompositeValuesSourceBuilder<?>> compositeAggSubjectSources = new ArrayList(); List<CompositeValuesSourceBuilder<?>> compositeAggSubjectSources = new ArrayList();
compositeAggSubjectSources.add(subjectValuesBuilder); compositeAggSubjectSources.add(subjectValuesBuilder);
CompositeAggregationBuilder compositeAggregationSubjectBuilder = new CompositeAggregationBuilder("group_by_subject", compositeAggSubjectSources); CompositeAggregationBuilder compositeAggregationSubjectBuilder = new CompositeAggregationBuilder(GROUP_BY_SUBJECT, compositeAggSubjectSources);
compositeAggregationSubjectBuilder.subAggregation(observationCodeAggregationBuilder); compositeAggregationSubjectBuilder.subAggregation(observationCodeAggregationBuilder);
compositeAggregationSubjectBuilder.size(theMaximumResultSetSize); compositeAggregationSubjectBuilder.size(10000);
return compositeAggregationSubjectBuilder; return compositeAggregationSubjectBuilder;
} }
private TermsAggregationBuilder createTermsAggregationBuilder(int theMaximumResultSetSize, int theMaxNumberObservationsPerCode, String[] theTopHitsInclude) { private SearchResponse executeSearchRequest(SearchRequest searchRequest) throws IOException {
TermsAggregationBuilder observationCodeAggregationBuilder = new TermsAggregationBuilder("group_by_code", ValueType.STRING).field("codeconceptid");
// Top Hits Aggregation
observationCodeAggregationBuilder.subAggregation(AggregationBuilders.topHits("most_recent_effective")
.sort("effectivedtm", SortOrder.DESC).fetchSource(theTopHitsInclude, null).size(theMaxNumberObservationsPerCode));
observationCodeAggregationBuilder.size(theMaximumResultSetSize);
TermsAggregationBuilder subjectsBuilder = new TermsAggregationBuilder("group_by_subject", ValueType.STRING).field("subject");
subjectsBuilder.subAggregation(observationCodeAggregationBuilder);
subjectsBuilder.size(theMaximumResultSetSize);
return subjectsBuilder;
}
public SearchResponse executeSearchRequest(SearchRequest searchRequest) throws IOException {
return myRestHighLevelClient.search(searchRequest, RequestOptions.DEFAULT); return myRestHighLevelClient.search(searchRequest, RequestOptions.DEFAULT);
} }
public List<ObservationJson> buildObservationCompositeResults(SearchResponse theSearchResponse) throws IOException {
private List<String> buildObservationIdList(SearchResponse theSearchResponse) throws IOException {
List<String> theObservationList = new ArrayList<>();
for (ParsedComposite.ParsedBucket subjectBucket : getSubjectBuckets(theSearchResponse)) {
for (Terms.Bucket observationCodeBucket : getObservationCodeBuckets(subjectBucket)) {
for (SearchHit lastNMatch : getLastNMatches(observationCodeBucket)) {
String indexedObservation = lastNMatch.getSourceAsString();
ObservationJson observationJson = objectMapper.readValue(indexedObservation, ObservationJson.class);
theObservationList.add(observationJson.getIdentifier());
}
}
}
return theObservationList;
}
private List<ObservationJson> buildObservationDocumentList(SearchResponse theSearchResponse) throws IOException {
List<ObservationJson> theObservationList = new ArrayList<>();
for (ParsedComposite.ParsedBucket subjectBucket : getSubjectBuckets(theSearchResponse)) {
for (Terms.Bucket observationCodeBucket : getObservationCodeBuckets(subjectBucket)) {
for (SearchHit lastNMatch : getLastNMatches(observationCodeBucket)) {
String indexedObservation = lastNMatch.getSourceAsString();
ObservationJson observationJson = objectMapper.readValue(indexedObservation, ObservationJson.class);
theObservationList.add(observationJson);
}
}
}
return theObservationList;
}
private List<ParsedComposite.ParsedBucket> getSubjectBuckets(SearchResponse theSearchResponse) {
Aggregations responseAggregations = theSearchResponse.getAggregations(); Aggregations responseAggregations = theSearchResponse.getAggregations();
ParsedComposite aggregatedSubjects = responseAggregations.get("group_by_subject"); ParsedComposite aggregatedSubjects = responseAggregations.get(GROUP_BY_SUBJECT);
List<ParsedComposite.ParsedBucket> subjectBuckets = aggregatedSubjects.getBuckets(); return aggregatedSubjects.getBuckets();
List<ObservationJson> codes = new ArrayList<>(); }
for(ParsedComposite.ParsedBucket subjectBucket : subjectBuckets) {
Aggregations observationCodeAggregations = subjectBucket.getAggregations(); private List<? extends Terms.Bucket> getObservationCodeBuckets(ParsedComposite.ParsedBucket theSubjectBucket) {
ParsedTerms aggregatedObservationCodes = observationCodeAggregations.get("group_by_code"); Aggregations observationCodeAggregations = theSubjectBucket.getAggregations();
List<? extends Terms.Bucket> observationCodeBuckets = aggregatedObservationCodes.getBuckets(); ParsedTerms aggregatedObservationCodes = observationCodeAggregations.get(GROUP_BY_CODE);
for (Terms.Bucket observationCodeBucket : observationCodeBuckets) { return aggregatedObservationCodes.getBuckets();
Aggregations topHitObservationCodes = observationCodeBucket.getAggregations(); }
private SearchHit[] getLastNMatches(Terms.Bucket theObservationCodeBucket) {
Aggregations topHitObservationCodes = theObservationCodeBucket.getAggregations();
ParsedTopHits parsedTopHits = topHitObservationCodes.get("most_recent_effective"); ParsedTopHits parsedTopHits = topHitObservationCodes.get("most_recent_effective");
SearchHit[] topHits = parsedTopHits.getHits().getHits(); return parsedTopHits.getHits().getHits();
for (SearchHit topHit : topHits) {
String sources = topHit.getSourceAsString();
ObservationJson code = objectMapper.readValue(sources, ObservationJson.class);
codes.add(code);
}
}
}
return codes;
} }
private List<ResourcePersistentId> buildObservationIdList(SearchResponse theSearchResponse, IdHelperService theIdHelperService) throws IOException { private List<CodeJson> buildCodeResult(SearchResponse theSearchResponse) throws JsonProcessingException {
Aggregations responseAggregations = theSearchResponse.getAggregations();
ParsedComposite aggregatedSubjects = responseAggregations.get("group_by_subject");
List<ParsedComposite.ParsedBucket> subjectBuckets = aggregatedSubjects.getBuckets();
List<ResourcePersistentId> myObservationIds = new ArrayList<>();
for(ParsedComposite.ParsedBucket subjectBucket : subjectBuckets) {
Aggregations observationCodeAggregations = subjectBucket.getAggregations();
ParsedTerms aggregatedObservationCodes = observationCodeAggregations.get("group_by_code");
List<? extends Terms.Bucket> observationCodeBuckets = aggregatedObservationCodes.getBuckets();
for (Terms.Bucket observationCodeBucket : observationCodeBuckets) {
Aggregations topHitObservationCodes = observationCodeBucket.getAggregations();
ParsedTopHits parsedTopHits = topHitObservationCodes.get("most_recent_effective");
SearchHit[] topHits = parsedTopHits.getHits().getHits();
for (SearchHit topHit : topHits) {
String sources = topHit.getSourceAsString();
ObservationJson code = objectMapper.readValue(sources, ObservationJson.class);
myObservationIds.add(theIdHelperService.resolveResourcePersistentIds("Observation", code.getIdentifier()));
}
}
}
return myObservationIds;
}
public List<ObservationJson> buildObservationTermsResults(SearchResponse theSearchResponse) throws IOException {
Aggregations responseAggregations = theSearchResponse.getAggregations();
ParsedTerms aggregatedSubjects = responseAggregations.get("group_by_subject");
List<? extends Terms.Bucket> subjectBuckets = aggregatedSubjects.getBuckets();
List<ObservationJson> codes = new ArrayList<>();
for (Terms.Bucket subjectBucket : subjectBuckets) {
Aggregations observationCodeAggregations = subjectBucket.getAggregations();
ParsedTerms aggregatedObservationCodes = observationCodeAggregations.get("group_by_code");
List<? extends Terms.Bucket> observationCodeBuckets = aggregatedObservationCodes.getBuckets();
for (Terms.Bucket observationCodeBucket : observationCodeBuckets) {
Aggregations topHitObservationCodes = observationCodeBucket.getAggregations();
ParsedTopHits parsedTopHits = topHitObservationCodes.get("most_recent_effective");
SearchHit[] topHits = parsedTopHits.getHits().getHits();
for (SearchHit topHit : topHits) {
String sources = topHit.getSourceAsString();
ObservationJson code = objectMapper.readValue(sources,ObservationJson.class);
codes.add(code);
}
}
}
return codes;
}
public List<CodeJson> buildCodeResult(SearchResponse theSearchResponse) throws JsonProcessingException {
SearchHits codeHits = theSearchResponse.getHits(); SearchHits codeHits = theSearchResponse.getHits();
List<CodeJson> codes = new ArrayList<>(); List<CodeJson> codes = new ArrayList<>();
for (SearchHit codeHit : codeHits) { for (SearchHit codeHit : codeHits) {
@ -338,27 +315,6 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
return codes; return codes;
} }
public SearchRequest buildObservationAllFieldsCompositeSearchRequest(int maxResultSetSize, SearchParameterMap theSearchParameterMap, int theMaxObservationsPerCode) {
return buildObservationsSearchRequest(theSearchParameterMap, createCompositeAggregationBuilder(maxResultSetSize, theMaxObservationsPerCode, null));
}
public SearchRequest buildObservationCompositeSearchRequest(int maxResultSetSize, SearchParameterMap theSearchParameterMap, int theMaxObservationsPerCode) {
// Return only identifiers
String[] topHitsInclude = {"identifier","subject","effectivedtm","codeconceptid"};
return buildObservationsSearchRequest(theSearchParameterMap, createCompositeAggregationBuilder(maxResultSetSize, theMaxObservationsPerCode, topHitsInclude));
}
public SearchRequest buildObservationAllFieldsTermsSearchRequest(int maxResultSetSize, SearchParameterMap theSearchParameterMap, int theMaxObservationsPerCode) {
return buildObservationsSearchRequest(theSearchParameterMap, createTermsAggregationBuilder(maxResultSetSize, theMaxObservationsPerCode, null));
}
public SearchRequest buildObservationTermsSearchRequest(int maxResultSetSize, SearchParameterMap theSearchParameterMap, int theMaxObservationsPerCode) {
// Return only identifiers
String[] topHitsInclude = {"identifier","subject","effectivedtm","codeconceptid"};
return buildObservationsSearchRequest(theSearchParameterMap, createTermsAggregationBuilder(maxResultSetSize, theMaxObservationsPerCode, topHitsInclude));
}
private SearchRequest buildObservationsSearchRequest(SearchParameterMap theSearchParameterMap, AggregationBuilder theAggregationBuilder) { private SearchRequest buildObservationsSearchRequest(SearchParameterMap theSearchParameterMap, AggregationBuilder theAggregationBuilder) {
SearchRequest searchRequest = new SearchRequest(IndexConstants.OBSERVATION_INDEX); SearchRequest searchRequest = new SearchRequest(IndexConstants.OBSERVATION_INDEX);
SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder(); SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
@ -383,19 +339,19 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
private Boolean searchParamsHaveLastNCriteria(SearchParameterMap theSearchParameterMap) { private Boolean searchParamsHaveLastNCriteria(SearchParameterMap theSearchParameterMap) {
return theSearchParameterMap != null && return theSearchParameterMap != null &&
(theSearchParameterMap.containsKey("patient") || theSearchParameterMap.containsKey("subject") || (theSearchParameterMap.containsKey(IndexConstants.PATIENT_SEARCH_PARAM) || theSearchParameterMap.containsKey(IndexConstants.SUBJECT_SEARCH_PARAM) ||
theSearchParameterMap.containsKey("category") || theSearchParameterMap.containsKey("code")); theSearchParameterMap.containsKey(IndexConstants.CATEGORY_SEARCH_PARAM) || theSearchParameterMap.containsKey(IndexConstants.CODE_SEARCH_PARAM));
} }
private void addSubjectsCriteria(BoolQueryBuilder theBoolQueryBuilder, SearchParameterMap theSearchParameterMap) { private void addSubjectsCriteria(BoolQueryBuilder theBoolQueryBuilder, SearchParameterMap theSearchParameterMap) {
if (theSearchParameterMap.containsKey("patient") || theSearchParameterMap.containsKey("subject")) { if (theSearchParameterMap.containsKey(IndexConstants.PATIENT_SEARCH_PARAM) || theSearchParameterMap.containsKey(IndexConstants.SUBJECT_SEARCH_PARAM)) {
ArrayList<String> subjectReferenceCriteria = new ArrayList<>(); ArrayList<String> subjectReferenceCriteria = new ArrayList<>();
List<List<IQueryParameterType>> andOrParams = new ArrayList<>(); List<List<IQueryParameterType>> andOrParams = new ArrayList<>();
if (theSearchParameterMap.get("patient") != null) { if (theSearchParameterMap.get(IndexConstants.PATIENT_SEARCH_PARAM) != null) {
andOrParams.addAll(theSearchParameterMap.get("patient")); andOrParams.addAll(theSearchParameterMap.get(IndexConstants.PATIENT_SEARCH_PARAM));
} }
if (theSearchParameterMap.get("subject") != null) { if (theSearchParameterMap.get(IndexConstants.SUBJECT_SEARCH_PARAM) != null) {
andOrParams.addAll(theSearchParameterMap.get("subject")); andOrParams.addAll(theSearchParameterMap.get(IndexConstants.SUBJECT_SEARCH_PARAM));
} }
for (List<? extends IQueryParameterType> nextAnd : andOrParams) { for (List<? extends IQueryParameterType> nextAnd : andOrParams) {
subjectReferenceCriteria.addAll(getReferenceValues(nextAnd)); subjectReferenceCriteria.addAll(getReferenceValues(nextAnd));
@ -425,12 +381,12 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
} }
private void addCategoriesCriteria(BoolQueryBuilder theBoolQueryBuilder, SearchParameterMap theSearchParameterMap) { private void addCategoriesCriteria(BoolQueryBuilder theBoolQueryBuilder, SearchParameterMap theSearchParameterMap) {
if (theSearchParameterMap.containsKey("category")) { if (theSearchParameterMap.containsKey(IndexConstants.CATEGORY_SEARCH_PARAM)) {
ArrayList<String> codeSystemHashList = new ArrayList<>(); ArrayList<String> codeSystemHashList = new ArrayList<>();
ArrayList<String> codeOnlyList = new ArrayList<>(); ArrayList<String> codeOnlyList = new ArrayList<>();
ArrayList<String> systemOnlyList = new ArrayList<>(); ArrayList<String> systemOnlyList = new ArrayList<>();
ArrayList<String> textOnlyList = new ArrayList<>(); ArrayList<String> textOnlyList = new ArrayList<>();
List<List<IQueryParameterType>> andOrParams = theSearchParameterMap.get("category"); List<List<IQueryParameterType>> andOrParams = theSearchParameterMap.get(IndexConstants.CATEGORY_SEARCH_PARAM);
for (List<? extends IQueryParameterType> nextAnd : andOrParams) { for (List<? extends IQueryParameterType> nextAnd : andOrParams) {
codeSystemHashList.addAll(getCodingCodeSystemValues(nextAnd)); codeSystemHashList.addAll(getCodingCodeSystemValues(nextAnd));
codeOnlyList.addAll(getCodingCodeOnlyValues(nextAnd)); codeOnlyList.addAll(getCodingCodeOnlyValues(nextAnd));
@ -522,12 +478,12 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
} }
private void addObservationCodeCriteria(BoolQueryBuilder theBoolQueryBuilder, SearchParameterMap theSearchParameterMap) { private void addObservationCodeCriteria(BoolQueryBuilder theBoolQueryBuilder, SearchParameterMap theSearchParameterMap) {
if (theSearchParameterMap.containsKey("code")) { if (theSearchParameterMap.containsKey(IndexConstants.CODE_SEARCH_PARAM)) {
ArrayList<String> codeSystemHashList = new ArrayList<>(); ArrayList<String> codeSystemHashList = new ArrayList<>();
ArrayList<String> codeOnlyList = new ArrayList<>(); ArrayList<String> codeOnlyList = new ArrayList<>();
ArrayList<String> systemOnlyList = new ArrayList<>(); ArrayList<String> systemOnlyList = new ArrayList<>();
ArrayList<String> textOnlyList = new ArrayList<>(); ArrayList<String> textOnlyList = new ArrayList<>();
List<List<IQueryParameterType>> andOrParams = theSearchParameterMap.get("code"); List<List<IQueryParameterType>> andOrParams = theSearchParameterMap.get(IndexConstants.CODE_SEARCH_PARAM);
for (List<? extends IQueryParameterType> nextAnd : andOrParams) { for (List<? extends IQueryParameterType> nextAnd : andOrParams) {
codeSystemHashList.addAll(getCodingCodeSystemValues(nextAnd)); codeSystemHashList.addAll(getCodingCodeSystemValues(nextAnd));
codeOnlyList.addAll(getCodingCodeOnlyValues(nextAnd)); codeOnlyList.addAll(getCodingCodeOnlyValues(nextAnd));
@ -555,22 +511,11 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
} }
@VisibleForTesting
void deleteAllDocuments(String theIndexName) throws IOException { void deleteAllDocuments(String theIndexName) throws IOException {
DeleteByQueryRequest deleteByQueryRequest = new DeleteByQueryRequest(theIndexName); DeleteByQueryRequest deleteByQueryRequest = new DeleteByQueryRequest(theIndexName);
deleteByQueryRequest.setQuery(QueryBuilders.matchAllQuery()); deleteByQueryRequest.setQuery(QueryBuilders.matchAllQuery());
myRestHighLevelClient.deleteByQuery(deleteByQueryRequest, RequestOptions.DEFAULT); myRestHighLevelClient.deleteByQuery(deleteByQueryRequest, RequestOptions.DEFAULT);
} }
/* @Override
public IBundleProvider lastN(HttpServletRequest theServletRequest, RequestDetails theRequestDetails) {
return null;
}
@Override
public IBundleProvider uniqueCodes(HttpServletRequest theServletRequest, RequestDetails theRequestDetails) {
return null;
}
*/
} }

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/IElasticsearchSvc.java
View File

@ -1,20 +1,10 @@
package ca.uhn.fhir.jpa.search.lastn; package ca.uhn.fhir.jpa.search.lastn;
//import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import java.util.List; import java.util.List;
public interface IElasticsearchSvc { public interface IElasticsearchSvc {
List<String> executeLastN(SearchParameterMap theSearchParameterMap, Integer theMaxObservationsPerCode);
// IBundleProvider lastN(javax.servlet.http.HttpServletRequest theServletRequest, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails);
// IBundleProvider uniqueCodes(javax.servlet.http.HttpServletRequest theServletRequest, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails);
List<ResourcePersistentId> executeLastN(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails, IdHelperService theIdHelperService);
} }

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/IndexConstants.java
View File

@ -6,4 +6,10 @@ public class IndexConstants {
public static final String CODE_INDEX = "code_index"; public static final String CODE_INDEX = "code_index";
public static final String OBSERVATION_DOCUMENT_TYPE = "ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedSearchParamLastNEntity"; public static final String OBSERVATION_DOCUMENT_TYPE = "ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedSearchParamLastNEntity";
public static final String CODE_DOCUMENT_TYPE = "ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedCodeCodeableConceptEntity"; public static final String CODE_DOCUMENT_TYPE = "ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedCodeCodeableConceptEntity";
public static final String SUBJECT_SEARCH_PARAM = "subject";
public static final String PATIENT_SEARCH_PARAM = "patient";
public static final String CODE_SEARCH_PARAM = "code";
public static final String CATEGORY_SEARCH_PARAM = "category";
} }

122
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/cli/MulticodeObservationsIntoElasticSearch.java
View File

@ -1,122 +0,0 @@
package ca.uhn.fhir.jpa.search.lastn.cli;
import ca.uhn.fhir.jpa.search.lastn.json.IdJson;
import ca.uhn.fhir.jpa.search.lastn.json.IndexJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.UUID;
public class MulticodeObservationsIntoElasticSearch {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MulticodeObservationsIntoElasticSearch.class);
private static final ObjectMapper ourMapperNonPrettyPrint;
static {
ourMapperNonPrettyPrint = new ObjectMapper();
ourMapperNonPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
ourMapperNonPrettyPrint.disable(SerializationFeature.INDENT_OUTPUT);
ourMapperNonPrettyPrint.disable(JsonGenerator.Feature.AUTO_CLOSE_TARGET);
}
public static void main(String[] theArgs) {
for (int patientCount = 0; patientCount < 10 ; patientCount++) {
String subject = "Patient/"+UUID.randomUUID().toString();
for ( int entryCount = 0; entryCount < 10 ; entryCount++ ) {
String nextResourceId = UUID.randomUUID().toString();
IdJson id = new IdJson(nextResourceId);
IndexJson documentIndex = new IndexJson(id);
ObservationJson observationDocument = new ObservationJson();
observationDocument.setIdentifier(nextResourceId);
observationDocument.setSubject(subject);
// Add three CodeableConcepts for category
List<CodeableConcept> category = new ArrayList<>();
// Create three codings and first category CodeableConcept
Coding categoryCoding1_1 = new Coding("http://mycodes.org/fhir/observation-category", "test-heart-rate", "test heart-rate");
Coding categoryCoding1_2 = new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-heart-rate", "test alternate heart-rate");
Coding categoryCoding1_3 = new Coding("http://mysecondaltcodes.org/fhir/observation-category", "test-2nd-alt-heart-rate", "test second alternate heart-rate");
CodeableConcept categoryCodeableConcept1 = new CodeableConcept();
categoryCodeableConcept1.getCoding().add(categoryCoding1_1);
categoryCodeableConcept1.getCoding().add(categoryCoding1_2);
categoryCodeableConcept1.getCoding().add(categoryCoding1_3);
categoryCodeableConcept1.setText("Heart Rate Codeable Concept");
category.add(categoryCodeableConcept1);
// Create three codings and second category CodeableConcept
Coding categoryCoding2_1 = new Coding("http://mycodes.org/fhir/observation-category", "test-vital-signs", "test vital signs");
Coding categoryCoding2_2 = new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-vitals", "test alternate vital signs");
Coding categoryCoding2_3 = new Coding("http://mysecondaltcodes.org/fhir/observation-category", "test-2nd-alt-vitals", "test second alternate vital signs");
CodeableConcept categoryCodeableConcept2 = new CodeableConcept();
categoryCodeableConcept2.getCoding().add(categoryCoding2_1);
categoryCodeableConcept2.getCoding().add(categoryCoding2_2);
categoryCodeableConcept2.getCoding().add(categoryCoding2_3);
categoryCodeableConcept2.setText("Vital Signs Codeable Concept");
category.add(categoryCodeableConcept2);
// Create three codings and third category CodeableConcept
Coding categoryCoding3_1 = new Coding("http://mycodes.org/fhir/observation-category", "test-vitals-panel", "test vital signs panel");
Coding categoryCoding3_2 = new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-vitals-panel", "test alternate vital signs panel");
Coding categoryCoding3_3 = new Coding("http://mysecondaltcodes.org/fhir/observation-category", "test-2nd-alt-vitals-panel", "test second alternate vital signs panel");
CodeableConcept categoryCodeableConcept3 = new CodeableConcept();
categoryCodeableConcept3.getCoding().add(categoryCoding3_1);
categoryCodeableConcept3.getCoding().add(categoryCoding3_2);
categoryCodeableConcept3.getCoding().add(categoryCoding3_3);
categoryCodeableConcept3.setText("Vital Signs Panel Codeable Concept");
category.add(categoryCodeableConcept3);
observationDocument.setCategories(category);
Coding codeCoding1 = new Coding("http://mycodes.org/fhir/observation-code", "test-code", "test observation code");
Coding codeCoding2 = new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code", "test observation code");
Coding codeCoding3 = new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code", "test observation code");
CodeableConcept code = new CodeableConcept();
code.getCoding().add(codeCoding1);
code.getCoding().add(codeCoding2);
code.getCoding().add(codeCoding3);
code.setText("Observation code CodeableConcept");
observationDocument.setCode(code);
observationDocument.setCode_concept_id("multicode_test_normalized_code");
Date effectiveDtm = new Date();
observationDocument.setEffectiveDtm(effectiveDtm);
StringWriter stringWriter = new StringWriter();
File outputFile = new File("Observations_multiplecodes.json");
try {
FileOutputStream outputStream = new FileOutputStream(outputFile, true);
ourMapperNonPrettyPrint.writeValue(stringWriter, documentIndex);
stringWriter.append('\n');
ourMapperNonPrettyPrint.writeValue(stringWriter, observationDocument);
ourMapperNonPrettyPrint.writeValue(outputStream, documentIndex);
outputStream.write('\n');
ourMapperNonPrettyPrint.writeValue(outputStream, observationDocument);
outputStream.write('\n');
outputStream.flush();
outputStream.close();
} catch (IOException theE) {
theE.printStackTrace();
}
}
}
ourLog.info("Upload complete");
}
}

128
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/cli/OneMillionPatientsIntoElasticSearch.java
View File

@ -1,128 +0,0 @@
package ca.uhn.fhir.jpa.search.lastn.cli;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchBulkIndexSvcImpl;
import ca.uhn.fhir.jpa.search.lastn.IndexConstants;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.search.lastn.util.SimpleStopWatch;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import org.apache.commons.lang3.RandomStringUtils;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import java.io.IOException;
import java.util.*;
public class OneMillionPatientsIntoElasticSearch {
// private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(OneMillionPatientsIntoElasticSearch.class);
private static final ObjectMapper ourMapperNonPrettyPrint;
static {
ourMapperNonPrettyPrint = new ObjectMapper();
ourMapperNonPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
ourMapperNonPrettyPrint.disable(SerializationFeature.INDENT_OUTPUT);
ourMapperNonPrettyPrint.disable(JsonGenerator.Feature.AUTO_CLOSE_TARGET);
}
public static void main(String[] theArgs) throws IOException {
ElasticsearchBulkIndexSvcImpl elasticsearchSvc = new ElasticsearchBulkIndexSvcImpl("localhost",9301, "elastic", "changeme");
try {
SimpleStopWatch stopwatch = new SimpleStopWatch();
List<String> observationCodeIds = new ArrayList<>();
List<CodeableConcept> observationCodes = new ArrayList<>();
for (int codeCount = 0; codeCount < 1000; codeCount++) {
String code = RandomStringUtils.random(10,true,true);
Coding codeCoding = new Coding("http://mycodes.org/fhir/observation-code", code, "test observation code " + code);
CodeableConcept codeConcept = new CodeableConcept();
codeConcept.getCoding().add(codeCoding);
codeConcept.setText("test observation code concept " + code);
String codeableConceptId = UUID.randomUUID().toString();
observationCodeIds.add(codeableConceptId);
observationCodes.add(codeConcept);
CodeJson codeDocument = new CodeJson(codeConcept, codeableConceptId);
String printedObservationDocument = ourMapperNonPrettyPrint.writeValueAsString(codeDocument);
System.out.println(printedObservationDocument);
System.out.println(codeableConceptId);
elasticsearchSvc.addToBulkIndexRequest("code_index", codeableConceptId, printedObservationDocument, IndexConstants.CODE_DOCUMENT_TYPE);
if ((codeCount+1)%250 == 0) {
elasticsearchSvc.executeBulkIndex();
long elapsedTime = stopwatch.getElapsedTime();
stopwatch.restart();
System.out.println("Elapsed processing time = " + elapsedTime/1000 + "s");
System.out.println("Average processing time/code = " + elapsedTime/5000 + "ms");
}
}
for (int patientCount = 0; patientCount < 1000000 ; patientCount++) {
String subject = "Patient/"+UUID.randomUUID().toString();
ArrayList<CodeableConcept> observationCodesSubSet = new ArrayList<>();
ArrayList<String> observationCodeIdsSubSet = new ArrayList<>();
for (int observationCount = 0; observationCount < 15 ; observationCount++) {
int codeIndex = (int) (1000 * Math.random());
observationCodesSubSet.add(observationCodes.get(codeIndex));
observationCodeIdsSubSet.add(observationCodeIds.get(codeIndex));
}
int repeatedCodeIndex = (int) (1000 * Math.random());
CodeableConcept repeatedCoding = observationCodes.get(repeatedCodeIndex);
for (int observationCount = 0; observationCount < 10 ; observationCount++ ) {
observationCodesSubSet.add(repeatedCoding);
observationCodeIdsSubSet.add(observationCodeIds.get(repeatedCodeIndex));
}
int entryCount = 0;
for (int codingCount=0; codingCount<observationCodesSubSet.size(); codingCount++) {
String nextResourceId = UUID.randomUUID().toString();
ObservationJson observationDocument = new ObservationJson();
observationDocument.setIdentifier(nextResourceId);
observationDocument.setSubject(subject);
List<CodeableConcept> category = new ArrayList<>();
Coding categoryCoding = new Coding("http://mycodes.org/fhir/category-code", "test-category-code", "test category display");
CodeableConcept categoryCodeableConcept = new CodeableConcept();
categoryCodeableConcept.getCoding().add(categoryCoding);
categoryCodeableConcept.setText("Test Category CodeableConcept Text");
category.add(categoryCodeableConcept);
observationDocument.setCategories(category);
observationDocument.setCode(observationCodesSubSet.get(codingCount));
observationDocument.setCode_concept_id(observationCodeIdsSubSet.get(codingCount));
Calendar observationDate = new GregorianCalendar();
observationDate.add(Calendar.HOUR, -10 + entryCount);
entryCount++;
Date effectiveDtm = observationDate.getTime();
observationDocument.setEffectiveDtm(effectiveDtm);
String printedObservationDocument = ourMapperNonPrettyPrint.writeValueAsString(observationDocument);
elasticsearchSvc.addToBulkIndexRequest("observation_index", nextResourceId, printedObservationDocument, IndexConstants.OBSERVATION_DOCUMENT_TYPE );
}
if ((patientCount+1)%100 == 0) {
System.out.println("Entries created = " + (patientCount+1)*25);
}
if ((patientCount+1)%250 == 0) {
elasticsearchSvc.executeBulkIndex();
long elapsedTime = stopwatch.getElapsedTime();
stopwatch.restart();
System.out.println("Elapsed processing time = " + elapsedTime/1000 + "s");
System.out.println("Average processing time/observation = " + elapsedTime/5000 + "ms");
}
}
if (elasticsearchSvc.bulkRequestPending()) {
elasticsearchSvc.executeBulkIndex();
}
// ourLog.info("Upload complete");
} finally {
elasticsearchSvc.closeClient();
}
}
}

116
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/cli/OneThousandObservationsIntoElasticSearch.java
View File

@ -1,116 +0,0 @@
package ca.uhn.fhir.jpa.search.lastn.cli;
import ca.uhn.fhir.jpa.search.lastn.json.IdJson;
import ca.uhn.fhir.jpa.search.lastn.json.IndexJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.UUID;
public class OneThousandObservationsIntoElasticSearch {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(OneThousandObservationsIntoElasticSearch.class);
private static final ObjectMapper ourMapperNonPrettyPrint;
static {
ourMapperNonPrettyPrint = new ObjectMapper();
ourMapperNonPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
ourMapperNonPrettyPrint.disable(SerializationFeature.INDENT_OUTPUT);
ourMapperNonPrettyPrint.disable(JsonGenerator.Feature.AUTO_CLOSE_TARGET);
}
public static void main(String[] theArgs) {
for (int patientCount = 0; patientCount < 3 ; patientCount++) {
String subject = "Patient/"+UUID.randomUUID().toString();
for ( int entryCount = 0; entryCount < 1100 ; entryCount++ ) {
String nextResourceId = UUID.randomUUID().toString();
IdJson id = new IdJson(nextResourceId);
IndexJson documentIndex = new IndexJson(id);
ObservationJson observationDocument = new ObservationJson();
observationDocument.setIdentifier(nextResourceId);
observationDocument.setSubject(subject);
// Add three CodeableConcepts for category
List<CodeableConcept> category = new ArrayList<>();
// Create three codings and first category CodeableConcept
Coding categoryCoding1_1 = new Coding("http://mycodes.org/fhir/observation-category", "test-heart-rate", "test heart-rate");
Coding categoryCoding1_2 = new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-heart-rate", "test alternate heart-rate");
CodeableConcept categoryCodeableConcept1 = new CodeableConcept();
categoryCodeableConcept1.getCoding().add(categoryCoding1_1);
categoryCodeableConcept1.getCoding().add(categoryCoding1_2);
categoryCodeableConcept1.setText("Heart Rate CodeableConcept");
category.add(categoryCodeableConcept1);
// Create three codings and second category CodeableConcept
Coding categoryCoding2_1 = new Coding("http://mycodes.org/fhir/observation-category", "test-vital-signs", "test vital signs");
Coding categoryCoding2_2 = new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-vitals", "test alternate vital signs");
CodeableConcept categoryCodeableConcept2 = new CodeableConcept();
categoryCodeableConcept2.getCoding().add(categoryCoding2_1);
categoryCodeableConcept2.getCoding().add(categoryCoding2_2);
categoryCodeableConcept2.setText("Vital Signs CodeableConcept");
category.add(categoryCodeableConcept2);
// Create three codings and third category CodeableConcept
Coding categoryCoding3_1 = new Coding("http://mycodes.org/fhir/observation-category", "test-vitals-panel", "test vital signs panel");
Coding categoryCoding3_2 = new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-vitals-panel", "test alternate vital signs panel");
CodeableConcept categoryCodeableConcept3 = new CodeableConcept();
categoryCodeableConcept3.getCoding().add(categoryCoding3_1);
categoryCodeableConcept3.getCoding().add(categoryCoding3_2);
categoryCodeableConcept3.setText("Vital Signs Panel CodeableConcept");
category.add(categoryCodeableConcept3);
observationDocument.setCategories(category);
Coding codeCoding1 = new Coding("http://mycodes.org/fhir/observation-code", "test-code_" + entryCount, "test observation code");
Coding codeCoding2 = new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code_" + entryCount, "test observation code");
Coding codeCoding3 = new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code" + entryCount, "test observation code");
CodeableConcept code = new CodeableConcept();
code.getCoding().add(codeCoding1);
code.getCoding().add(codeCoding2);
code.getCoding().add(codeCoding3);
code.setText("Observation code CodeableConcept " + entryCount);
observationDocument.setCode(code);
observationDocument.setCode_concept_id("multicode_test_normalized_code_" + entryCount);
Date effectiveDtm = new Date();
observationDocument.setEffectiveDtm(effectiveDtm);
StringWriter stringWriter = new StringWriter();
File outputFile = new File("one_thousand_observations.json");
try {
FileOutputStream outputStream = new FileOutputStream(outputFile, true);
ourMapperNonPrettyPrint.writeValue(stringWriter, documentIndex);
stringWriter.append('\n');
ourMapperNonPrettyPrint.writeValue(stringWriter, observationDocument);
ourMapperNonPrettyPrint.writeValue(outputStream, documentIndex);
outputStream.write('\n');
ourMapperNonPrettyPrint.writeValue(outputStream, observationDocument);
outputStream.write('\n');
outputStream.flush();
outputStream.close();
} catch (IOException theE) {
theE.printStackTrace();
}
}
}
ourLog.info("Upload complete");
}
}

153
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/cli/UploadSampleDatasetIntoElasticSearch.java
View File

@ -1,153 +0,0 @@
package ca.uhn.fhir.jpa.search.lastn.cli;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.jpa.search.lastn.json.IdJson;
import ca.uhn.fhir.jpa.search.lastn.json.IndexJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import com.google.common.base.Charsets;
import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.springframework.core.io.Resource;
import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
import java.io.*;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import java.util.concurrent.atomic.AtomicInteger;
public class UploadSampleDatasetIntoElasticSearch {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UploadSampleDatasetIntoElasticSearch.class);
private static final ObjectMapper ourMapperNonPrettyPrint;
static {
ourMapperNonPrettyPrint = new ObjectMapper();
ourMapperNonPrettyPrint.setSerializationInclusion(JsonInclude.Include.NON_NULL);
ourMapperNonPrettyPrint.disable(SerializationFeature.INDENT_OUTPUT);
ourMapperNonPrettyPrint.disable(JsonGenerator.Feature.AUTO_CLOSE_TARGET);
}
public static void main(String[] theArgs) {
FhirContext myFhirCtx = FhirContext.forR4();
myFhirCtx.getRestfulClientFactory().setSocketTimeout(120000);
PathMatchingResourcePatternResolver provider = new PathMatchingResourcePatternResolver();
final Resource[] bundleResources;
try {
bundleResources = provider.getResources("*.json.bz2");
} catch (IOException e) {
throw new RuntimeException("Unexpected error during transmission: " + e.toString(), e);
}
AtomicInteger index = new AtomicInteger();
Arrays.stream(bundleResources).forEach(
resource -> {
index.incrementAndGet();
InputStream resIs = null;
String nextBundleString;
try {
resIs = resource.getInputStream();
resIs = new BZip2CompressorInputStream(resIs);
nextBundleString = IOUtils.toString(resIs, Charsets.UTF_8);
} catch (IOException e) {
ourLog.error("Failure reading: {}", resource.getFilename(), e);
return;
} finally {
try {
if (resIs != null) {
resIs.close();
}
} catch (final IOException ioe) {
// ignore
}
}
ourLog.info("Uploading {}/{} - {} ({} bytes)", index, bundleResources.length, resource.getFilename(), nextBundleString.length());
/*
* SMART demo apps rely on the use of LOINC 3141-9 (Body Weight Measured)
* instead of LOINC 29463-7 (Body Weight)
*/
nextBundleString = nextBundleString.replace("\"29463-7\"", "\"3141-9\"");
IParser parser = myFhirCtx.newJsonParser();
parser.setParserErrorHandler(new LenientErrorHandler(false));
Bundle bundle = parser.parseResource(Bundle.class, nextBundleString);
for (BundleEntryComponent nextEntry : bundle.getEntry()) {
/*
* Synthea gives resources UUIDs with urn:uuid: prefix, which is only
* used for placeholders. We're going to use these as the actual resource
* IDs, so we strip the prefix.
*/
String nextResourceId = nextEntry.getFullUrl();
if (nextResourceId == null) {
nextResourceId = UUID.randomUUID().toString();
}
nextResourceId = nextResourceId.replace("urn:uuid:", "");
nextEntry.getResource().setId(nextResourceId);
nextEntry.setFullUrl(nextResourceId);
if (nextEntry.getResource().getResourceType().equals(ResourceType.Observation)) {
IdJson id = new IdJson(nextResourceId);
IndexJson documentIndex = new IndexJson(id);
org.hl7.fhir.r4.model.Observation observation = (Observation) nextEntry.getResource();
ObservationJson observationDocument = new ObservationJson();
observationDocument.setIdentifier(nextResourceId);
String subject = "Patient/"+observation.getSubject().getReference();
observationDocument.setSubject(subject);
List<CodeableConcept> category = observation.getCategory();
observationDocument.setCategories(category);
observationDocument.setCode_concept_id(category.get(0).getCodingFirstRep().getSystem() + "/" + category.get(0).getCodingFirstRep().getCode());
CodeableConcept code = observation.getCode();
observationDocument.setCode(code);
Date effectiveDtm = observation.getEffectiveDateTimeType().getValue();
observationDocument.setEffectiveDtm(effectiveDtm);
StringWriter stringWriter = new StringWriter();
File outputFile = new File("Observations.json");
try {
FileOutputStream outputStream = new FileOutputStream(outputFile, true);
ourMapperNonPrettyPrint.writeValue(stringWriter, documentIndex);
stringWriter.append('\n');
ourMapperNonPrettyPrint.writeValue(stringWriter, observationDocument);
ourMapperNonPrettyPrint.writeValue(outputStream, documentIndex);
outputStream.write('\n');
ourMapperNonPrettyPrint.writeValue(outputStream, observationDocument);
outputStream.write('\n');
outputStream.flush();
outputStream.close();
} catch (IOException theE) {
theE.printStackTrace();
}
System.out.println(stringWriter.toString());
}
}
}
);
ourLog.info("Upload complete");
}
}

11
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticSearch.java
View File

@ -22,6 +22,10 @@ public class TestR4ConfigWithElasticSearch extends TestR4Config {
private static final Logger ourLog = LoggerFactory.getLogger(TestR4ConfigWithElasticSearch.class); private static final Logger ourLog = LoggerFactory.getLogger(TestR4ConfigWithElasticSearch.class);
private static final String ELASTIC_VERSION = "6.5.4"; private static final String ELASTIC_VERSION = "6.5.4";
protected final String elasticsearchHost = "localhost";
protected final String elasticsearchUserId = "";
protected final String elasticsearchPassword = "";
@Override @Override
@Bean @Bean
@ -38,9 +42,9 @@ public class TestR4ConfigWithElasticSearch extends TestR4Config {
.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE) .setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE)
.setIndexManagementWaitTimeoutMillis(10000) .setIndexManagementWaitTimeoutMillis(10000)
.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW) .setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW)
.setRestUrl("http://localhost:" + httpPort) .setRestUrl("http://"+ elasticsearchHost + ":" + httpPort)
.setUsername("") .setUsername(elasticsearchUserId)
.setPassword("") .setPassword(elasticsearchPassword)
.apply(retVal); .apply(retVal);
return retVal; return retVal;
@ -65,7 +69,6 @@ public class TestR4ConfigWithElasticSearch extends TestR4Config {
return embeddedElastic; return embeddedElastic;
} }
@PreDestroy @PreDestroy
public void stop() { public void stop() {
embeddedElasticSearch().stop(); embeddedElasticSearch().stop();

16
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticsearchClient.java Normal file
View File

@ -0,0 +1,16 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class TestR4ConfigWithElasticsearchClient extends TestR4ConfigWithElasticSearch {
@Bean()
public ElasticsearchSvcImpl myElasticsearchSvc() {
int elasticsearchPort = embeddedElasticSearch().getHttpPort();
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
}
}

43
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/lastn/IntegratedObservationIndexedSearchParamLastNTest.java
View File

@ -2,20 +2,16 @@ package ca.uhn.fhir.jpa.dao.lastn;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao; import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.lastn.config.TestIntegratedObservationIndexSearchConfig; import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticsearchClient;
import ca.uhn.fhir.jpa.dao.data.IObservationIndexedCodeCodeableConceptSearchParamDao; import ca.uhn.fhir.jpa.dao.data.IObservationIndexedCodeCodeableConceptSearchParamDao;
import ca.uhn.fhir.jpa.dao.data.IObservationIndexedSearchParamLastNDao; import ca.uhn.fhir.jpa.dao.data.IObservationIndexedSearchParamLastNDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.parser.IParser; import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.LenientErrorHandler; import ca.uhn.fhir.parser.LenientErrorHandler;
import ca.uhn.fhir.rest.param.ReferenceParam; import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import com.google.common.base.Charsets; import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.shadehapi.elasticsearch.action.search.SearchRequest;
import org.shadehapi.elasticsearch.action.search.SearchResponse;
import org.hl7.fhir.r4.model.*; import org.hl7.fhir.r4.model.*;
import org.junit.After; import org.junit.After;
import org.junit.Before; import org.junit.Before;
@ -34,7 +30,7 @@ import java.util.concurrent.atomic.AtomicInteger;
import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertEquals;
@RunWith(SpringJUnit4ClassRunner.class) @RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = { TestIntegratedObservationIndexSearchConfig.class }) @ContextConfiguration(classes = { TestR4ConfigWithElasticsearchClient.class })
public class IntegratedObservationIndexedSearchParamLastNTest { public class IntegratedObservationIndexedSearchParamLastNTest {
@Autowired @Autowired
@ -128,29 +124,16 @@ public class IntegratedObservationIndexedSearchParamLastNTest {
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", SUBJECTID); ReferenceParam subjectParam = new ReferenceParam("Patient", "", SUBJECTID);
searchParameterMap.add("subject", subjectParam); searchParameterMap.add(Observation.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().addOr(subjectParam)));
TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE); TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE);
searchParameterMap.add("category", categoryParam); searchParameterMap.add(Observation.SP_CATEGORY, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(categoryParam)));
TokenParam codeParam = new TokenParam(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE); TokenParam codeParam = new TokenParam(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE);
searchParameterMap.add("code", codeParam); searchParameterMap.add(Observation.SP_CODE, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(codeParam)));
// execute Observation ID search - Terms Aggregation List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, 3);
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationAllFieldsTermsSearchRequest(1000, searchParameterMap, 3);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationTermsResults(responseIds);
assertEquals(1, observationIdsOnly.size()); assertEquals(1, observationIdsOnly.size());
ObservationJson observationIdOnly = observationIdsOnly.get(0); assertEquals(RESOURCEPID, observationIdsOnly.get(0));
assertEquals(RESOURCEPID, observationIdOnly.getIdentifier());
// execute Observation ID search - Composite Aggregation
searchRequestIdsOnly = elasticsearchSvc.buildObservationAllFieldsCompositeSearchRequest(1000, searchParameterMap, 3);
responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(1, observationIdsOnly.size());
observationIdOnly = observationIdsOnly.get(0);
assertEquals(RESOURCEPID, observationIdOnly.getIdentifier());
} }
@ -278,19 +261,13 @@ public class IntegratedObservationIndexedSearchParamLastNTest {
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
// execute Observation ID search - Composite Aggregation // execute Observation ID search - Composite Aggregation
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationAllFieldsCompositeSearchRequest(1000, searchParameterMap, 1); List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap,1);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(20, observationIdsOnly.size()); assertEquals(20, observationIdsOnly.size());
ObservationJson observationIdOnly = observationIdsOnly.get(0);
searchRequestIdsOnly = elasticsearchSvc.buildObservationAllFieldsCompositeSearchRequest(1000, searchParameterMap, 3); observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, 3);
responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(38, observationIdsOnly.size()); assertEquals(38, observationIdsOnly.size());
observationIdOnly = observationIdsOnly.get(0);
} }

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/lastn/PersistObservationIndexedSearchParamLastNTest.java
View File

@ -1,6 +1,6 @@
package ca.uhn.fhir.jpa.dao.lastn; package ca.uhn.fhir.jpa.dao.lastn;
import ca.uhn.fhir.jpa.dao.lastn.config.TestObservationIndexSearchConfig; import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticSearch;
import ca.uhn.fhir.jpa.dao.data.IObservationIndexedCodeCodeableConceptSearchParamDao; import ca.uhn.fhir.jpa.dao.data.IObservationIndexedCodeCodeableConceptSearchParamDao;
import ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedCodeCodeableConceptEntity; import ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedCodeCodeableConceptEntity;
import ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedSearchParamLastNEntity; import ca.uhn.fhir.jpa.dao.lastn.entity.ObservationIndexedSearchParamLastNEntity;
@ -19,7 +19,7 @@ import java.util.*;
import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertEquals;
@RunWith(SpringJUnit4ClassRunner.class) @RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = { TestObservationIndexSearchConfig.class }) @ContextConfiguration(classes = { TestR4ConfigWithElasticSearch.class })
public class PersistObservationIndexedSearchParamLastNTest { public class PersistObservationIndexedSearchParamLastNTest {
@Autowired @Autowired

23
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/lastn/config/TestIntegratedObservationIndexSearchConfig.java
View File

@ -1,23 +0,0 @@
package ca.uhn.fhir.jpa.dao.lastn.config;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import java.io.IOException;
@Configuration
@EnableJpaRepositories(entityManagerFactoryRef = "entityManagerFactory",
basePackages = {"ca.uhn.fhir.jpa.dao.data"})
@EnableTransactionManagement
public class TestIntegratedObservationIndexSearchConfig extends TestObservationIndexSearchConfig {
@Bean()
public ElasticsearchSvcImpl myElasticsearchSvc() throws IOException {
int elasticsearchPort = embeddedElasticSearch().getHttpPort();
return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
}
}

93
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/lastn/config/TestObservationIndexSearchConfig.java
View File

@ -1,93 +0,0 @@
package ca.uhn.fhir.jpa.dao.lastn.config;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.jpa.config.TestR4Config;
import ca.uhn.fhir.jpa.config.r4.BaseR4Config;
import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import org.hibernate.cfg.AvailableSettings;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.transaction.annotation.EnableTransactionManagement;
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
@EnableJpaRepositories(entityManagerFactoryRef = "entityManagerFactory",
basePackages = {"ca.uhn.fhir.jpa.dao.data"})
@EnableTransactionManagement
public class TestObservationIndexSearchConfig extends TestR4Config {
final String elasticsearchHost = "127.0.0.1";
final String elasticsearchUserId = "";
final String elasticsearchPassword = "";
private static final String ELASTIC_VERSION = "6.5.4";
@Override
public Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.dialect", org.hibernate.dialect.H2Dialect.class);
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put(AvailableSettings.HBM2DDL_AUTO, "update");
extraProperties.put("hibernate.jdbc.batch_size", "5000");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");
extraProperties.put("hibernate.cache.use_structured_entries", "false");
extraProperties.put("hibernate.cache.use_minimal_puts", "false");
extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
extraProperties.put("hibernate.search.default.worker.execution", "sync");
int elasticsearchPort = embeddedElasticSearch().getHttpPort();
new ElasticsearchHibernatePropertiesBuilder()
.setDebugRefreshAfterWrite(true)
.setDebugPrettyPrintJsonLog(true)
.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE)
.setIndexManagementWaitTimeoutMillis(10000)
.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW)
.setRestUrl("http://" + elasticsearchHost + ":" + elasticsearchPort)
.setUsername(elasticsearchUserId)
.setPassword(elasticsearchPassword)
.apply(extraProperties);
extraProperties.setProperty("hibernate.search.default.elasticsearch.refresh_after_write", "true");
return extraProperties;
}
@Bean
public EmbeddedElastic embeddedElasticSearch() {
EmbeddedElastic embeddedElastic;
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();
}
}

134
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LastNTest.java
View File

@ -1,134 +0,0 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.*;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.lastn.config.TestIntegratedObservationIndexSearchConfig;
import ca.uhn.fhir.jpa.dao.BaseJpaTest;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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.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.servlet.http.HttpServletRequest;
import java.util.*;
import static org.junit.Assert.*;
import static org.mockito.Mockito.when;
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = { TestIntegratedObservationIndexSearchConfig.class })
public class FhirResourceDaoR4LastNTest extends BaseJpaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4LastNTest.class);
@Autowired
@Qualifier("myPatientDaoR4")
protected IFhirResourceDaoPatient<Patient> myPatientDao;
@Autowired
@Qualifier("myObservationDaoR4")
protected IFhirResourceDaoObservation<Observation> myObservationDao;
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
protected FhirContext myFhirCtx;
@Autowired
protected PlatformTransactionManager myPlatformTransactionManager;
@Override
protected FhirContext getContext() {
return myFhirCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myPlatformTransactionManager;
}
@Before
public void beforeDisableResultReuse() {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
private ServletRequestDetails mockSrd() {
return mySrd;
}
@Test
public void testLastN() {
Patient pt = new Patient();
pt.addName().setFamily("Lastn").addGiven("Arthur");
IIdType ptId = myPatientDao.create(pt, mockSrd()).getId().toUnqualifiedVersionless();
Map<String, String[]> requestParameters = new HashMap<>();
String[] maxParam = new String[1];
maxParam[0] = "1";
requestParameters.put("max", maxParam);
when(mySrd.getParameters()).thenReturn(requestParameters);
Map<IIdType, CodeableConcept> observationIds = new HashMap<>();
for(int observationIdx = 0 ; observationIdx < 20 ; observationIdx++) {
Calendar observationDate = new GregorianCalendar();
String idxSuffix = String.valueOf(observationIdx);
Observation obs = new Observation();
obs.getText().setDivAsString("<div>OBSTEXT0_" + idxSuffix + "</div>");
obs.getSubject().setReferenceElement(ptId);
obs.getCode().addCoding().setCode("CODE_" + idxSuffix).setSystem("http://mycode.com");
obs.setValue(new StringType("obsvalue0_" + idxSuffix));
observationDate.add(Calendar.HOUR, -2);
Date effectiveDtm = observationDate.getTime();
obs.setEffective(new DateTimeType(effectiveDtm));
observationIds.put(myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless(), obs.getCode());
obs = new Observation();
obs.getText().setDivAsString("<div>OBSTEXT1_" + idxSuffix + "</div>");
obs.getSubject().setReferenceElement(ptId);
obs.getCode().addCoding().setCode("CODE_" + idxSuffix).setSystem("http://mycode.com");
obs.setValue(new StringType("obsvalue1_" + idxSuffix));
observationDate.add(Calendar.HOUR, -1);
effectiveDtm = observationDate.getTime();
obs.setEffective(new DateTimeType(effectiveDtm));
observationIds.put(myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless(), obs.getCode());
obs = new Observation();
obs.getText().setDivAsString("<div>OBSTEXT2_" + idxSuffix + "</div>");
obs.getSubject().setReferenceElement(ptId);
obs.getCode().addCoding().setCode("CODE_" + idxSuffix).setSystem("http://mycode.com");
obs.setValue(new StringType("obsvalue2_" + idxSuffix));
observationDate.add(Calendar.HOUR, -0);
effectiveDtm = observationDate.getTime();
obs.setEffective(new DateTimeType(effectiveDtm));
observationIds.put(myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless(), obs.getCode());
}
HttpServletRequest request;
List<String> actual;
SearchParameterMap params = new SearchParameterMap();
params.setLastN(true);
actual = toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(),null));
assertEquals(20, actual.size());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

472
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNTest.java Normal file
View File

@ -0,0 +1,472 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.*;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticsearchClient;
import ca.uhn.fhir.jpa.dao.BaseJpaTest;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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.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 java.util.*;
import static org.junit.Assert.*;
import static org.mockito.Mockito.when;
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = { TestR4ConfigWithElasticsearchClient.class })
public class FhirResourceDaoR4SearchLastNTest extends BaseJpaTest {
@Autowired
@Qualifier("myPatientDaoR4")
protected IFhirResourceDaoPatient<Patient> myPatientDao;
@Autowired
@Qualifier("myObservationDaoR4")
protected IFhirResourceDaoObservation<Observation> myObservationDao;
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
protected FhirContext myFhirCtx;
@Autowired
protected PlatformTransactionManager myPlatformTransactionManager;
@Override
protected FhirContext getContext() {
return myFhirCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myPlatformTransactionManager;
}
private final String observationCd0 = "code0";
private final String observationCd1 = "code1";
private final String observationCd2 = "code2";
private final String categoryCd0 = "category0";
private final String categoryCd1 = "category1";
private final String categoryCd2 = "category2";
private final String codeSystem = "http://mycode.com";
private final String categorySystem = "http://mycategory.com";
// Using static variables including the flag below so that we can initalize the database and indexes once
// (all of the tests only read from the DB and indexes and so no need to re-initialze them for each test).
private static boolean dataLoaded = false;
private static IIdType patient0Id = null;
private static IIdType patient1Id = null;
private static IIdType patient2Id = null;
private static final Map<String, String> observationPatientMap = new HashMap<>();
private static final Map<String, String> observationCategoryMap = new HashMap<>();
private static final Map<String, String> observationCodeMap = new HashMap<>();
private static final Map<String, Date> observationEffectiveMap = new HashMap<>();
@Before
public void beforeCreateTestPatientsAndObservations() {
// Using a static flag here to ensure that load is only done once. Reason for this is that we cannot
// access Autowired objects in @BeforeClass method.
if(!dataLoaded) {
Patient pt = new Patient();
pt.addName().setFamily("Lastn").addGiven("Arthur");
patient0Id = myPatientDao.create(pt, mockSrd()).getId().toUnqualifiedVersionless();
createObservationsForPatient(patient0Id);
pt = new Patient();
pt.addName().setFamily("Lastn").addGiven("Johnathan");
patient1Id = myPatientDao.create(pt, mockSrd()).getId().toUnqualifiedVersionless();
createObservationsForPatient(patient1Id);
pt = new Patient();
pt.addName().setFamily("Lastn").addGiven("Michael");
patient2Id = myPatientDao.create(pt, mockSrd()).getId().toUnqualifiedVersionless();
createObservationsForPatient(patient2Id);
dataLoaded = true;
}
}
private void createObservationsForPatient(IIdType thePatientId) {
createFiveObservationsForPatientCodeCategory(thePatientId,observationCd0, categoryCd0, 15);
createFiveObservationsForPatientCodeCategory(thePatientId,observationCd0, categoryCd1, 10);
createFiveObservationsForPatientCodeCategory(thePatientId,observationCd0, categoryCd2, 5);
createFiveObservationsForPatientCodeCategory(thePatientId,observationCd1, categoryCd0, 10);
createFiveObservationsForPatientCodeCategory(thePatientId,observationCd1, categoryCd1, 5);
createFiveObservationsForPatientCodeCategory(thePatientId,observationCd2, categoryCd2, 5);
}
private void createFiveObservationsForPatientCodeCategory(IIdType thePatientId, String theObservationCode, String theCategoryCode,
Integer theTimeOffset) {
Calendar observationDate = new GregorianCalendar();
for (int idx=0; idx<5; idx++ ) {
Observation obs = new Observation();
obs.getSubject().setReferenceElement(thePatientId);
obs.getCode().addCoding().setCode(theObservationCode).setSystem(codeSystem);
obs.setValue(new StringType(theObservationCode + "_0"));
observationDate.add(Calendar.HOUR, -theTimeOffset+idx);
Date effectiveDtm = observationDate.getTime();
obs.setEffective(new DateTimeType(effectiveDtm));
obs.getCategoryFirstRep().addCoding().setCode(theCategoryCode).setSystem(categorySystem);
String observationId = myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless().getValue();
observationPatientMap.put(observationId, thePatientId.getValue());
observationCategoryMap.put(observationId, theCategoryCode);
observationCodeMap.put(observationId, theObservationCode);
observationEffectiveMap.put(observationId, effectiveDtm);
}
}
private ServletRequestDetails mockSrd() {
return mySrd;
}
@Test
public void testLastNNoParams() {
SearchParameterMap params = new SearchParameterMap();
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient1Id.getValue());
sortedPatients.add(patient2Id.getValue());
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd1);
sortedObservationCodes.add(observationCd2);
executeTestCase(params, sortedPatients, sortedObservationCodes, null,90);
}
private void executeTestCase(SearchParameterMap params, List<String> sortedPatients, List<String> sortedObservationCodes, List<String> theCategories, int expectedObservationCount) {
List<String> actual;
params.setLastN(true);
Map<String, String[]> requestParameters = new HashMap<>();
String[] maxParam = new String[1];
maxParam[0] = "100";
requestParameters.put("max", maxParam);
when(mySrd.getParameters()).thenReturn(requestParameters);
actual = toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(),null));
assertEquals(expectedObservationCount, actual.size());
validateSorting(actual, sortedPatients, sortedObservationCodes, theCategories);
}
private void validateSorting(List<String> theObservationIds, List<String> thePatientIds, List<String> theCodes, List<String> theCategores) {
int theNextObservationIdx = 0;
// Validate patient grouping
for (String patientId : thePatientIds) {
assertEquals(patientId, observationPatientMap.get(theObservationIds.get(theNextObservationIdx)));
theNextObservationIdx = validateSortingWithinPatient(theObservationIds,theNextObservationIdx,theCodes, theCategores, patientId);
}
assertEquals(theObservationIds.size(), theNextObservationIdx);
}
private int validateSortingWithinPatient(List<String> theObservationIds, int theFirstObservationIdxForPatient, List<String> theCodes,
List<String> theCategories, String thePatientId) {
int theNextObservationIdx = theFirstObservationIdxForPatient;
for (String codeValue : theCodes) {
assertEquals(codeValue, observationCodeMap.get(theObservationIds.get(theNextObservationIdx)));
// Validate sorting within code group
theNextObservationIdx = validateSortingWithinCode(theObservationIds,theNextObservationIdx,
observationCodeMap.get(theObservationIds.get(theNextObservationIdx)), theCategories, thePatientId);
}
return theNextObservationIdx;
}
private int validateSortingWithinCode(List<String> theObservationIds, int theFirstObservationIdxForPatientAndCode, String theObservationCode,
List<String> theCategories, String thePatientId) {
int theNextObservationIdx = theFirstObservationIdxForPatientAndCode;
Date lastEffectiveDt = observationEffectiveMap.get(theObservationIds.get(theNextObservationIdx));
theNextObservationIdx++;
while(theObservationCode.equals(observationCodeMap.get(theObservationIds.get(theNextObservationIdx)))
&& thePatientId.equals(observationPatientMap.get(theObservationIds.get(theNextObservationIdx)))) {
// Check that effective date is before that of the previous observation.
assertTrue(lastEffectiveDt.compareTo(observationEffectiveMap.get(theObservationIds.get(theNextObservationIdx))) > 0);
lastEffectiveDt = observationEffectiveMap.get(theObservationIds.get(theNextObservationIdx));
// Check that observation is in one of the specified categories (if applicable)
if (theCategories != null && !theCategories.isEmpty()) {
assertTrue(theCategories.contains(observationCategoryMap.get(theObservationIds.get(theNextObservationIdx))));
}
theNextObservationIdx++;
if (theNextObservationIdx >= theObservationIds.size()) {
// Have reached the end of the Observation list.
break;
}
}
return theNextObservationIdx;
}
@Test
public void testLastNSinglePatient() {
SearchParameterMap params = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", patient0Id.getValue());
params.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd1);
sortedObservationCodes.add(observationCd2);
executeTestCase(params, sortedPatients,sortedObservationCodes, null,30);
params = new SearchParameterMap();
ReferenceParam patientParam = new ReferenceParam("Patient", "", patient0Id.getValue());
params.add(Observation.SP_PATIENT, buildReferenceAndListParam(patientParam));
sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd1);
sortedObservationCodes.add(observationCd2);
executeTestCase(params, sortedPatients,sortedObservationCodes, null,30);
}
private ReferenceAndListParam buildReferenceAndListParam(ReferenceParam... theReference) {
ReferenceOrListParam myReferenceOrListParam = new ReferenceOrListParam();
for (ReferenceParam referenceParam : theReference) {
myReferenceOrListParam.addOr(referenceParam);
}
return new ReferenceAndListParam().addAnd(myReferenceOrListParam);
}
@Test
public void testLastNMultiplePatients() {
// Two Subject parameters.
SearchParameterMap params = new SearchParameterMap();
ReferenceParam subjectParam1 = new ReferenceParam("Patient", "", patient0Id.getValue());
ReferenceParam subjectParam2 = new ReferenceParam("Patient", "", patient1Id.getValue());
params.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam1, subjectParam2));
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient1Id.getValue());
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd1);
sortedObservationCodes.add(observationCd2);
executeTestCase(params, sortedPatients, sortedObservationCodes, null,60);
// Two Patient parameters
params = new SearchParameterMap();
ReferenceParam patientParam1 = new ReferenceParam("Patient", "", patient0Id.getValue());
ReferenceParam patientParam3 = new ReferenceParam("Patient", "", patient2Id.getValue());
params.add(Observation.SP_SUBJECT, buildReferenceAndListParam(patientParam1, patientParam3));
sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient2Id.getValue());
executeTestCase(params,sortedPatients, sortedObservationCodes, null,60);
}
@Test
public void testLastNSingleCategory() {
// One category parameter.
SearchParameterMap params = new SearchParameterMap();
TokenParam categoryParam = new TokenParam(categorySystem, categoryCd0);
params.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
List<String> myCategories = new ArrayList<>();
myCategories.add(categoryCd0);
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient1Id.getValue());
sortedPatients.add(patient2Id.getValue());
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd1);
executeTestCase(params, sortedPatients, sortedObservationCodes, myCategories, 30);
// Another category parameter.
params = new SearchParameterMap();
categoryParam = new TokenParam(categorySystem, categoryCd2);
params.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
myCategories = new ArrayList<>();
myCategories.add(categoryCd2);
sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd2);
executeTestCase(params, sortedPatients, sortedObservationCodes, myCategories, 30);
}
@Test
public void testLastNMultipleCategories() {
// Two category parameters.
SearchParameterMap params = new SearchParameterMap();
TokenParam categoryParam1 = new TokenParam(categorySystem, categoryCd0);
TokenParam categoryParam2 = new TokenParam(categorySystem, categoryCd1);
params.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam1, categoryParam2));
List<String> myCategories = new ArrayList<>();
myCategories.add(categoryCd0);
myCategories.add(categoryCd1);
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient1Id.getValue());
sortedPatients.add(patient2Id.getValue());
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd1);
executeTestCase(params, sortedPatients, sortedObservationCodes, myCategories, 60);
}
@Test
public void testLastNSingleCode() {
// One code parameter.
SearchParameterMap params = new SearchParameterMap();
TokenParam code = new TokenParam(codeSystem, observationCd0);
params.add(Observation.SP_CODE, buildTokenAndListParam(code));
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient1Id.getValue());
sortedPatients.add(patient2Id.getValue());
executeTestCase(params, sortedPatients, sortedObservationCodes, null, 45);
// Another code parameter.
params = new SearchParameterMap();
code = new TokenParam(codeSystem, observationCd2);
params.add(Observation.SP_CODE, buildTokenAndListParam(code));
sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd2);
executeTestCase(params, sortedPatients, sortedObservationCodes, null, 15);
}
@Test
public void testLastNMultipleCodes() {
// Two code parameters.
SearchParameterMap params = new SearchParameterMap();
TokenParam codeParam1 = new TokenParam(codeSystem, observationCd0);
TokenParam codeParam2 = new TokenParam(codeSystem, observationCd1);
params.add(Observation.SP_CODE, buildTokenAndListParam(codeParam1, codeParam2));
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd1);
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient1Id.getValue());
sortedPatients.add(patient2Id.getValue());
executeTestCase(params, sortedPatients, sortedObservationCodes, null, 75);
}
@Test
public void testLastNSinglePatientCategoryCode() {
// One patient, category and code.
SearchParameterMap params = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", patient0Id.getValue());
params.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
TokenParam code = new TokenParam(codeSystem, observationCd0);
params.add(Observation.SP_CODE, buildTokenAndListParam(code));
TokenParam category = new TokenParam(categorySystem, categoryCd2);
params.add(Observation.SP_CATEGORY, buildTokenAndListParam(category));
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
List<String> myCategories = new ArrayList<>();
myCategories.add(categoryCd2);
executeTestCase(params, sortedPatients, sortedObservationCodes, myCategories, 5);
}
@Test
public void testLastNMultiplePatientsCategoriesCodes() {
// Two patients, categories and codes.
SearchParameterMap params = new SearchParameterMap();
ReferenceParam subjectParam1 = new ReferenceParam("Patient", "", patient0Id.getValue());
ReferenceParam subjectParam2 = new ReferenceParam("Patient", "", patient1Id.getValue());
params.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam1, subjectParam2));
List<String> sortedPatients = new ArrayList<>();
sortedPatients.add(patient0Id.getValue());
sortedPatients.add(patient1Id.getValue());
TokenParam codeParam1 = new TokenParam(codeSystem, observationCd0);
TokenParam codeParam2 = new TokenParam(codeSystem, observationCd2);
params.add(Observation.SP_CODE, buildTokenAndListParam(codeParam1, codeParam2));
List<String> sortedObservationCodes = new ArrayList<>();
sortedObservationCodes.add(observationCd0);
sortedObservationCodes.add(observationCd2);
TokenParam categoryParam1 = new TokenParam(categorySystem, categoryCd1);
TokenParam categoryParam2 = new TokenParam(categorySystem, categoryCd2);
params.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam1, categoryParam2));
List<String> myCategories = new ArrayList<>();
myCategories.add(categoryCd1);
myCategories.add(categoryCd2);
executeTestCase(params, sortedPatients, sortedObservationCodes, myCategories, 30);
}
private TokenAndListParam buildTokenAndListParam(TokenParam... theToken) {
TokenOrListParam myTokenOrListParam = new TokenOrListParam();
for (TokenParam tokenParam : theToken) {
myTokenOrListParam.addOr(tokenParam);
}
return new TokenAndListParam().addAnd(myTokenOrListParam);
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

177
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsTest.java
View File

@ -1,9 +1,7 @@
package ca.uhn.fhir.jpa.search.lastn; package ca.uhn.fhir.jpa.search.lastn;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.param.ReferenceParam; import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.jpa.search.lastn.config.TestElasticsearchConfig; import ca.uhn.fhir.jpa.search.lastn.config.TestElasticsearchConfig;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson; import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson; import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
@ -11,9 +9,8 @@ import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonGenerator; import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature; import com.fasterxml.jackson.databind.SerializationFeature;
import org.hl7.fhir.r4.model.Observation;
import org.junit.*; import org.junit.*;
import org.shadehapi.elasticsearch.action.search.SearchRequest;
import org.shadehapi.elasticsearch.action.search.SearchResponse;
import org.hl7.fhir.r4.model.CodeableConcept; import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding; import org.hl7.fhir.r4.model.Coding;
import org.junit.runner.RunWith; import org.junit.runner.RunWith;
@ -36,7 +33,7 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
private static ObjectMapper ourMapperNonPrettyPrint; private static ObjectMapper ourMapperNonPrettyPrint;
private Map<String,Map<String,List<Date>>> createdPatientObservationMap = new HashMap<>(); private final Map<String, Map<String, List<Date>>> createdPatientObservationMap = new HashMap<>();
@BeforeClass @BeforeClass
@ -59,27 +56,12 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
} }
@Test @Test
public void testLastNNoCriteriaQuery() throws IOException { public void testLastNNoCriteriaQuery() {
// execute Observation ID search (Terms Aggregation) last 3 observations for each patient
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationTermsSearchRequest(1000, null, 3);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationTermsResults(responseIds);
validateQueryResponse(observationIdsOnly);
// execute Observation ID search (Composite Aggregation) last 3 observations for each patient // execute Observation ID search (Composite Aggregation) last 3 observations for each patient
searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, null, 3); List<ObservationJson> observations = elasticsearchSvc.executeLastNWithAllFields(null, 3);
responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
validateQueryResponse(observationIdsOnly); validateQueryResponse(observations);
// Retrieve all Observation codes
SearchRequest searchRequest = elasticsearchSvc.buildObservationCodesSearchRequest(1000);
SearchResponse response = elasticsearchSvc.executeSearchRequest(searchRequest);
List<CodeJson> codes = elasticsearchSvc.buildCodeResult(response);
assertEquals(2, codes.size());
} }
@ -141,80 +123,149 @@ public class LastNElasticsearchSvcMultipleObservationsTest {
} }
@Test @Test
public void testLastNMultiPatientMultiCodeHashMultiCategoryHash() throws IOException { public void testLastNMultiPatientMultiCodeHashMultiCategoryHash() {
// Include subject and patient // Multiple Subject references
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", "3"); ReferenceParam subjectParam1 = new ReferenceParam("Patient", "", "3");
searchParameterMap.add("subject", subjectParam); ReferenceParam subjectParam2 = new ReferenceParam("Patient", "", "5");
ReferenceParam patientParam = new ReferenceParam("Patient", "", "8"); searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam1, subjectParam2));
searchParameterMap.add("patient", patientParam); TokenParam categoryParam1 = new TokenParam("http://mycodes.org/fhir/observation-category", "test-heart-rate");
TokenParam categoryParam = new TokenParam("http://mycodes.org/fhir/observation-category", "test-heart-rate"); TokenParam categoryParam2 = new TokenParam("http://mycodes.org/fhir/observation-category", "test-vital-signs");
searchParameterMap.add("category", categoryParam); searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam1, categoryParam2));
TokenParam codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-1"); TokenParam codeParam1 = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-1");
searchParameterMap.add("code", codeParam); TokenParam codeParam2 = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-2");
searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam1, codeParam2));
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100); List<String> observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(10, observationIdsOnly.size()); assertEquals(20, observations.size());
// Repeat with multiple Patient parameter
searchParameterMap = new SearchParameterMap();
ReferenceParam patientParam1 = new ReferenceParam("Patient", "", "8");
ReferenceParam patientParam2 = new ReferenceParam("Patient", "", "6");
searchParameterMap.add(Observation.SP_PATIENT, buildReferenceAndListParam(patientParam1, patientParam2));
searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam1, categoryParam2));
searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam1, codeParam2));
observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
assertEquals(20, observations.size());
} }
private ReferenceAndListParam buildReferenceAndListParam(ReferenceParam... theReference) {
ReferenceOrListParam myReferenceOrListParam = new ReferenceOrListParam();
for (ReferenceParam referenceParam : theReference) {
myReferenceOrListParam.addOr(referenceParam);
}
return new ReferenceAndListParam().addAnd(myReferenceOrListParam);
}
private TokenAndListParam buildTokenAndListParam(TokenParam... theToken) {
TokenOrListParam myTokenOrListParam = new TokenOrListParam();
for (TokenParam tokenParam : theToken) {
myTokenOrListParam.addOr(tokenParam);
}
return new TokenAndListParam().addAnd(myTokenOrListParam);
}
@Test @Test
public void testLastNCodeCodeOnlyCategoryCodeOnly() throws IOException { public void testLastNCodeCodeOnlyCategoryCodeOnly() {
// Include subject and patient // Include subject
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", "3"); ReferenceParam subjectParam = new ReferenceParam("Patient", "", "3");
searchParameterMap.add("subject", subjectParam); searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
TokenParam categoryParam = new TokenParam("test-heart-rate"); TokenParam categoryParam = new TokenParam("test-heart-rate");
searchParameterMap.add("category", categoryParam); searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
TokenParam codeParam = new TokenParam("test-code-1"); TokenParam codeParam = new TokenParam("test-code-1");
searchParameterMap.add("code", codeParam); searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam));
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100); List<String> observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(5, observationIdsOnly.size()); assertEquals(5, observations.size());
} }
@Test @Test
public void testLastNCodeSystemOnlyCategorySystemOnly() throws IOException { public void testLastNCodeSystemOnlyCategorySystemOnly() {
// Include subject and patient // Include subject and patient
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", "3"); ReferenceParam subjectParam = new ReferenceParam("Patient", "", "3");
searchParameterMap.add("subject", subjectParam); searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
TokenParam categoryParam = new TokenParam("http://mycodes.org/fhir/observation-category", null); TokenParam categoryParam = new TokenParam("http://mycodes.org/fhir/observation-category", null);
searchParameterMap.add("category", categoryParam); searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
TokenParam codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", null); TokenParam codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", null);
searchParameterMap.add("code", codeParam); searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam));
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100); List<String> observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(10, observationIdsOnly.size()); assertEquals(10, observations.size());
} }
@Test @Test
public void testLastNCodeCodeTextCategoryTextOnly() throws IOException { public void testLastNCodeCodeTextCategoryTextOnly() {
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", "3"); ReferenceParam subjectParam = new ReferenceParam("Patient", "", "3");
searchParameterMap.add("subject", subjectParam); searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
TokenParam categoryParam = new TokenParam("test-heart-rate display"); TokenParam categoryParam = new TokenParam("test-heart-rate display");
categoryParam.setModifier(TokenParamModifier.TEXT); categoryParam.setModifier(TokenParamModifier.TEXT);
searchParameterMap.add("category", categoryParam); searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
TokenParam codeParam = new TokenParam("test-code-1 display"); TokenParam codeParam = new TokenParam("test-code-1 display");
codeParam.setModifier(TokenParamModifier.TEXT); codeParam.setModifier(TokenParamModifier.TEXT);
searchParameterMap.add("code", codeParam); searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam));
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 100); List<String> observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(5, observationIdsOnly.size()); assertEquals(5, observations.size());
}
@Test
public void testLastNNoMatchQueries() {
// Invalid Patient
SearchParameterMap searchParameterMap = new SearchParameterMap();
ReferenceParam patientParam = new ReferenceParam("Patient", "", "10");
searchParameterMap.add(Observation.SP_PATIENT, buildReferenceAndListParam(patientParam));
TokenParam categoryParam = new TokenParam("http://mycodes.org/fhir/observation-category", "test-heart-rate");
searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
TokenParam codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-1");
searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam));
List<String> observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
assertEquals(0, observations.size());
// Invalid subject
searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", "10");
searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
categoryParam = new TokenParam("http://mycodes.org/fhir/observation-category", "test-heart-rate");
searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-1");
searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam));
observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
assertEquals(0, observations.size());
// Invalid observation code
searchParameterMap = new SearchParameterMap();
subjectParam = new ReferenceParam("Patient", "", "9");
searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
categoryParam = new TokenParam("http://mycodes.org/fhir/observation-category", "test-heart-rate");
searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-999");
searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam));
observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
assertEquals(0, observations.size());
// Invalid category code
searchParameterMap = new SearchParameterMap();
subjectParam = new ReferenceParam("Patient", "", "9");
searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
categoryParam = new TokenParam("http://mycodes.org/fhir/observation-category", "test-not-a-category");
searchParameterMap.add(Observation.SP_CATEGORY, buildTokenAndListParam(categoryParam));
codeParam = new TokenParam("http://mycodes.org/fhir/observation-code", "test-code-1");
searchParameterMap.add(Observation.SP_CODE, buildTokenAndListParam(codeParam));
observations = elasticsearchSvc.executeLastN(searchParameterMap, 100);
assertEquals(0, observations.size());
} }

57
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcSingleObservationTest.java
View File

@ -5,14 +5,12 @@ import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson; import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash; import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap; import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.param.ReferenceParam; import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.rest.param.TokenParam; import ca.uhn.fhir.rest.param.*;
import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonGenerator; import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature; import com.fasterxml.jackson.databind.SerializationFeature;
import org.shadehapi.elasticsearch.action.search.SearchRequest;
import org.shadehapi.elasticsearch.action.search.SearchResponse;
import org.hl7.fhir.r4.model.CodeableConcept; import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding; import org.hl7.fhir.r4.model.Coding;
import org.junit.*; import org.junit.*;
@ -37,8 +35,6 @@ public class LastNElasticsearchSvcSingleObservationTest {
static ObjectMapper ourMapperNonPrettyPrint; static ObjectMapper ourMapperNonPrettyPrint;
final String RESOURCEPID = "123"; final String RESOURCEPID = "123";
// final String SUBJECTID = "4567";
// final String SUBJECTTYPEANDID = "Patient/4567";
final String SUBJECTID = "Patient/4567"; final String SUBJECTID = "Patient/4567";
final Date EFFECTIVEDTM = new Date(); final Date EFFECTIVEDTM = new Date();
final String FIRSTCATEGORYTEXT = "Test Codeable Concept Field for first category"; final String FIRSTCATEGORYTEXT = "Test Codeable Concept Field for first category";
@ -87,12 +83,6 @@ public class LastNElasticsearchSvcSingleObservationTest {
} }
// @Before
public void before() throws IOException {
elasticsearchSvc.deleteAllDocuments(IndexConstants.OBSERVATION_INDEX);
elasticsearchSvc.deleteAllDocuments(IndexConstants.CODE_INDEX);
}
@After @After
public void after() throws IOException { public void after() throws IOException {
elasticsearchSvc.deleteAllDocuments(IndexConstants.OBSERVATION_INDEX); elasticsearchSvc.deleteAllDocuments(IndexConstants.OBSERVATION_INDEX);
@ -106,41 +96,20 @@ public class LastNElasticsearchSvcSingleObservationTest {
SearchParameterMap searchParameterMap = new SearchParameterMap(); SearchParameterMap searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", SUBJECTID); ReferenceParam subjectParam = new ReferenceParam("Patient", "", SUBJECTID);
searchParameterMap.add("subject", subjectParam); searchParameterMap.add(Observation.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().addOr(subjectParam)));
TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE); TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE);
searchParameterMap.add("category", categoryParam); searchParameterMap.add(Observation.SP_CATEGORY, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(categoryParam)));
TokenParam codeParam = new TokenParam(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE); TokenParam codeParam = new TokenParam(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE);
searchParameterMap.add("code", codeParam); searchParameterMap.add(Observation.SP_CODE, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(codeParam)));
// execute Observation ID search - Terms Aggregation // execute Observation ID search
SearchRequest searchRequestIdsOnly = elasticsearchSvc.buildObservationTermsSearchRequest(1000, searchParameterMap, 3); List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, 3);
SearchResponse responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
List<ObservationJson> observationIdsOnly = elasticsearchSvc.buildObservationTermsResults(responseIds);
assertEquals(1, observationIdsOnly.size()); assertEquals(1, observationIdsOnly.size());
ObservationJson observationIdOnly = observationIdsOnly.get(0); assertEquals(RESOURCEPID, observationIdsOnly.get(0));
assertEquals(RESOURCEPID, observationIdOnly.getIdentifier());
// execute Observation ID search - Composite Aggregation // execute Observation search for all search fields
searchRequestIdsOnly = elasticsearchSvc.buildObservationCompositeSearchRequest(1000, searchParameterMap, 3); List<ObservationJson> observations = elasticsearchSvc.executeLastNWithAllFields(searchParameterMap, 3);
responseIds = elasticsearchSvc.executeSearchRequest(searchRequestIdsOnly);
observationIdsOnly = elasticsearchSvc.buildObservationCompositeResults(responseIds);
assertEquals(1, observationIdsOnly.size());
observationIdOnly = observationIdsOnly.get(0);
assertEquals(RESOURCEPID, observationIdOnly.getIdentifier());
// execute full Observation search - Terms Aggregation
SearchRequest searchRequestAllFields = elasticsearchSvc.buildObservationAllFieldsTermsSearchRequest(1000, searchParameterMap, 3);
SearchResponse response = elasticsearchSvc.executeSearchRequest(searchRequestAllFields);
List<ObservationJson> observations = elasticsearchSvc.buildObservationTermsResults(response);
validateFullObservationSearch(observations);
// execute full Observation search - Composite Aggregation
searchRequestAllFields= elasticsearchSvc.buildObservationAllFieldsCompositeSearchRequest(1000, searchParameterMap, 3);
response = elasticsearchSvc.executeSearchRequest(searchRequestAllFields);
observations = elasticsearchSvc.buildObservationCompositeResults(response);
validateFullObservationSearch(observations); validateFullObservationSearch(observations);
} }
@ -151,7 +120,6 @@ public class LastNElasticsearchSvcSingleObservationTest {
ObservationJson observation = observations.get(0); ObservationJson observation = observations.get(0);
assertEquals(RESOURCEPID, observation.getIdentifier()); assertEquals(RESOURCEPID, observation.getIdentifier());
// assertEquals(SUBJECTTYPEANDID, observation.getSubject());
assertEquals(SUBJECTID, observation.getSubject()); assertEquals(SUBJECTID, observation.getSubject());
assertEquals(RESOURCEPID, observation.getIdentifier()); assertEquals(RESOURCEPID, observation.getIdentifier());
assertEquals(EFFECTIVEDTM, observation.getEffectiveDtm()); assertEquals(EFFECTIVEDTM, observation.getEffectiveDtm());
@ -275,9 +243,7 @@ public class LastNElasticsearchSvcSingleObservationTest {
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE)), code_coding_code_system_hash); assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE)), code_coding_code_system_hash);
// Retrieve all Observation codes // Retrieve all Observation codes
SearchRequest searchRequest = elasticsearchSvc.buildObservationCodesSearchRequest(1000); List<CodeJson> codes = elasticsearchSvc.queryAllIndexedObservationCodes(1000);
SearchResponse response = elasticsearchSvc.executeSearchRequest(searchRequest);
List<CodeJson> codes = elasticsearchSvc.buildCodeResult(response);
assertEquals(1, codes.size()); assertEquals(1, codes.size());
CodeJson persistedObservationCode = codes.get(0); CodeJson persistedObservationCode = codes.get(0);
@ -324,7 +290,6 @@ public class LastNElasticsearchSvcSingleObservationTest {
private void createSingleObservation() throws IOException { private void createSingleObservation() throws IOException {
ObservationJson indexedObservation = new ObservationJson(); ObservationJson indexedObservation = new ObservationJson();
indexedObservation.setIdentifier(RESOURCEPID); indexedObservation.setIdentifier(RESOURCEPID);
// indexedObservation.setSubject(SUBJECTTYPEANDID);
indexedObservation.setSubject(SUBJECTID); indexedObservation.setSubject(SUBJECTID);
indexedObservation.setEffectiveDtm(EFFECTIVEDTM); indexedObservation.setEffectiveDtm(EFFECTIVEDTM);

53
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/config/TestElasticsearchV5Config.java
View File

@ -1,53 +0,0 @@
package ca.uhn.fhir.jpa.search.lastn.config;
import ca.uhn.fhir.context.ConfigurationException;
//import ca.uhn.fhir.jpa.search.lastn.ElasticsearchV5SvcImpl;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import pl.allegro.tech.embeddedelasticsearch.EmbeddedElastic;
import pl.allegro.tech.embeddedelasticsearch.PopularProperties;
import java.io.IOException;
import java.util.UUID;
import java.util.concurrent.TimeUnit;
//@Configuration
//@EnableJpaRepositories(entityManagerFactoryRef = "entityManagerFactory")
//@EnableTransactionManagement
public class TestElasticsearchV5Config {
private final String elasticsearchHost = "127.0.0.1";
private final String elasticsearchUserId = "";
private final String elasticsearchPassword = "";
private static final String ELASTIC_VERSION = "5.6.16";
/*
@Bean()
public ElasticsearchV5SvcImpl myElasticsearchSvc() throws IOException {
int elasticsearchPort = embeddedElasticSearch().getHttpPort();
return new ElasticsearchV5SvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
}
@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;
}
*/
}