Issue 3450 there is no way to recreate freetext indexes for terminology entities (#3463)
* Add reindex-terminology batch command * Handle number of thread throttling and concurrency with other terminology batch operations * Add required dbcp2 dependency * Fix test * Improve ConnectionPoolInfoProvider setup. Handle maximum connections. * Remove java higher version construction * Remove unused config * Add reindex terminology integration test. Reset termConcept counters before pre-expanding, which otherwise accumulate if it was pre-expanded before. Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto
GitHub
parent
17cf1ed9ce
commit
e45f7ee9cb
|
|
@ -25,7 +25,7 @@ public final class Msg {
|
|||
|
||||
/**
|
||||
* IMPORTANT: Please update the following comment after you add a new code
|
||||
* Last code value: 2071
|
||||
* Last code value: 2072
|
||||
*/
|
||||
|
||||
private Msg() {}
|
||||
|
|
|
|||
|
|
@ -259,6 +259,11 @@
|
|||
<artifactId>jarchivelib</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.springframework</groupId>
|
||||
<artifactId>spring-test</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
</dependencies>
|
||||
|
||||
|
|
|
|||
|
|
@ -188,6 +188,7 @@ public abstract class BaseApp {
|
|||
commands.add(new HapiFlywayMigrateDatabaseCommand());
|
||||
commands.add(new CreatePackageCommand());
|
||||
commands.add(new BulkImportCommand());
|
||||
commands.add(new ReindexTerminologyCommand());
|
||||
return commands;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,111 @@
|
|||
package ca.uhn.fhir.cli;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR - Command Line Client - API
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
|
||||
* %%
|
||||
* 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.rest.client.api.IGenericClient;
|
||||
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
|
||||
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
|
||||
import ca.uhn.fhir.util.ParametersUtil;
|
||||
import org.apache.commons.cli.CommandLine;
|
||||
import org.apache.commons.cli.ParseException;
|
||||
import org.hl7.fhir.instance.model.api.IBaseParameters;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
import static ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider.RESP_PARAM_SUCCESS;
|
||||
|
||||
public class ReindexTerminologyCommand extends BaseRequestGeneratingCommand {
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ReindexTerminologyCommand.class);
|
||||
|
||||
static final String REINDEX_TERMINOLOGY = "reindex-terminology";
|
||||
|
||||
|
||||
@Override
|
||||
public String getCommandDescription() {
|
||||
return "Recreates freetext-indexes for terminology data.";
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getCommandName() {
|
||||
return REINDEX_TERMINOLOGY;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public void run(CommandLine theCommandLine) throws ParseException {
|
||||
parseFhirContext(theCommandLine);
|
||||
|
||||
IGenericClient client = newClient(theCommandLine);
|
||||
|
||||
if (theCommandLine.hasOption(VERBOSE_LOGGING_PARAM)) {
|
||||
client.registerInterceptor(new LoggingInterceptor(true));
|
||||
}
|
||||
|
||||
invokeOperation(client);
|
||||
}
|
||||
|
||||
|
||||
private void invokeOperation(IGenericClient theClient) {
|
||||
IBaseParameters inputParameters = ParametersUtil.newInstance(myFhirCtx);
|
||||
|
||||
ourLog.info("Beginning freetext indexing - This may take a while...");
|
||||
|
||||
IBaseParameters response;
|
||||
try {
|
||||
response = theClient
|
||||
.operation()
|
||||
.onServer()
|
||||
.named(REINDEX_TERMINOLOGY)
|
||||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
|
||||
} catch (BaseServerResponseException e) {
|
||||
if (e.getOperationOutcome() != null) {
|
||||
ourLog.error("Received the following response: {}{}", NL,
|
||||
myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
|
||||
}
|
||||
throw e;
|
||||
}
|
||||
|
||||
Optional<String> isSuccessResponse = ParametersUtil.getNamedParameterValueAsString(myFhirCtx, response, RESP_PARAM_SUCCESS);
|
||||
if ( ! isSuccessResponse.isPresent() ) {
|
||||
ParametersUtil.addParameterToParametersBoolean(myFhirCtx, response, RESP_PARAM_SUCCESS, false);
|
||||
ParametersUtil.addParameterToParametersString(myFhirCtx, response, "message",
|
||||
"Internal error. Command result unknown. Check system logs for details");
|
||||
ourLog.info("Response:{}{}", NL, myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
|
||||
return;
|
||||
}
|
||||
|
||||
boolean succeeded = Boolean.parseBoolean( isSuccessResponse.get() );
|
||||
if ( ! succeeded) {
|
||||
ourLog.info("Response:{}{}", NL, myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
|
||||
return;
|
||||
}
|
||||
|
||||
ourLog.info("Recreation of terminology freetext indexes complete!");
|
||||
ourLog.info("Response:{}{}", NL, myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
|
||||
}
|
||||
|
||||
|
||||
public static final String NL = System.getProperty("line.separator");
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,135 @@
|
|||
package ca.uhn.fhir.cli;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider;
|
||||
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
|
||||
import ca.uhn.fhir.util.ParametersUtil;
|
||||
import org.hl7.fhir.instance.model.api.IBaseParameters;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.junit.jupiter.api.extension.RegisterExtension;
|
||||
import org.mockito.Spy;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import java.io.ByteArrayOutputStream;
|
||||
import java.io.PrintStream;
|
||||
|
||||
import static ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider.RESP_PARAM_SUCCESS;
|
||||
import static org.hamcrest.CoreMatchers.containsString;
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||
import static org.mockito.ArgumentMatchers.any;
|
||||
import static org.mockito.Mockito.doReturn;
|
||||
import static org.mockito.Mockito.spy;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class ReindexTerminologyCommandTest {
|
||||
|
||||
private final FhirContext myContext = FhirContext.forR4();
|
||||
|
||||
@Spy
|
||||
private BaseJpaSystemProvider<?, ?> myProvider = spy(new BaseJpaSystemProvider<>());
|
||||
|
||||
@RegisterExtension
|
||||
public final RestfulServerExtension myRestfulServerExtension =
|
||||
new RestfulServerExtension(myContext, myProvider);
|
||||
|
||||
|
||||
private final PrintStream standardOut = System.out;
|
||||
private final ByteArrayOutputStream outputStreamCaptor = new ByteArrayOutputStream();
|
||||
|
||||
static {
|
||||
System.setProperty("test", "true");
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testProviderMethodInvoked() {
|
||||
System.setOut(new PrintStream(outputStreamCaptor));
|
||||
IBaseParameters retVal = ParametersUtil.newInstance(myContext);
|
||||
ParametersUtil.addParameterToParametersBoolean(myContext, retVal, RESP_PARAM_SUCCESS, true);
|
||||
doReturn(retVal).when(myProvider).reindexTerminology(any());
|
||||
|
||||
App.main(new String[]{
|
||||
ReindexTerminologyCommand.REINDEX_TERMINOLOGY,
|
||||
"-v", "r4",
|
||||
"-t", myRestfulServerExtension.getBaseUrl()
|
||||
});
|
||||
|
||||
assertThat(outputStreamCaptor.toString().trim(),
|
||||
outputStreamCaptor.toString().trim(), containsString("<valueBoolean value=\"true\"/>"));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testNoVersionThrows() {
|
||||
IBaseParameters retVal = ParametersUtil.newInstance(myContext);
|
||||
ParametersUtil.addParameterToParametersBoolean(myContext, retVal, RESP_PARAM_SUCCESS, true);
|
||||
doReturn(retVal).when(myProvider).reindexTerminology(any());
|
||||
|
||||
Error thrown = assertThrows(Error.class, () ->
|
||||
App.main(new String[]{
|
||||
ReindexTerminologyCommand.REINDEX_TERMINOLOGY,
|
||||
"-t", myRestfulServerExtension.getBaseUrl()
|
||||
})
|
||||
);
|
||||
assertThat(thrown.getMessage(), containsString("Missing required option: v"));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testNoTargetThrows() {
|
||||
IBaseParameters retVal = ParametersUtil.newInstance(myContext);
|
||||
ParametersUtil.addParameterToParametersBoolean(myContext, retVal, RESP_PARAM_SUCCESS, true);
|
||||
doReturn(retVal).when(myProvider).reindexTerminology(any());
|
||||
|
||||
Error thrown = assertThrows(Error.class, () ->
|
||||
App.main(new String[]{ReindexTerminologyCommand.REINDEX_TERMINOLOGY, "-v", "r4"})
|
||||
);
|
||||
assertThat(thrown.getMessage(), containsString("Missing required option: t"));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testHandleUnexpectedResponse() {
|
||||
System.setOut(new PrintStream(outputStreamCaptor));
|
||||
IBaseParameters retVal = ParametersUtil.newInstance(myContext);
|
||||
doReturn(retVal).when(myProvider).reindexTerminology(any());
|
||||
|
||||
App.main(new String[]{
|
||||
ReindexTerminologyCommand.REINDEX_TERMINOLOGY,
|
||||
"-v", "r4",
|
||||
"-t", myRestfulServerExtension.getBaseUrl()
|
||||
});
|
||||
|
||||
assertThat(outputStreamCaptor.toString().trim(),
|
||||
outputStreamCaptor.toString().trim(), containsString("<valueBoolean value=\"false\"/>"));
|
||||
assertThat(outputStreamCaptor.toString().trim(),
|
||||
outputStreamCaptor.toString().trim(), containsString("<valueString value=\"Internal error. " +
|
||||
"Command result unknown. Check system logs for details\"/>"));
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testHandleServiceError() {
|
||||
System.setOut(new PrintStream(outputStreamCaptor));
|
||||
IBaseParameters retVal = ParametersUtil.newInstance(myContext);
|
||||
ParametersUtil.addParameterToParametersBoolean(myContext, retVal, RESP_PARAM_SUCCESS, false);
|
||||
ParametersUtil.addParameterToParametersString(myContext, retVal, "message",
|
||||
"Freetext service is not configured. Operation didn't run.");
|
||||
doReturn(retVal).when(myProvider).reindexTerminology(any());
|
||||
|
||||
App.main(new String[]{
|
||||
ReindexTerminologyCommand.REINDEX_TERMINOLOGY,
|
||||
"-v", "r4",
|
||||
"-t", myRestfulServerExtension.getBaseUrl()
|
||||
});
|
||||
|
||||
assertThat(outputStreamCaptor.toString().trim(),
|
||||
outputStreamCaptor.toString().trim(), containsString("<valueBoolean value=\"false\"/>"));
|
||||
assertThat(outputStreamCaptor.toString().trim(),
|
||||
outputStreamCaptor.toString().trim(), containsString("<valueString value=\"Freetext service is not configured. Operation didn't run.\"/>"));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
---
|
||||
type: fix
|
||||
issue: 3450
|
||||
title: "There was no way to recreate freetext indexes for terminology entities. Command line operation
|
||||
reindex-terminology was added for this purpose."
|
||||
|
|
@ -142,6 +142,18 @@
|
|||
<artifactId>hapi-fhir-storage-batch2-jobs</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-dbcp2</artifactId>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>commons-logging</groupId>
|
||||
<artifactId>commons-logging</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-storage</artifactId>
|
||||
|
|
@ -272,17 +284,6 @@
|
|||
<artifactId>h2</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.commons</groupId>
|
||||
<artifactId>commons-dbcp2</artifactId>
|
||||
<scope>test</scope>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>commons-logging</groupId>
|
||||
<artifactId>commons-logging</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-test-utilities</artifactId>
|
||||
|
|
|
|||
|
|
@ -29,6 +29,8 @@ import org.hibernate.search.engine.cfg.BackendSettings;
|
|||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
|
||||
|
||||
import javax.sql.DataSource;
|
||||
|
||||
public class HibernatePropertiesProvider {
|
||||
|
||||
@Autowired
|
||||
|
|
@ -61,4 +63,9 @@ public class HibernatePropertiesProvider {
|
|||
}
|
||||
return myHibernateSearchBackend;
|
||||
}
|
||||
|
||||
|
||||
public DataSource getDataSource() {
|
||||
return myEntityManagerFactory.getDataSource();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,33 @@
|
|||
package ca.uhn.fhir.jpa.config.util;
|
||||
|
||||
import org.apache.commons.dbcp2.BasicDataSource;
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
/**
|
||||
* Utility class to hide the complexities of obtaining ConnectionPool information
|
||||
*/
|
||||
public class BasicDataSourceConnectionPoolInfoProvider implements IConnectionPoolInfoProvider {
|
||||
|
||||
public final BasicDataSource myDataSource;
|
||||
|
||||
public BasicDataSourceConnectionPoolInfoProvider(BasicDataSource theDataSource) {
|
||||
myDataSource = theDataSource;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Optional<Integer> getTotalConnectionSize() {
|
||||
return Optional.of( myDataSource.getMaxTotal() );
|
||||
}
|
||||
|
||||
@Override
|
||||
public Optional<Integer> getActiveConnections() {
|
||||
return Optional.of( myDataSource.getNumActive() );
|
||||
}
|
||||
|
||||
@Override
|
||||
public Optional<Long> getMaxWaitMillis() {
|
||||
return Optional.of( myDataSource.getMaxWaitMillis() );
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
package ca.uhn.fhir.jpa.config.util;
|
||||
|
||||
import net.ttddyy.dsproxy.support.ProxyDataSource;
|
||||
import org.apache.commons.dbcp2.BasicDataSource;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import javax.sql.DataSource;
|
||||
import java.sql.SQLException;
|
||||
import java.util.Optional;
|
||||
|
||||
/**
|
||||
* Utility to hide complexity involved in obtaining connection pool information
|
||||
*/
|
||||
public class ConnectionPoolInfoProvider implements IConnectionPoolInfoProvider {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(ConnectionPoolInfoProvider.class);
|
||||
|
||||
private IConnectionPoolInfoProvider provider;
|
||||
|
||||
|
||||
public ConnectionPoolInfoProvider(DataSource theDataSource) {
|
||||
if (theDataSource.getClass().isAssignableFrom(BasicDataSource.class)) {
|
||||
provider = new BasicDataSourceConnectionPoolInfoProvider((BasicDataSource) theDataSource);
|
||||
return;
|
||||
}
|
||||
|
||||
if ( theDataSource.getClass().isAssignableFrom(ProxyDataSource.class)) {
|
||||
boolean basiDataSourceWrapped = false;
|
||||
try {
|
||||
basiDataSourceWrapped = theDataSource.isWrapperFor(BasicDataSource.class);
|
||||
if (basiDataSourceWrapped) {
|
||||
BasicDataSource basicDataSource = theDataSource.unwrap(BasicDataSource.class);
|
||||
provider = new BasicDataSourceConnectionPoolInfoProvider(basicDataSource);
|
||||
}
|
||||
} catch (SQLException ignored) { }
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public Optional<Integer> getTotalConnectionSize() {
|
||||
return provider == null ? Optional.empty() : provider.getTotalConnectionSize();
|
||||
}
|
||||
|
||||
@Override
|
||||
public Optional<Integer> getActiveConnections() {
|
||||
return provider == null ? Optional.empty() : provider.getActiveConnections();
|
||||
}
|
||||
|
||||
@Override
|
||||
public Optional<Long> getMaxWaitMillis() {
|
||||
return provider == null ? Optional.empty() : provider.getMaxWaitMillis();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
package ca.uhn.fhir.jpa.config.util;
|
||||
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
public interface IConnectionPoolInfoProvider {
|
||||
Optional<Integer> getTotalConnectionSize();
|
||||
|
||||
Optional<Integer> getActiveConnections();
|
||||
|
||||
Optional<Long> getMaxWaitMillis();
|
||||
}
|
||||
|
|
@ -20,11 +20,14 @@ package ca.uhn.fhir.jpa.provider;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
|
||||
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
|
||||
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
|
||||
import ca.uhn.fhir.jpa.model.util.JpaConstants;
|
||||
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ReindexTerminologyResult;
|
||||
import ca.uhn.fhir.rest.annotation.At;
|
||||
import ca.uhn.fhir.rest.annotation.History;
|
||||
import ca.uhn.fhir.rest.annotation.Offset;
|
||||
|
|
@ -34,9 +37,14 @@ import ca.uhn.fhir.rest.annotation.Since;
|
|||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.param.DateRangeParam;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
|
||||
import ca.uhn.fhir.util.ParametersUtil;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import org.hl7.fhir.instance.model.api.IBaseParameters;
|
||||
import org.hl7.fhir.instance.model.api.IPrimitiveType;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Required;
|
||||
|
||||
|
|
@ -44,6 +52,9 @@ import javax.servlet.http.HttpServletRequest;
|
|||
import java.util.Date;
|
||||
|
||||
public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider implements IJpaSystemProvider {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(BaseJpaSystemProvider.class);
|
||||
|
||||
public static final String RESP_PARAM_SUCCESS = "success";
|
||||
|
||||
/**
|
||||
* @see ProviderConstants#OPERATION_REINDEX
|
||||
|
|
@ -62,6 +73,10 @@ public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider implements IJp
|
|||
@Autowired
|
||||
private IResourceReindexingSvc myResourceReindexingSvc;
|
||||
|
||||
@Autowired
|
||||
private ITermReadSvc myTermReadSvc;
|
||||
|
||||
|
||||
public BaseJpaSystemProvider() {
|
||||
// nothing
|
||||
}
|
||||
|
|
@ -116,4 +131,36 @@ public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider implements IJp
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
@Operation(name = ProviderConstants.OPERATION_REINDEX_TERMINOLOGY, idempotent = false)
|
||||
public IBaseParameters reindexTerminology(RequestDetails theRequestDetails) {
|
||||
|
||||
ReindexTerminologyResult result;
|
||||
StopWatch sw = new StopWatch();
|
||||
try {
|
||||
result = myTermReadSvc.reindexTerminology();
|
||||
|
||||
} catch (Exception theE) {
|
||||
throw new InternalErrorException(Msg.code(2072) +
|
||||
"Re-creating terminology freetext indexes failed with exception: " + theE.getMessage());
|
||||
}
|
||||
|
||||
IBaseParameters retVal = ParametersUtil.newInstance(getContext());
|
||||
if ( ! result.equals(ReindexTerminologyResult.SUCCESS) ) {
|
||||
ParametersUtil.addParameterToParametersBoolean(getContext(), retVal, RESP_PARAM_SUCCESS, false);
|
||||
String msg = result.equals(ReindexTerminologyResult.SEARCH_SVC_DISABLED)
|
||||
? "Freetext service is not configured. Operation didn't run."
|
||||
: "Operation was cancelled because other terminology background tasks are currently running. Try again in a few minutes.";
|
||||
ParametersUtil.addParameterToParametersString(getContext(), retVal, "message", msg);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
ParametersUtil.addParameterToParametersBoolean(getContext(), retVal, RESP_PARAM_SUCCESS, true);
|
||||
ourLog.info("Re-creating terminology freetext indexes took {}", sw);
|
||||
return retVal;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -34,6 +34,8 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
|||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
|
||||
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
|
||||
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
|
||||
import ca.uhn.fhir.jpa.config.util.ConnectionPoolInfoProvider;
|
||||
import ca.uhn.fhir.jpa.config.util.IConnectionPoolInfoProvider;
|
||||
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
|
||||
|
|
@ -67,6 +69,7 @@ import ca.uhn.fhir.jpa.search.ElasticsearchNestedQueryBuilderUtil;
|
|||
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ReindexTerminologyResult;
|
||||
import ca.uhn.fhir.jpa.term.ex.ExpansionTooCostlyException;
|
||||
import ca.uhn.fhir.jpa.util.LogicUtil;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
|
|
@ -98,6 +101,7 @@ import org.apache.lucene.search.BooleanQuery;
|
|||
import org.apache.lucene.search.Query;
|
||||
import org.apache.lucene.search.RegexpQuery;
|
||||
import org.apache.lucene.search.TermQuery;
|
||||
import org.hibernate.CacheMode;
|
||||
import org.hibernate.search.backend.elasticsearch.ElasticsearchExtension;
|
||||
import org.hibernate.search.backend.lucene.LuceneExtension;
|
||||
import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep;
|
||||
|
|
@ -106,6 +110,7 @@ import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
|
|||
import org.hibernate.search.engine.search.query.SearchQuery;
|
||||
import org.hibernate.search.mapper.orm.Search;
|
||||
import org.hibernate.search.mapper.orm.common.EntityReference;
|
||||
import org.hibernate.search.mapper.orm.massindexing.impl.LoggingMassIndexingMonitor;
|
||||
import org.hibernate.search.mapper.orm.session.SearchSession;
|
||||
import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
|
||||
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
|
||||
|
|
@ -135,6 +140,7 @@ import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
|
|||
import org.quartz.JobExecutionContext;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Lazy;
|
||||
import org.springframework.data.domain.PageRequest;
|
||||
import org.springframework.data.domain.Pageable;
|
||||
import org.springframework.data.domain.Slice;
|
||||
|
|
@ -215,6 +221,12 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
private static final String IDX_PROP_VALUE_STRING = IDX_PROPERTIES + ".myValueString";
|
||||
private static final String IDX_PROP_DISPLAY_STRING = IDX_PROPERTIES + ".myDisplayString";
|
||||
|
||||
public static final int DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS = 2;
|
||||
// doesn't seem to be much gain by using more threads than this value
|
||||
public static final int MAX_MASS_INDEXER_OBJECT_LOADING_THREADS = 6;
|
||||
|
||||
private boolean myPreExpandingValueSets = false;
|
||||
|
||||
private final Cache<String, TermCodeSystemVersion> myCodeSystemCurrentVersionCache = Caffeine.newBuilder().expireAfterWrite(1, TimeUnit.MINUTES).build();
|
||||
@Autowired
|
||||
protected DaoRegistry myDaoRegistry;
|
||||
|
|
@ -270,6 +282,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
@Autowired
|
||||
private HibernatePropertiesProvider myHibernatePropertiesProvider;
|
||||
|
||||
|
||||
private boolean isFullTextSetToUseElastic() {
|
||||
return "elasticsearch".equalsIgnoreCase(myHibernatePropertiesProvider.getHibernateSearchBackend());
|
||||
}
|
||||
|
|
@ -1945,6 +1958,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
TermValueSet termValueSet = optionalTermValueSet.get();
|
||||
termValueSet.setTotalConcepts(0L);
|
||||
termValueSet.setTotalConceptDesignations(0L);
|
||||
termValueSet.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
|
||||
return myTermValueSetDao.saveAndFlush(termValueSet);
|
||||
});
|
||||
|
|
@ -1953,6 +1968,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
}
|
||||
|
||||
// We have a ValueSet to pre-expand.
|
||||
setPreExpandingValueSets(true);
|
||||
try {
|
||||
ValueSet valueSet = txTemplate.execute(t -> {
|
||||
TermValueSet refreshedValueSetToExpand = myTermValueSetDao.findById(valueSetToExpand.getId()).orElseThrow(() -> new IllegalStateException("Unknown VS ID: " + valueSetToExpand.getId()));
|
||||
|
|
@ -1982,10 +1998,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
myTermValueSetDao.saveAndFlush(valueSetToExpand);
|
||||
|
||||
});
|
||||
|
||||
} finally {
|
||||
setPreExpandingValueSets(false);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private synchronized void setPreExpandingValueSets(boolean thePreExpandingValueSets) {
|
||||
myPreExpandingValueSets = thePreExpandingValueSets;
|
||||
}
|
||||
|
||||
private synchronized boolean isPreExpandingValueSets() {
|
||||
return myPreExpandingValueSets;
|
||||
}
|
||||
|
||||
@Override
|
||||
@Transactional
|
||||
public CodeValidationResult validateCode(ConceptValidationOptions theOptions, IIdType theValueSetId, String theValueSetIdentifier, String theCodeSystemIdentifierToValidate, String theCodeToValidate, String theDisplayToValidate, IBaseDatatype theCodingToValidate, IBaseDatatype theCodeableConceptToValidate) {
|
||||
|
|
@ -2642,6 +2669,79 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
|
|||
return Optional.of(cs);
|
||||
}
|
||||
|
||||
|
||||
private static final int SECONDS_IN_MINUTE = 60;
|
||||
private static final int INDEXED_ROOTS_LOGGING_COUNT = 50_000;
|
||||
|
||||
|
||||
@Transactional
|
||||
@Override
|
||||
public ReindexTerminologyResult reindexTerminology() throws InterruptedException {
|
||||
if (myFulltextSearchSvc == null) {
|
||||
return ReindexTerminologyResult.SEARCH_SVC_DISABLED;
|
||||
}
|
||||
|
||||
if (isBatchTerminologyTasksRunning()) {
|
||||
return ReindexTerminologyResult.OTHER_BATCH_TERMINOLOGY_TASKS_RUNNING;
|
||||
}
|
||||
|
||||
// disallow pre-expanding ValueSets while reindexing
|
||||
myDeferredStorageSvc.setProcessDeferred(false);
|
||||
|
||||
int objectLoadingThreadNumber = calculateObjectLoadingThreadNumber();
|
||||
ourLog.info("Using {} threads to load objects", objectLoadingThreadNumber);
|
||||
|
||||
try {
|
||||
SearchSession searchSession = getSearchSession();
|
||||
searchSession
|
||||
.massIndexer( TermConcept.class )
|
||||
.dropAndCreateSchemaOnStart( true )
|
||||
.purgeAllOnStart( false )
|
||||
.batchSizeToLoadObjects( 100 )
|
||||
.cacheMode( CacheMode.IGNORE )
|
||||
.threadsToLoadObjects( 6 )
|
||||
.transactionTimeout( 60 * SECONDS_IN_MINUTE )
|
||||
.monitor( new LoggingMassIndexingMonitor(INDEXED_ROOTS_LOGGING_COUNT) )
|
||||
.startAndWait();
|
||||
|
||||
} finally {
|
||||
myDeferredStorageSvc.setProcessDeferred(true);
|
||||
}
|
||||
|
||||
return ReindexTerminologyResult.SUCCESS;
|
||||
}
|
||||
|
||||
|
||||
@VisibleForTesting
|
||||
boolean isBatchTerminologyTasksRunning() {
|
||||
return isNotSafeToPreExpandValueSets() || isPreExpandingValueSets();
|
||||
}
|
||||
|
||||
|
||||
@VisibleForTesting
|
||||
int calculateObjectLoadingThreadNumber() {
|
||||
IConnectionPoolInfoProvider connectionPoolInfoProvider =
|
||||
new ConnectionPoolInfoProvider(myHibernatePropertiesProvider.getDataSource());
|
||||
Optional<Integer> maxConnectionsOpt = connectionPoolInfoProvider.getTotalConnectionSize();
|
||||
if ( ! maxConnectionsOpt.isPresent() ) {
|
||||
return DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS;
|
||||
}
|
||||
|
||||
int maxConnections = maxConnectionsOpt.get();
|
||||
int usableThreads = maxConnections < 6 ? 1 : maxConnections - 5;
|
||||
int objectThreads = Math.min(usableThreads, MAX_MASS_INDEXER_OBJECT_LOADING_THREADS);
|
||||
ourLog.debug("Data source connection pool has {} connections allocated, so reindexing will use {} object " +
|
||||
"loading threads (each using a connection)", maxConnections, objectThreads);
|
||||
return objectThreads;
|
||||
}
|
||||
|
||||
|
||||
@VisibleForTesting
|
||||
SearchSession getSearchSession() {
|
||||
return Search.session( myEntityManager );
|
||||
}
|
||||
|
||||
|
||||
@VisibleForTesting
|
||||
public static void setForceDisableHibernateSearchForUnitTest(boolean theForceDisableHibernateSearchForUnitTest) {
|
||||
ourForceDisableHibernateSearchForUnitTest = theForceDisableHibernateSearchForUnitTest;
|
||||
|
|
|
|||
|
|
@ -133,4 +133,10 @@ public interface ITermReadSvc extends IValidationSupport {
|
|||
*/
|
||||
Optional<IBaseResource> readCodeSystemByForcedId(String theForcedId);
|
||||
|
||||
/**
|
||||
* Version independent
|
||||
* Recreates freetext indexes for TermConcept and nested TermConceptProperty
|
||||
*/
|
||||
ReindexTerminologyResult reindexTerminology() throws InterruptedException;
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,11 @@
|
|||
package ca.uhn.fhir.jpa.term.api;
|
||||
|
||||
public enum ReindexTerminologyResult {
|
||||
SUCCESS,
|
||||
|
||||
// search service is not enabled
|
||||
SEARCH_SVC_DISABLED,
|
||||
|
||||
// batch terminology tasks other than re-indexing are currently running
|
||||
OTHER_BATCH_TERMINOLOGY_TASKS_RUNNING
|
||||
}
|
||||
|
|
@ -155,7 +155,7 @@ public class TestR4Config {
|
|||
// .logQueryBySlf4j(level)
|
||||
.logSlowQueryBySlf4j(10, TimeUnit.SECONDS, level)
|
||||
.beforeQuery(new BlockLargeNumbersOfParamsListener())
|
||||
.beforeQuery(new MandatoryTransactionListener())
|
||||
.beforeQuery( getMandatoryTransactionListener() )
|
||||
.afterQuery(captureQueriesListener())
|
||||
.afterQuery(new CurrentThreadCaptureQueriesListener())
|
||||
.countQuery(singleQueryCountHolder())
|
||||
|
|
@ -170,6 +170,12 @@ public class TestR4Config {
|
|||
return new SingleQueryCountHolder();
|
||||
}
|
||||
|
||||
@Bean
|
||||
public ProxyDataSourceBuilder.SingleQueryExecution getMandatoryTransactionListener() {
|
||||
return new MandatoryTransactionListener();
|
||||
}
|
||||
|
||||
|
||||
@Bean
|
||||
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
|
||||
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,144 @@
|
|||
package ca.uhn.fhir.jpa.config.util;
|
||||
|
||||
import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
|
||||
import net.ttddyy.dsproxy.support.ProxyDataSource;
|
||||
import org.apache.commons.dbcp2.BasicDataSource;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Nested;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.springframework.test.util.ReflectionTestUtils;
|
||||
|
||||
import javax.sql.DataSource;
|
||||
import java.util.Optional;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class ConnectionPoolInfoProviderTest {
|
||||
|
||||
public static final long MAX_WAIT_MILLIS = 10_000;
|
||||
public static final int MAX_CONNECTIONS_TOTAL = 50;
|
||||
|
||||
private IConnectionPoolInfoProvider tested;
|
||||
|
||||
|
||||
@Nested
|
||||
public class TestBasiDataSourceImplementation {
|
||||
|
||||
@BeforeEach
|
||||
void setUp() {
|
||||
BasicDataSource myDataSource = new BasicDataSource();
|
||||
myDataSource.setMaxWaitMillis(MAX_WAIT_MILLIS);
|
||||
myDataSource.setMaxTotal(MAX_CONNECTIONS_TOTAL);
|
||||
tested = new BasicDataSourceConnectionPoolInfoProvider(myDataSource);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void testGetMaxWaitMillis() {
|
||||
Optional<Long> resOpt = tested.getMaxWaitMillis();
|
||||
assertTrue(resOpt.isPresent());
|
||||
assertEquals(MAX_WAIT_MILLIS, resOpt.get());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testGetMaxConnectionSize() {
|
||||
Optional<Integer> resOpt = tested.getTotalConnectionSize();
|
||||
assertTrue(resOpt.isPresent());
|
||||
assertEquals(MAX_CONNECTIONS_TOTAL, resOpt.get());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Nested
|
||||
public class TestFailedProviderSetup {
|
||||
|
||||
@Mock DataSource unknownDataSource;
|
||||
|
||||
@BeforeEach
|
||||
void setUp() {
|
||||
tested = new ConnectionPoolInfoProvider(unknownDataSource);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void testGetMaxWaitMillis() {
|
||||
Optional<Long> resOpt = tested.getMaxWaitMillis();
|
||||
assertFalse(resOpt.isPresent());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testGetMaxConnectionSize() {
|
||||
Optional<Integer> resOpt = tested.getTotalConnectionSize();
|
||||
assertFalse(resOpt.isPresent());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testGetActiveConnections() {
|
||||
Optional<Integer> resOpt = tested.getActiveConnections();
|
||||
assertFalse(resOpt.isPresent());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class TestConfig {
|
||||
|
||||
@Mock DataSource unknownDataSource;
|
||||
|
||||
@Test
|
||||
void dataSourceIsBasicDataSource() {
|
||||
DataSource ds = new BasicDataSource();
|
||||
|
||||
IConnectionPoolInfoProvider provider = new ConnectionPoolInfoProvider(ds);
|
||||
|
||||
IConnectionPoolInfoProvider instantiatedProvider =
|
||||
(IConnectionPoolInfoProvider) ReflectionTestUtils.getField(provider, "provider");
|
||||
|
||||
assertNotNull(instantiatedProvider);
|
||||
assertTrue(instantiatedProvider.getClass().isAssignableFrom(BasicDataSourceConnectionPoolInfoProvider.class));
|
||||
}
|
||||
|
||||
@Test
|
||||
void dataSourceIsProxyDataSourceWrappingBasicDataSource() {
|
||||
DataSource ds = new BasicDataSource();
|
||||
ProxyDataSource proxyDs = new ProxyDataSource(ds);
|
||||
|
||||
IConnectionPoolInfoProvider provider = new ConnectionPoolInfoProvider(proxyDs);
|
||||
|
||||
IConnectionPoolInfoProvider instantiatedProvider =
|
||||
(IConnectionPoolInfoProvider) ReflectionTestUtils.getField(provider, "provider");
|
||||
assertNotNull(instantiatedProvider);
|
||||
assertTrue(instantiatedProvider.getClass().isAssignableFrom(BasicDataSourceConnectionPoolInfoProvider.class));
|
||||
}
|
||||
|
||||
@Test
|
||||
void dataSourceIsProxyDataSourceWrappingNotBasicDataSource() {
|
||||
ProxyDataSource proxyDs = new ProxyDataSource(unknownDataSource);
|
||||
|
||||
IConnectionPoolInfoProvider provider = new ConnectionPoolInfoProvider(proxyDs);
|
||||
IConnectionPoolInfoProvider instantiatedProvider =
|
||||
(IConnectionPoolInfoProvider) ReflectionTestUtils.getField(provider, "provider");
|
||||
assertNull(instantiatedProvider);
|
||||
}
|
||||
|
||||
@Test
|
||||
void dataSourceIsNotBasicDataSourceOrProxyDataSource() {
|
||||
IConnectionPoolInfoProvider provider = new ConnectionPoolInfoProvider(unknownDataSource);
|
||||
|
||||
IConnectionPoolInfoProvider instantiatedProvider =
|
||||
(IConnectionPoolInfoProvider) ReflectionTestUtils.getField(provider, "provider");
|
||||
assertNull(instantiatedProvider);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,103 @@
|
|||
package ca.uhn.fhir.jpa.provider;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ReindexTerminologyResult;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.util.ParametersUtil;
|
||||
import org.hl7.fhir.instance.model.api.IBaseParameters;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.InjectMocks;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.springframework.test.util.ReflectionTestUtils;
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
import static ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider.RESP_PARAM_SUCCESS;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
public class TerminologyFreetextIndexingProviderTest {
|
||||
|
||||
private final FhirContext myContext = FhirContext.forR4();
|
||||
|
||||
@Mock private ITermReadSvc myTermReadSvc;
|
||||
@Mock private SystemRequestDetails myRequestDetails;
|
||||
|
||||
@InjectMocks
|
||||
private BaseJpaSystemProvider<?, ?> testedProvider = new BaseJpaSystemProvider<>();
|
||||
|
||||
@BeforeEach
|
||||
void setUp() {
|
||||
ReflectionTestUtils.setField(testedProvider, "myContext", myContext);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testNoSearchEnabled() throws InterruptedException {
|
||||
when(myTermReadSvc.reindexTerminology()).thenReturn(ReindexTerminologyResult.SEARCH_SVC_DISABLED);
|
||||
|
||||
IBaseParameters retVal = testedProvider.reindexTerminology(myRequestDetails);
|
||||
|
||||
assertNotNull(retVal);
|
||||
Optional<String> successValueOpt = ParametersUtil.getNamedParameterValueAsString(myContext, retVal, RESP_PARAM_SUCCESS);
|
||||
assertTrue(successValueOpt.isPresent());
|
||||
assertEquals("false", successValueOpt.get());
|
||||
Optional<String> msgOpt = ParametersUtil.getNamedParameterValueAsString(myContext, retVal, "message");
|
||||
assertTrue(msgOpt.isPresent());
|
||||
assertEquals("Freetext service is not configured. Operation didn't run.", msgOpt.get());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void testOtherTerminologyTasksRunning() throws InterruptedException {
|
||||
when(myTermReadSvc.reindexTerminology()).thenReturn(ReindexTerminologyResult.OTHER_BATCH_TERMINOLOGY_TASKS_RUNNING);
|
||||
|
||||
IBaseParameters retVal = testedProvider.reindexTerminology(myRequestDetails);
|
||||
|
||||
assertNotNull(retVal);
|
||||
Optional<String> successValueOpt = ParametersUtil.getNamedParameterValueAsString(myContext, retVal, RESP_PARAM_SUCCESS);
|
||||
assertTrue(successValueOpt.isPresent());
|
||||
assertEquals("false", successValueOpt.get());
|
||||
Optional<String> msgOpt = ParametersUtil.getNamedParameterValueAsString(myContext, retVal, "message");
|
||||
assertTrue(msgOpt.isPresent());
|
||||
assertEquals("Operation was cancelled because other terminology background tasks are currently running. Try again in a few minutes.", msgOpt.get());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void testServiceWorks() throws InterruptedException {
|
||||
when(myTermReadSvc.reindexTerminology()).thenReturn(ReindexTerminologyResult.SUCCESS);
|
||||
|
||||
IBaseParameters retVal = testedProvider.reindexTerminology(myRequestDetails);
|
||||
|
||||
assertNotNull(retVal);
|
||||
Optional<String> successValueOpt = ParametersUtil.getNamedParameterValueAsString(myContext, retVal, RESP_PARAM_SUCCESS);
|
||||
assertTrue(successValueOpt.isPresent());
|
||||
assertEquals("true", successValueOpt.get());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void testServiceThroes() throws InterruptedException {
|
||||
String exceptionMsg = "some msg";
|
||||
when(myTermReadSvc.reindexTerminology()).thenThrow(new InterruptedException(exceptionMsg));
|
||||
|
||||
InternalErrorException thrown = assertThrows(InternalErrorException.class,
|
||||
() -> testedProvider.reindexTerminology(myRequestDetails));
|
||||
|
||||
assertEquals(Msg.code(2072) + "Re-creating terminology freetext indexes " +
|
||||
"failed with exception: " + exceptionMsg, thrown.getMessage());
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package ca.uhn.fhir.jpa.term.api;
|
||||
package ca.uhn.fhir.jpa.term;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
|
|
@ -22,12 +22,18 @@ package ca.uhn.fhir.jpa.term.api;
|
|||
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
|
||||
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
|
||||
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.term.TermReadSvcR4;
|
||||
import ca.uhn.fhir.jpa.term.TermReadSvcUtil;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
import com.google.common.collect.Lists;
|
||||
import net.ttddyy.dsproxy.support.ProxyDataSource;
|
||||
import org.apache.commons.dbcp2.BasicDataSource;
|
||||
import org.hibernate.search.mapper.orm.massindexing.MassIndexer;
|
||||
import org.hibernate.search.mapper.orm.session.SearchSession;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
|
|
@ -35,26 +41,35 @@ import org.junit.jupiter.api.Nested;
|
|||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Answers;
|
||||
import org.mockito.InjectMocks;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.Spy;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.springframework.data.domain.Pageable;
|
||||
import org.springframework.test.util.ReflectionTestUtils;
|
||||
|
||||
import javax.persistence.EntityManager;
|
||||
import javax.persistence.NonUniqueResultException;
|
||||
import javax.sql.DataSource;
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
import static ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS;
|
||||
import static ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.MAX_MASS_INDEXER_OBJECT_LOADING_THREADS;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.mockito.ArgumentMatchers.any;
|
||||
import static org.mockito.ArgumentMatchers.anyString;
|
||||
import static org.mockito.ArgumentMatchers.eq;
|
||||
import static org.mockito.ArgumentMatchers.isA;
|
||||
import static org.mockito.Mockito.doReturn;
|
||||
import static org.mockito.Mockito.never;
|
||||
import static org.mockito.Mockito.spy;
|
||||
import static org.mockito.Mockito.times;
|
||||
import static org.mockito.Mockito.verify;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
|
@ -257,9 +272,10 @@ class ITermReadSvcTest {
|
|||
|
||||
List<TermConcept> termConcepts = Lists.newArrayList(termConceptCode1, termConceptCode3, termConceptCode4);
|
||||
List<String> values = Arrays.asList(CODE_1, CODE_2, CODE_3, CODE_4, CODE_5);
|
||||
String msg = (String) ReflectionTestUtils.invokeMethod(
|
||||
String msg = ReflectionTestUtils.invokeMethod(
|
||||
testedClass, "getTermConceptsFetchExceptionMsg", termConcepts, values);
|
||||
|
||||
assertNotNull(msg);
|
||||
assertTrue(msg.contains("No TermConcept(s) were found"));
|
||||
assertFalse(msg.contains(CODE_1));
|
||||
assertTrue(msg.contains(CODE_2));
|
||||
|
|
@ -276,13 +292,101 @@ class ITermReadSvcTest {
|
|||
when(termConceptCode3.getId()).thenReturn(3L);
|
||||
|
||||
List<TermConcept> termConcepts = Lists.newArrayList(termConceptCode1, termConceptCode3);
|
||||
List<String> values = Arrays.asList(CODE_3);
|
||||
String msg = (String) ReflectionTestUtils.invokeMethod(
|
||||
List<String> values = List.of(CODE_3);
|
||||
String msg = ReflectionTestUtils.invokeMethod(
|
||||
testedClass, "getTermConceptsFetchExceptionMsg", termConcepts, values);
|
||||
|
||||
assertNotNull(msg);
|
||||
assertTrue(msg.contains("More TermConcepts were found than indicated codes"));
|
||||
assertFalse(msg.contains("Queried codes: [" + CODE_3 + "]"));
|
||||
assertTrue(msg.contains("Obtained TermConcept IDs, codes: [1, code-1; 3, code-3]"));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Nested
|
||||
public class TestReindexTerminology {
|
||||
@Mock private SearchSession mySearchSession;
|
||||
|
||||
@Mock(answer = Answers.RETURNS_DEEP_STUBS)
|
||||
private MassIndexer myMassIndexer;
|
||||
|
||||
@Mock private IFulltextSearchSvc myFulltextSearchSvc;
|
||||
@Mock private ITermDeferredStorageSvc myDeferredStorageSvc;
|
||||
@Mock private HibernatePropertiesProvider myHibernatePropertiesProvider;
|
||||
|
||||
@InjectMocks
|
||||
@Spy private BaseTermReadSvcImpl myTermReadSvc = (BaseTermReadSvcImpl) spy(testedClass);
|
||||
|
||||
|
||||
@Test
|
||||
void testReindexTerminology() throws InterruptedException {
|
||||
doReturn(mySearchSession).when(myTermReadSvc).getSearchSession();
|
||||
doReturn(false).when(myTermReadSvc).isBatchTerminologyTasksRunning();
|
||||
doReturn(10).when(myTermReadSvc).calculateObjectLoadingThreadNumber();
|
||||
when(mySearchSession.massIndexer(TermConcept.class)).thenReturn(myMassIndexer);
|
||||
|
||||
myTermReadSvc.reindexTerminology();
|
||||
verify(mySearchSession, times(1)).massIndexer(TermConcept.class);
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class TestCalculateObjectLoadingThreadNumber {
|
||||
|
||||
private final BasicDataSource myBasicDataSource = new BasicDataSource();
|
||||
private final ProxyDataSource myProxyDataSource = new ProxyDataSource(myBasicDataSource) ;
|
||||
|
||||
@BeforeEach
|
||||
void setUp() {
|
||||
doReturn(myProxyDataSource).when(myHibernatePropertiesProvider).getDataSource();
|
||||
}
|
||||
|
||||
@Test
|
||||
void testLessThanSix() {
|
||||
myBasicDataSource.setMaxTotal(5);
|
||||
|
||||
int retMaxConnectionSize = myTermReadSvc.calculateObjectLoadingThreadNumber();
|
||||
|
||||
assertEquals(1, retMaxConnectionSize);
|
||||
}
|
||||
|
||||
@Test
|
||||
void testMoreThanSixButLessThanLimit() {
|
||||
myBasicDataSource.setMaxTotal(10);
|
||||
|
||||
int retMaxConnectionSize = myTermReadSvc.calculateObjectLoadingThreadNumber();
|
||||
|
||||
assertEquals(5, retMaxConnectionSize);
|
||||
}
|
||||
|
||||
@Test
|
||||
void testMoreThanSixAndMoreThanLimit() {
|
||||
myBasicDataSource.setMaxTotal(35);
|
||||
|
||||
int retMaxConnectionSize = myTermReadSvc.calculateObjectLoadingThreadNumber();
|
||||
|
||||
assertEquals(MAX_MASS_INDEXER_OBJECT_LOADING_THREADS, retMaxConnectionSize);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class TestCalculateObjectLoadingThreadNumberDefault {
|
||||
|
||||
@Mock private DataSource myDataSource = new BasicDataSource();
|
||||
|
||||
@BeforeEach
|
||||
void setUp() {
|
||||
doReturn(myDataSource).when(myHibernatePropertiesProvider).getDataSource();
|
||||
}
|
||||
|
||||
@Test
|
||||
void testDefaultWhenCantGetMaxConnections() {
|
||||
int retMaxConnectionSize = myTermReadSvc.calculateObjectLoadingThreadNumber();
|
||||
|
||||
assertEquals(DEFAULT_MASS_INDEXER_OBJECT_LOADING_THREADS, retMaxConnectionSize);
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,342 @@
|
|||
package ca.uhn.fhir.jpa.term.freetext;
|
||||
|
||||
import ca.uhn.fhir.jpa.config.TestHibernateSearchAddInConfig;
|
||||
import ca.uhn.fhir.jpa.config.TestR4Config;
|
||||
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
|
||||
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
|
||||
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.entity.TermValueSet;
|
||||
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
|
||||
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
|
||||
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import net.ttddyy.dsproxy.ExecutionInfo;
|
||||
import net.ttddyy.dsproxy.QueryInfo;
|
||||
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
|
||||
import org.hibernate.search.engine.search.predicate.dsl.PredicateFinalStep;
|
||||
import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
|
||||
import org.hibernate.search.engine.search.query.SearchQuery;
|
||||
import org.hibernate.search.mapper.orm.Search;
|
||||
import org.hibernate.search.mapper.orm.common.EntityReference;
|
||||
import org.hibernate.search.mapper.orm.mapping.SearchMapping;
|
||||
import org.hibernate.search.mapper.orm.session.SearchSession;
|
||||
import org.hibernate.search.mapper.orm.work.SearchWorkspace;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.junit.jupiter.SpringExtension;
|
||||
import org.springframework.util.ResourceUtils;
|
||||
|
||||
import javax.persistence.EntityManager;
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
|
||||
import static java.util.Map.entry;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@ContextConfiguration(classes = {TestR4Config.class, TestHibernateSearchAddInConfig.LuceneFilesystem.class
|
||||
,ReindexTerminologyFreetextR4Test.NoopMandatoryTransactionListener.class
|
||||
})
|
||||
public class ReindexTerminologyFreetextR4Test extends BaseJpaR4Test {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(ReindexTerminologyFreetextR4Test.class);
|
||||
|
||||
public static final String LOINC_URL = "http://loinc.org";
|
||||
public static final String TEST_FILES_CLASSPATH = "loinc-reindex/";
|
||||
public static final String NULL = "'null'";
|
||||
|
||||
// set to false to avoid cleanup for debugging purposes
|
||||
public static final boolean CLEANUP_DATA = true;
|
||||
|
||||
public static final String CS_VERSION = "2.68";
|
||||
public static final int CS_CONCEPTS_NUMBER = 81;
|
||||
|
||||
public static final String LOINC_PROPERTIES_CLASSPATH =
|
||||
ResourceUtils.CLASSPATH_URL_PREFIX + TEST_FILES_CLASSPATH + "Loinc_small_v68.zip";
|
||||
|
||||
public static final String LOINC_ZIP_CLASSPATH =
|
||||
ResourceUtils.CLASSPATH_URL_PREFIX + TEST_FILES_CLASSPATH + "v268_loincupload.properties";
|
||||
|
||||
|
||||
@Autowired private EntityManager myEntityManager;
|
||||
@Autowired private TermLoaderSvcImpl myTermLoaderSvc;
|
||||
@Autowired private ITermReadSvc myITermReadSvc;
|
||||
@Autowired private ITermConceptDao myTermConceptDao;
|
||||
@Autowired private ITermReadSvc myTermReadSvc;
|
||||
|
||||
|
||||
long termCodeSystemVersionWithVersionId;
|
||||
long termCodeSystemVersionWithNoVersionId;
|
||||
|
||||
Map<String, Long> conceptCounts = Map.ofEntries(
|
||||
entry("http://loinc.org/vs", 81L),
|
||||
entry("http://loinc.org/vs/LG100-4", 0L),
|
||||
entry("http://loinc.org/vs/LG1695-8", 0L),
|
||||
entry("http://loinc.org/vs/LL1000-0", 3L),
|
||||
entry("http://loinc.org/vs/LL1001-8", 7L),
|
||||
entry("http://loinc.org/vs/LL1892-0", 0L),
|
||||
entry("http://loinc.org/vs/loinc-document-ontology", 1L),
|
||||
entry("http://loinc.org/vs/loinc-imaging-document-codes", 1L),
|
||||
entry("http://loinc.org/vs/loinc-rsna-radiology-playbook", 1L),
|
||||
entry("http://loinc.org/vs/loinc-universal-order-set", 0L),
|
||||
entry("http://loinc.org/vs/top-2000-lab-observations-si", 0L),
|
||||
entry("http://loinc.org/vs/top-2000-lab-observations-us", 0L)
|
||||
);
|
||||
|
||||
Map<String, Long> conceptDesignationCounts = Map.ofEntries(
|
||||
entry("http://loinc.org/vs", 55L),
|
||||
entry("http://loinc.org/vs/LG100-4", 0L),
|
||||
entry("http://loinc.org/vs/LG1695-8", 0L),
|
||||
entry("http://loinc.org/vs/LL1000-0", 0L),
|
||||
entry("http://loinc.org/vs/LL1001-8", 0L),
|
||||
entry("http://loinc.org/vs/LL1892-0", 0L),
|
||||
entry("http://loinc.org/vs/loinc-document-ontology", 0L),
|
||||
entry("http://loinc.org/vs/loinc-imaging-document-codes", 1L),
|
||||
entry("http://loinc.org/vs/loinc-rsna-radiology-playbook", 1L),
|
||||
entry("http://loinc.org/vs/loinc-universal-order-set", 0L),
|
||||
entry("http://loinc.org/vs/top-2000-lab-observations-si", 0L),
|
||||
entry("http://loinc.org/vs/top-2000-lab-observations-us", 0L)
|
||||
);
|
||||
|
||||
|
||||
|
||||
|
||||
@Test()
|
||||
public void uploadLoincCodeSystem() throws FileNotFoundException, InterruptedException {
|
||||
List<ITermLoaderSvc.FileDescriptor> myFileDescriptors = buildFileDescriptors();
|
||||
|
||||
// upload terminology
|
||||
myTermLoaderSvc.loadLoinc(myFileDescriptors, mySrd);
|
||||
|
||||
// save all deferred concepts, properties, links, etc
|
||||
myTerminologyDeferredStorageSvc.saveAllDeferred();
|
||||
validateSavedConceptsCount();
|
||||
|
||||
// check the number of freetext-indexed TermConcepts
|
||||
validateFreetextCounts();
|
||||
|
||||
// pre-expand ValueSets
|
||||
myTermReadSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
// pre-expansion uses freetext so check is to make sure all valuesets have the right number of concepts
|
||||
validateValueSetPreexpansion();
|
||||
|
||||
// run reindexing operation
|
||||
reFreetextIndexTerminology();
|
||||
|
||||
// validate again after reindexing the number of freetext-indexed TermConcepts
|
||||
validateFreetextCounts();
|
||||
|
||||
// remove ValueSet pre-expansions
|
||||
removeValueSetPreExpansions();
|
||||
|
||||
// pre-expand ValueSets again, after freetext reindexing
|
||||
myTermReadSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
|
||||
// pre-expansion uses freetext so check is to make sure all valuesets have the right number of concepts
|
||||
validateValueSetPreexpansion();
|
||||
}
|
||||
|
||||
|
||||
private void removeValueSetPreExpansions() {
|
||||
List<TermValueSet> termValueSets = myTermValueSetDao.findAll();
|
||||
for (TermValueSet termValueSet : termValueSets) {
|
||||
myTermReadSvc.invalidatePreCalculatedExpansion(termValueSet.getResource().getIdDt(), new SystemRequestDetails());
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* check number of TermConcepts (DB vs freetext-indexed)
|
||||
*/
|
||||
private void validateFreetextCounts() {
|
||||
int dbTermConceptCountForVersion = runInTransaction(() ->
|
||||
myTermConceptDao.countByCodeSystemVersion(termCodeSystemVersionWithVersionId) );
|
||||
assertEquals(CS_CONCEPTS_NUMBER, dbTermConceptCountForVersion);
|
||||
|
||||
long termConceptCountForVersion = searchAllIndexedTermConceptCount(termCodeSystemVersionWithVersionId);
|
||||
ourLog.info("=================> Number of freetext found concepts after re-indexing for version {}: {}",
|
||||
CS_VERSION, termConceptCountForVersion);
|
||||
assertEquals(CS_CONCEPTS_NUMBER, termConceptCountForVersion);
|
||||
|
||||
|
||||
int dbTermConceptCountForNullVersion = runInTransaction(() ->
|
||||
myTermConceptDao.countByCodeSystemVersion(termCodeSystemVersionWithNoVersionId) );
|
||||
assertEquals(CS_CONCEPTS_NUMBER, dbTermConceptCountForNullVersion);
|
||||
|
||||
long termConceptCountNullVersion = searchAllIndexedTermConceptCount(termCodeSystemVersionWithVersionId);
|
||||
ourLog.info("=================> Number of freetext found concepts after re-indexing for version {}: {}",
|
||||
NULL, termConceptCountNullVersion);
|
||||
assertEquals(CS_CONCEPTS_NUMBER, termConceptCountNullVersion);
|
||||
}
|
||||
|
||||
|
||||
|
||||
private void validateFreetextIndexesEmpty() {
|
||||
long termConceptCountVersioned = searchAllIndexedTermConceptCount(termCodeSystemVersionWithVersionId);
|
||||
assertEquals(0, termConceptCountVersioned);
|
||||
|
||||
long termConceptCountNotVersioned = searchAllIndexedTermConceptCount(termCodeSystemVersionWithNoVersionId);
|
||||
assertEquals(0, termConceptCountNotVersioned);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks the number of VS Concepts and ConceptDesignations against test pre-specified values
|
||||
*/
|
||||
private void validateValueSetPreexpansion() {
|
||||
List<TermValueSet> termValueSets = myTermValueSetDao.findAll();
|
||||
for (TermValueSet termValueSet : termValueSets) {
|
||||
ourLog.debug("=================> testing ValueSet: {}", termValueSet.getUrl());
|
||||
long conceptCount = conceptCounts.get( termValueSet.getUrl() );
|
||||
assertEquals(conceptCount, termValueSet.getTotalConcepts());
|
||||
long conceptDesignationCount = conceptDesignationCounts.get( termValueSet.getUrl() );
|
||||
assertEquals(conceptDesignationCount, termValueSet.getTotalConceptDesignations());
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void validateSavedConceptsCount() {
|
||||
termCodeSystemVersionWithVersionId = getTermCodeSystemVersionNotNullId();
|
||||
int dbVersionedTermConceptCount = runInTransaction(() ->
|
||||
myTermConceptDao.countByCodeSystemVersion(termCodeSystemVersionWithVersionId) );
|
||||
ourLog.info("=================> Number of stored concepts for version {}: {}", CS_VERSION, dbVersionedTermConceptCount);
|
||||
assertEquals(CS_CONCEPTS_NUMBER, dbVersionedTermConceptCount);
|
||||
|
||||
termCodeSystemVersionWithNoVersionId = getTermCodeSystemVersionNullId();
|
||||
int dbNotVersionedTermConceptCount = runInTransaction(() ->
|
||||
myTermConceptDao.countByCodeSystemVersion(termCodeSystemVersionWithNoVersionId) );
|
||||
ourLog.info("=================> Number of stored concepts for version {}: {}", NULL, dbNotVersionedTermConceptCount);
|
||||
assertEquals(CS_CONCEPTS_NUMBER, dbNotVersionedTermConceptCount);
|
||||
}
|
||||
|
||||
|
||||
private void reFreetextIndexTerminology() throws InterruptedException {
|
||||
myTermReadSvc.reindexTerminology();
|
||||
}
|
||||
|
||||
|
||||
private long getTermCodeSystemVersionNotNullId() {
|
||||
return runInTransaction(() -> {
|
||||
TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(LOINC_URL);
|
||||
TermCodeSystemVersion termCodeSystemVersion = myTermCodeSystemVersionDao
|
||||
.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), CS_VERSION);
|
||||
assertNotNull(termCodeSystemVersion);
|
||||
return termCodeSystemVersion.getPid();
|
||||
});
|
||||
}
|
||||
|
||||
|
||||
private long getTermCodeSystemVersionNullId() {
|
||||
return runInTransaction(() -> {
|
||||
TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(LOINC_URL);
|
||||
TermCodeSystemVersion termCodeSystemVersion = myTermCodeSystemVersionDao
|
||||
.findByCodeSystemPidVersionIsNull(myTermCodeSystem.getPid());
|
||||
assertNotNull(termCodeSystemVersion);
|
||||
return termCodeSystemVersion.getPid();
|
||||
});
|
||||
}
|
||||
|
||||
|
||||
private List<ITermLoaderSvc.FileDescriptor> buildFileDescriptors() throws FileNotFoundException {
|
||||
List<ITermLoaderSvc.FileDescriptor> fileDescriptors = new ArrayList<>();
|
||||
|
||||
File propsFile = ResourceUtils.getFile(LOINC_PROPERTIES_CLASSPATH);
|
||||
fileDescriptors.add( new TerminologyUploaderProvider.FileBackedFileDescriptor(propsFile) );
|
||||
|
||||
File zipFile = ResourceUtils.getFile(LOINC_ZIP_CLASSPATH);
|
||||
fileDescriptors.add( new TerminologyUploaderProvider.FileBackedFileDescriptor(zipFile) );
|
||||
|
||||
return fileDescriptors;
|
||||
}
|
||||
|
||||
|
||||
|
||||
private long searchAllIndexedTermConceptCount(long theCodeSystemVersionId) {
|
||||
return runInTransaction(() -> {
|
||||
SearchSession searchSession = Search.session(myEntityManager);
|
||||
SearchPredicateFactory predicate = searchSession.scope(TermConcept.class).predicate();
|
||||
PredicateFinalStep step = predicate.bool(b ->
|
||||
b.must(predicate.match().field("myCodeSystemVersionPid").matching(theCodeSystemVersionId)) );
|
||||
|
||||
SearchQuery<EntityReference> termConceptsQuery = searchSession
|
||||
.search(TermConcept.class)
|
||||
.selectEntityReference()
|
||||
.where(f -> step)
|
||||
.toQuery();
|
||||
|
||||
ourLog.trace("About to query: {}", termConceptsQuery.queryString());
|
||||
return termConceptsQuery.fetchTotalHitCount();
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* This configuration bypasses the MandatoryTransactionListener, which breaks this test
|
||||
* (I think it is because hibernate search massIndexer starts threads which don't participate of test transactions)
|
||||
*/
|
||||
@Configuration
|
||||
public static class NoopMandatoryTransactionListener {
|
||||
|
||||
@Bean
|
||||
public ProxyDataSourceBuilder.SingleQueryExecution getMandatoryTransactionListener() {
|
||||
return new ProxyDataSourceBuilder.SingleQueryExecution() {
|
||||
@Override
|
||||
public void execute(ExecutionInfo execInfo, List<QueryInfo> queryInfoList) {
|
||||
}
|
||||
};
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public void afterCleanupDao() {
|
||||
if (CLEANUP_DATA) {
|
||||
super.afterCleanupDao();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void afterResetInterceptors() {
|
||||
if (CLEANUP_DATA) {
|
||||
super.afterResetInterceptors();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void afterClearTerminologyCaches() {
|
||||
if (CLEANUP_DATA) {
|
||||
super.afterClearTerminologyCaches();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void afterPurgeDatabase() {
|
||||
if (CLEANUP_DATA) {
|
||||
super.afterPurgeDatabase();
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void afterEachClearCaches() {
|
||||
if (CLEANUP_DATA) {
|
||||
super.afterEachClearCaches();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Binary file not shown.
|
|
@ -0,0 +1,87 @@
|
|||
#################
|
||||
### MANDATORY ###
|
||||
#################
|
||||
|
||||
# Answer lists (ValueSets of potential answers/values for LOINC "questions")
|
||||
## File must be present
|
||||
loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
|
||||
# Answer list links (connects LOINC observation codes to answer list codes)
|
||||
## File must be present
|
||||
loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
|
||||
|
||||
# Document ontology
|
||||
## File must be present
|
||||
loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
|
||||
|
||||
# LOINC codes
|
||||
## File must be present
|
||||
loinc.file=LoincTable/Loinc.csv
|
||||
|
||||
# LOINC hierarchy
|
||||
## File must be present
|
||||
loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
|
||||
|
||||
# IEEE medical device codes
|
||||
## File must be present
|
||||
loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
|
||||
|
||||
# Imaging document codes
|
||||
## File must be present
|
||||
loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
|
||||
|
||||
# Part
|
||||
## File must be present
|
||||
loinc.part.file=AccessoryFiles/PartFile/Part.csv
|
||||
|
||||
# Part link
|
||||
## File must be present
|
||||
loinc.part.link.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
|
||||
loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
|
||||
|
||||
# Part related code mapping
|
||||
## File must be present
|
||||
loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
|
||||
|
||||
# RSNA playbook
|
||||
## File must be present
|
||||
loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
|
||||
|
||||
# Top 2000 codes - SI
|
||||
## File must be present
|
||||
loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
|
||||
# Top 2000 codes - US
|
||||
## File must be present
|
||||
loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
|
||||
|
||||
# Universal lab order ValueSet
|
||||
## File must be present
|
||||
loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
|
||||
|
||||
################
|
||||
### OPTIONAL ###
|
||||
################
|
||||
|
||||
# This is the version identifier for the LOINC code system
|
||||
## Key may be omitted if only a single version of LOINC is being kept.
|
||||
loinc.codesystem.version=2.68
|
||||
|
||||
# This is the version identifier for the answer list file
|
||||
## Key may be omitted
|
||||
loinc.answerlist.version=Beta.1
|
||||
|
||||
# This is the version identifier for uploaded ConceptMap resources
|
||||
## Key may be omitted
|
||||
loinc.conceptmap.version=Beta.1
|
||||
|
||||
# Group
|
||||
## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
|
||||
## File may be omitted
|
||||
loinc.group.file=AccessoryFiles/GroupFile/Group.csv
|
||||
# Group terms
|
||||
## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
|
||||
## File may be omitted
|
||||
loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
|
||||
# Parent group
|
||||
## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
|
||||
## File may be omitted
|
||||
loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv
|
||||
|
|
@ -191,6 +191,11 @@ public class ProviderConstants {
|
|||
*/
|
||||
public static final String OPERATION_MEMBER_MATCH = "$member-match";
|
||||
|
||||
/**
|
||||
* Operation name for the $reindex-terminology operation
|
||||
*/
|
||||
public static final String OPERATION_REINDEX_TERMINOLOGY = "$reindex-terminology";
|
||||
|
||||
@Deprecated
|
||||
public static final String MARK_ALL_RESOURCES_FOR_REINDEXING = "$mark-all-resources-for-reindexing";
|
||||
/**
|
||||
|
|
|
|||
Loading…
Reference in New Issue