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Renable elasticsearch tests (#3850) 

* Renable elasticsearch tests

Limit elasticsearch container to 512MB instead of the default 4GB.
This commit is contained in:
michaelabuckley 2022-08-07 03:09:12 -04:00 committed by GitHub
parent a5c4b0756b
commit 60a879c842
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
49 changed files with 633 additions and 334 deletions
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20
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/NumericParamRangeUtil.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.util;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* 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 org.apache.commons.lang3.tuple.Pair;
import java.math.BigDecimal;

5
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -140,8 +140,10 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
boolean haveCompressedContents = false;
try {
for (String nextDataFile : theDatafile) {
File dataFile = new File(nextDataFile);
ourLog.info("Reading {}", dataFile.getAbsolutePath());
try (FileInputStream fileInputStream = new FileInputStream(nextDataFile)) {
try (FileInputStream fileInputStream = new FileInputStream(dataFile)) {
boolean isFhirType = nextDataFile.endsWith(".json") || nextDataFile.endsWith(".xml");
if (nextDataFile.endsWith(".csv") || nextDataFile.endsWith(".properties") || isFhirType) {
@ -168,6 +170,7 @@ public class UploadTerminologyCommand extends BaseRequestGeneratingCommand {
IOUtils.copy(countingInputStream, zipOutputStream);
haveCompressedContents = true;
compressedSourceBytesCount += countingInputStream.getCount();
++compressedFileCount;
zipOutputStream.flush();
ourLog.info("Finished compressing {}", nextDataFile);

84
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HeaderPassthroughOptionTest.java
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@ -20,12 +20,15 @@ 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.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import java.util.concurrent.atomic.AtomicInteger;
import static org.hamcrest.CoreMatchers.hasItems;
import static org.hamcrest.MatcherAssert.assertThat;
@ -40,22 +43,23 @@ import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class HeaderPassthroughOptionTest {
private static final Logger ourLog = LoggerFactory.getLogger(HeaderPassthroughOptionTest.class);
final String FHIR_VERSION = "r4";
private FhirContext myCtx = FhirContext.forR4();
private Server myServer;
private int myPort;
private final String headerKey1 = "test-header-key-1";
private final String headerValue1 = "test header value-1";
private static final String myConceptsFileName = "target/concepts.csv";
private static File myConceptsFile = new File(myConceptsFileName);
private static final String myHierarchyFileName = "target/hierarchy.csv";
private static File myHierarchyFile = new File(myHierarchyFileName);
private static final String ourConceptsFileName = "target/concepts.csv";
private static final String ourHierarchyFileName = "target/hierarchy.csv";
private final CapturingInterceptor myCapturingInterceptor = new CapturingInterceptor();
private final UploadTerminologyCommand testedCommand =
new RequestCapturingUploadTerminologyCommand(myCapturingInterceptor);
@Mock
protected ITermLoaderSvc myTermLoaderSvc;
private static final AtomicInteger ourFilenameCounter = new AtomicInteger();
@BeforeEach
public void beforeEach() throws Exception {
@ -69,21 +73,22 @@ public class HeaderPassthroughOptionTest {
myServer.setHandler(proxyHandler);
JettyUtil.startServer(myServer);
myPort = JettyUtil.getPortForStartedServer(myServer);
writeConceptAndHierarchyFiles();
when(myTermLoaderSvc.loadCustom(eq("http://foo"), anyList(), any()))
.thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
}
@Test
public void oneHeader() throws Exception {
writeConceptAndHierarchyFiles();
String[] args = new String[] {
int filenameCounter = ourFilenameCounter.incrementAndGet();
writeConceptAndHierarchyFiles(filenameCounter);
String[] args = new String[]{
"-v", FHIR_VERSION,
"-m", "SNAPSHOT",
"-t", "http://localhost:" + myPort,
"-u", "http://foo",
"-d", myConceptsFileName,
"-d", myHierarchyFileName,
"-d", getConceptFilename(filenameCounter),
"-d", getHierarchyFilename(filenameCounter),
"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\""
};
@ -102,16 +107,18 @@ public class HeaderPassthroughOptionTest {
@Test
public void twoHeadersSameKey() throws Exception {
writeConceptAndHierarchyFiles();
int filenameCounter = ourFilenameCounter.incrementAndGet();
writeConceptAndHierarchyFiles(filenameCounter);
final String headerValue2 = "test header value-2";
String[] args = new String[] {
String[] args = new String[]{
"-v", FHIR_VERSION,
"-m", "SNAPSHOT",
"-t", "http://localhost:" + myPort,
"-u", "http://foo",
"-d", myConceptsFileName,
"-d", myHierarchyFileName,
"-d", getConceptFilename(filenameCounter),
"-d", getHierarchyFilename(filenameCounter),
"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
"-hp", "\"" + headerKey1 + ":" + headerValue2 + "\""
};
@ -133,17 +140,19 @@ public class HeaderPassthroughOptionTest {
@Test
public void twoHeadersDifferentKeys() throws Exception {
writeConceptAndHierarchyFiles();
int filenameCounter = ourFilenameCounter.incrementAndGet();
writeConceptAndHierarchyFiles(filenameCounter);
final String headerKey2 = "test-header-key-2";
final String headerValue2 = "test header value-2";
String[] args = new String[] {
String[] args = new String[]{
"-v", FHIR_VERSION,
"-m", "SNAPSHOT",
"-t", "http://localhost:" + myPort,
"-u", "http://foo",
"-d", myConceptsFileName,
"-d", myHierarchyFileName,
"-d", getConceptFilename(filenameCounter),
"-d", getHierarchyFilename(filenameCounter),
"-hp", "\"" + headerKey1 + ":" + headerValue1 + "\"",
"-hp", "\"" + headerKey2 + ":" + headerValue2 + "\""
};
@ -164,23 +173,34 @@ public class HeaderPassthroughOptionTest {
assertThat(allHeaders.get(headerKey2), hasItems(headerValue2));
}
private synchronized void writeConceptAndHierarchyFiles() throws IOException {
if (!myConceptsFile.exists()) {
try (FileWriter w = new FileWriter(myConceptsFile, false)) {
w.append("CODE,DISPLAY\n");
w.append("ANIMALS,Animals\n");
w.append("CATS,Cats\n");
w.append("DOGS,Dogs\n");
}
}
private static void writeConceptAndHierarchyFiles(int theFilenameCounter) throws IOException {
File conceptsFile = new File(getConceptFilename(theFilenameCounter));
File hierarchyFile = new File(getHierarchyFilename(theFilenameCounter));
if (!myHierarchyFile.exists()) {
try (FileWriter w = new FileWriter(myHierarchyFile, false)) {
w.append("PARENT,CHILD\n");
w.append("ANIMALS,CATS\n");
w.append("ANIMALS,DOGS\n");
}
ourLog.info("Writing {}", conceptsFile.getAbsolutePath());
try (FileWriter w = new FileWriter(conceptsFile, false)) {
w.append("CODE,DISPLAY\n");
w.append("ANIMALS,Animals\n");
w.append("CATS,Cats\n");
w.append("DOGS,Dogs\n");
}
ourLog.info("Can read {}: {}", ourConceptsFileName, conceptsFile.canRead());
ourLog.info("Writing {}", hierarchyFile.getAbsolutePath());
try (FileWriter w = new FileWriter(hierarchyFile, false)) {
w.append("PARENT,CHILD\n");
w.append("ANIMALS,CATS\n");
w.append("ANIMALS,DOGS\n");
}
ourLog.info("Can read {}: {}", ourHierarchyFileName, hierarchyFile.canRead());
}
private static String getConceptFilename(int theFilenameCounter) {
return ourConceptsFileName.replace(".csv", theFilenameCounter + ".csv");
}
private static String getHierarchyFilename(int theFilenameCounter) {
return ourHierarchyFileName.replace(".csv", theFilenameCounter + ".csv");
}
private class RequestCapturingUploadTerminologyCommand extends UploadTerminologyCommand {

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3878-fast-track-zero-chunk-jobs.yaml Normal file
View File

@ -0,0 +1,4 @@
type: fix
issue: 3878
title: "Previously, if an intermediate step of a gated batch job produced no output data, an exception would be thrown
and processing of the step would abort, leaving the batch job in an unrecoverable state. This has been fixed."

80
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImpl.java
View File

@ -27,10 +27,10 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.log.Logs;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.model.ActivateJobResult;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobJson;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.imprt.model.ActivateJobResult;
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobDao;
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobFileDao;
import ca.uhn.fhir.jpa.entity.BulkImportJobEntity;
@ -98,12 +98,12 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theJobDescription.getProcessingMode(), "Job File Processing mode must not be null");
ValidateUtil.isTrueOrThrowInvalidRequest(theJobDescription.getBatchSize() > 0, "Job File Batch Size must be > 0");
String jobId = UUID.randomUUID().toString();
String biJobId = UUID.randomUUID().toString();
ourLog.info("Creating new Bulk Import job with {} files, assigning job ID: {}", theInitialFiles.size(), jobId);
ourLog.info("Creating new Bulk Import job with {} files, assigning bijob ID: {}", theInitialFiles.size(), biJobId);
BulkImportJobEntity job = new BulkImportJobEntity();
job.setJobId(jobId);
job.setJobId(biJobId);
job.setFileCount(theInitialFiles.size());
job.setStatus(BulkImportJobStatusEnum.STAGING);
job.setJobDescription(theJobDescription.getJobDescription());
@ -114,17 +114,17 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
int nextSequence = 0;
addFilesToJob(theInitialFiles, job, nextSequence);
return jobId;
return biJobId;
}
@Override
@Transactional
public void addFilesToJob(String theJobId, List<BulkImportJobFileJson> theFiles) {
ourLog.info("Adding {} files to bulk import job: {}", theFiles.size(), theJobId);
public void addFilesToJob(String theBiJobId, List<BulkImportJobFileJson> theFiles) {
ourLog.info("Adding {} files to bulk import job with bijob id {}", theFiles.size(), theBiJobId);
BulkImportJobEntity job = findJobByJobId(theJobId);
BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
ValidateUtil.isTrueOrThrowInvalidRequest(job.getStatus() == BulkImportJobStatusEnum.STAGING, "Job %s has status %s and can not be added to", theJobId, job.getStatus());
ValidateUtil.isTrueOrThrowInvalidRequest(job.getStatus() == BulkImportJobStatusEnum.STAGING, "bijob id %s has status %s and can not be added to", theBiJobId, job.getStatus());
addFilesToJob(theFiles, job, job.getFileCount());
@ -132,20 +132,20 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
myJobDao.save(job);
}
private BulkImportJobEntity findJobByJobId(String theJobId) {
private BulkImportJobEntity findJobByBiJobId(String theBiJobId) {
BulkImportJobEntity job = myJobDao
.findByJobId(theJobId)
.orElseThrow(() -> new InvalidRequestException("Unknown job ID: " + theJobId));
.findByJobId(theBiJobId)
.orElseThrow(() -> new InvalidRequestException("Unknown bijob id: " + theBiJobId));
return job;
}
@Override
@Transactional
public void markJobAsReadyForActivation(String theJobId) {
ourLog.info("Activating bulk import job {}", theJobId);
public void markJobAsReadyForActivation(String theBiJobId) {
ourLog.info("Activating bulk import bijob {}", theBiJobId);
BulkImportJobEntity job = findJobByJobId(theJobId);
ValidateUtil.isTrueOrThrowInvalidRequest(job.getStatus() == BulkImportJobStatusEnum.STAGING, "Bulk import job %s can not be activated in status: %s", theJobId, job.getStatus());
BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
ValidateUtil.isTrueOrThrowInvalidRequest(job.getStatus() == BulkImportJobStatusEnum.STAGING, "Bulk import bijob %s can not be activated in status: %s", theBiJobId, job.getStatus());
job.setStatus(BulkImportJobStatusEnum.READY);
myJobDao.save(job);
@ -168,7 +168,9 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
}
try {
return doActivateNextReadyJob();
ActivateJobResult retval = doActivateNextReadyJob();
ourLog.info("Batch job submitted with batch job id {}", retval.jobId);
return retval;
} finally {
myRunningJobSemaphore.release();
}
@ -191,9 +193,9 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
BulkImportJobEntity bulkImportJobEntity = jobToProcessOpt.get();
String jobUuid = bulkImportJobEntity.getJobId();
String batchJobId = null;
String biJobId = null;
try {
batchJobId = processJob(bulkImportJobEntity);
biJobId = processJob(bulkImportJobEntity);
} catch (Exception e) {
ourLog.error("Failure while preparing bulk export extract", e);
myTxTemplate.execute(t -> {
@ -208,18 +210,18 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
});
}
return new ActivateJobResult(true, batchJobId);
return new ActivateJobResult(true, biJobId);
}
@Override
@Transactional
public void setJobToStatus(String theJobId, BulkImportJobStatusEnum theStatus) {
setJobToStatus(theJobId, theStatus, null);
public void setJobToStatus(String theBiJobId, BulkImportJobStatusEnum theStatus) {
setJobToStatus(theBiJobId, theStatus, null);
}
@Override
public void setJobToStatus(String theJobId, BulkImportJobStatusEnum theStatus, String theStatusMessage) {
BulkImportJobEntity job = findJobByJobId(theJobId);
public void setJobToStatus(String theBiJobId, BulkImportJobStatusEnum theStatus, String theStatusMessage) {
BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
job.setStatus(theStatus);
job.setStatusMessage(theStatusMessage);
myJobDao.save(job);
@ -227,14 +229,14 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
@Override
@Transactional
public BulkImportJobJson fetchJob(String theJobId) {
BulkImportJobEntity job = findJobByJobId(theJobId);
public BulkImportJobJson fetchJob(String theBiJobId) {
BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
return job.toJson();
}
@Override
public JobInfo getJobStatus(String theJobId) {
BulkImportJobEntity theJob = findJobByJobId(theJobId);
public JobInfo getJobStatus(String theBiJobId) {
BulkImportJobEntity theJob = findJobByBiJobId(theBiJobId);
return new JobInfo()
.setStatus(theJob.getStatus())
.setStatusMessage(theJob.getStatusMessage())
@ -243,28 +245,28 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
@Transactional
@Override
public BulkImportJobFileJson fetchFile(String theJobId, int theFileIndex) {
BulkImportJobEntity job = findJobByJobId(theJobId);
public BulkImportJobFileJson fetchFile(String theBiJobId, int theFileIndex) {
BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
return myJobFileDao
.findForJob(job, theFileIndex)
.map(t -> t.toJson())
.orElseThrow(() -> new IllegalArgumentException("Invalid index " + theFileIndex + " for job " + theJobId));
.orElseThrow(() -> new IllegalArgumentException("Invalid index " + theFileIndex + " for bijob " + theBiJobId));
}
@Transactional
@Override
public String getFileDescription(String theJobId, int theFileIndex) {
BulkImportJobEntity job = findJobByJobId(theJobId);
public String getFileDescription(String theBiJobId, int theFileIndex) {
BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
return myJobFileDao.findFileDescriptionForJob(job, theFileIndex).orElse("");
}
@Override
@Transactional
public void deleteJobFiles(String theJobId) {
BulkImportJobEntity job = findJobByJobId(theJobId);
List<Long> files = myJobFileDao.findAllIdsForJob(theJobId);
public void deleteJobFiles(String theBiJobId) {
BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
List<Long> files = myJobFileDao.findAllIdsForJob(theBiJobId);
for (Long next : files) {
myJobFileDao.deleteById(next);
}
@ -272,18 +274,18 @@ public class BulkDataImportSvcImpl implements IBulkDataImportSvc {
}
private String processJob(BulkImportJobEntity theBulkExportJobEntity) {
String jobId = theBulkExportJobEntity.getJobId();
String biJobId = theBulkExportJobEntity.getJobId();
int batchSize = theBulkExportJobEntity.getBatchSize();
Batch2BulkImportPullJobParameters jobParameters = new Batch2BulkImportPullJobParameters();
jobParameters.setJobId(jobId);
jobParameters.setJobId(biJobId);
jobParameters.setBatchSize(batchSize);
JobInstanceStartRequest request = new JobInstanceStartRequest();
request.setJobDefinitionId(BatchConstants.BULK_IMPORT_JOB_NAME);
request.setParameters(jobParameters);
ourLog.info("Submitting bulk import job {} to job scheduler", jobId);
ourLog.info("Submitting bulk import with bijob id {} to job scheduler", biJobId);
return myJobCoordinator.startInstance(request).getJobId();
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -166,14 +166,15 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private int getMaxFetchSize(SearchParameterMap theParams, Integer theMax) {
if (theParams.getCount() != null) {
return theParams.getCount();
}
if (theMax != null) {
return theMax;
}
// wipmb we should really pass this in.
if (theParams.getCount() != null) {
return theParams.getCount();
}
return DEFAULT_MAX_NON_PAGED_SIZE;
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/LastNAggregation.java
View File

@ -23,6 +23,8 @@ package ca.uhn.fhir.jpa.dao.search;
import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import java.util.List;
@ -36,6 +38,7 @@ import static ca.uhn.fhir.jpa.model.search.HSearchIndexWriter.SEARCH_PARAM_ROOT;
* Builds lastN aggregation, and parse the results
*/
public class LastNAggregation {
private static final Logger ourLog = LoggerFactory.getLogger(LastNAggregation.class);
static final String SP_SUBJECT = SEARCH_PARAM_ROOT + ".subject.reference.value";
private static final String SP_CODE_TOKEN_CODE_AND_SYSTEM = SEARCH_PARAM_ROOT + ".code.token.code-system";
private static final String SP_DATE_DT_UPPER = SEARCH_PARAM_ROOT + ".date.dt.upper";
@ -167,6 +170,7 @@ public class LastNAggregation {
* </pre>
*/
public List<Long> extractResourceIds(@Nonnull JsonObject theAggregationResult) {
ourLog.trace("extractResourceIds - hasSubject {} aggregation {}", myAggregateOnSubject, theAggregationResult);
Stream<JsonObject> resultBuckets = Stream.of(theAggregationResult);
// was it grouped by subject?

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ResourceNotFoundInIndexException.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao.search;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* 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%
*/
public class ResourceNotFoundInIndexException extends IllegalStateException {
private static final long serialVersionUID = 1L;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceReindexJobEntity.java
View File

@ -37,6 +37,9 @@ import javax.persistence.TemporalType;
import java.io.Serializable;
import java.util.Date;
/**
* @deprecated use new batch2 reindex job
*/
@Deprecated
@Entity
@Table(name = "HFJ_RES_REINDEX_JOB")

2
hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE27-SNAPSHOT</version>
<version>6.2.0-PRE1-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

17
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/config/ElasticsearchWithPrefixConfig.java
View File

@ -7,9 +7,10 @@ import ca.uhn.fhir.jpa.dao.r4.ElasticsearchPrefixTest;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
import ca.uhn.fhir.jpa.search.elastic.TestElasticsearchContainerHelper;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
import ca.uhn.fhir.jpa.test.config.BlockLargeNumbersOfParamsListener;
import ca.uhn.fhir.jpa.test.config.TestElasticsearchContainerHelper;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
@ -26,9 +27,11 @@ import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
@ -43,6 +46,7 @@ import java.util.concurrent.TimeUnit;
* We need to do this as it is during bean creation that HS bootstrapping occurs.
*/
@Configuration
@Import(TestHSearchAddInConfig.PooledElasticsearchContainerConfig.class)
public class ElasticsearchWithPrefixConfig {
@Bean
@ -93,6 +97,7 @@ public class ElasticsearchWithPrefixConfig {
return dataSource;
}
@Autowired ElasticsearchContainer myElasticsearchContainer;
@Bean
public Properties jpaProperties() {
Properties extraProperties = new Properties();
@ -102,8 +107,8 @@ public class ElasticsearchWithPrefixConfig {
extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
//Override default lucene settings
// Force elasticsearch to start first
int httpPort = elasticContainer().getMappedPort(9200);//9200 is the HTTP port
String host = elasticContainer().getHost();
int httpPort = myElasticsearchContainer.getMappedPort(9200);//9200 is the HTTP port
String host = myElasticsearchContainer.getHost();
// the below properties are used for ElasticSearch integration
extraProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "elasticsearch");
extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.ANALYSIS_CONFIGURER),
@ -137,10 +142,4 @@ public class ElasticsearchWithPrefixConfig {
return extraProperties;
}
@Bean
public ElasticsearchContainer elasticContainer() {
ElasticsearchContainer embeddedElasticSearch = TestElasticsearchContainerHelper.getEmbeddedElasticSearch();
embeddedElasticSearch.start();
return embeddedElasticSearch;
}
}

20
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticHSearch.java Normal file
View File

@ -0,0 +1,20 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
/**
* Combined config so we consistently share app contexts.
*
* Spring uses the context classes as the key for reuse between classes,
* so let's try to use the same config as much as we can.
*/
@Configuration
@Import({
TestR4Config.class,
TestHSearchAddInConfig.Elasticsearch.class
})
public class TestR4ConfigWithElasticHSearch {
}

59
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java
View File

@ -4,11 +4,10 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.param.DateAndListParam;
import ca.uhn.fhir.rest.param.DateOrListParam;
import ca.uhn.fhir.rest.param.DateParam;
@ -29,9 +28,12 @@ import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
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.beans.factory.annotation.Qualifier;
import org.springframework.boot.test.mock.mockito.SpyBean;
@ -54,19 +56,21 @@ import static org.mockito.Mockito.when;
@ExtendWith(SpringExtension.class)
@RequiresDocker
@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.Elasticsearch.class})
@ContextConfiguration(classes=TestR4ConfigWithElasticHSearch.class)
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
abstract public class BaseR4SearchLastN extends BaseJpaTest {
private static final Logger ourLog = LoggerFactory.getLogger(BaseR4SearchLastN.class);
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<>();
// wipmb make thise normal fields. This static setup wasn't working
protected static IIdType patient0Id = null;
protected static IIdType patient1Id = null;
protected static IIdType patient2Id = null;
// 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 Calendar observationDate = new GregorianCalendar();
protected final String observationCd0 = "code0";
protected final String observationCd1 = "code1";
@ -108,35 +112,35 @@ abstract public class BaseR4SearchLastN extends BaseJpaTest {
myDaoConfig.setLastNEnabled(new DaoConfig().isLastNEnabled());
}
@BeforeEach
@BeforeAll
public void beforeCreateTestPatientsAndObservations() throws IOException {
ourLog.info("setup Patients and Observations");
myDaoConfig.setLastNEnabled(true);
// enabled to also create extended lucene index during creation of test data
boolean hsearchSaved = myDaoConfig.isAdvancedHSearchIndexing();
myDaoConfig.setAdvancedHSearchIndexing(true);
// Using a static flag to ensure that test data and elasticsearch index is only created once.
// Creating this data and the index is time consuming and as such want to avoid having to repeat for each test.
// Normally would use a static @BeforeClass method for this purpose, but Autowired objects cannot be accessed in static methods.
if (!dataLoaded || patient0Id == null) {
// enabled to also create extended lucene index during creation of test data
myDaoConfig.setAdvancedHSearchIndexing(true);
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;
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
// turn off the setting enabled earlier
myDaoConfig.setAdvancedHSearchIndexing(false);
}
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);
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
// turn off the setting enabled earlier
myDaoConfig.setAdvancedHSearchIndexing(hsearchSaved);
}
@ -211,6 +215,7 @@ abstract public class BaseR4SearchLastN extends BaseJpaTest {
@Test
public void testLastNNoPatients() {
ourLog.info("testLastNNoPatients lastn {} hsearch {}", myDaoConfig.isLastNEnabled(), myDaoConfig.isAdvancedHSearchIndexing());
SearchParameterMap params = new SearchParameterMap();

4
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/ElasticsearchPrefixTest.java
View File

@ -11,6 +11,7 @@ import org.elasticsearch.client.RestHighLevelClient;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
@ -19,9 +20,12 @@ import java.io.IOException;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.springframework.test.annotation.DirtiesContext.ClassMode.AFTER_CLASS;
@RequiresDocker
@ExtendWith(SpringExtension.class)
// we don't reuse this context, so discard it and release our elastic container.
@DirtiesContext(classMode = AFTER_CLASS)
@ContextConfiguration(classes = {ElasticsearchWithPrefixConfig.class})
public class ElasticsearchPrefixTest {

2
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java
View File

@ -58,6 +58,8 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
SearchBuilder.setMaxPageSize50ForTest(true);
myDaoConfig.setLastNEnabled(true);
}
@AfterEach

6
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
View File

@ -11,6 +11,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.ArgumentCaptor;
@ -33,6 +34,11 @@ import static org.mockito.Mockito.when;
@ExtendWith(SpringExtension.class)
public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
@BeforeEach
public void enableAdvancedHSearchIndexing() {
myDaoConfig.setLastNEnabled(true);
}
@AfterEach
public void reset() {
SearchBuilder.setMaxPageSize50ForTest(false);

1
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNUsingExtendedHSearchIndexAsyncIT.java
View File

@ -15,6 +15,7 @@ public class FhirResourceDaoR4SearchLastNUsingExtendedHSearchIndexAsyncIT extend
@BeforeEach
public void enableAdvancedHSearchIndexing() {
myDaoConfig.setLastNEnabled(true);
myDaoConfig.setAdvancedHSearchIndexing(true);
}

6
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNUsingExtendedHSearchIndexIT.java
View File

@ -9,6 +9,8 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.Mockito;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.junit.jupiter.SpringExtension;
@ -22,6 +24,7 @@ import java.util.List;
*/
@ExtendWith(SpringExtension.class)
public class FhirResourceDaoR4SearchLastNUsingExtendedHSearchIndexIT extends FhirResourceDaoR4SearchLastNIT {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchLastNUsingExtendedHSearchIndexIT.class);
@Autowired
private TestHSearchEventDispatcher myHSearchEventDispatcher;
@ -32,8 +35,11 @@ public class FhirResourceDaoR4SearchLastNUsingExtendedHSearchIndexIT extends Fhi
@BeforeEach
public void enableAdvancedHSearchIndexing() {
myDaoConfig.setLastNEnabled(true);
myDaoConfig.setAdvancedHSearchIndexing(true);
myHSearchEventDispatcher.register(mySearchEventListener);
ourLog.info("enableAdvancedHSearchIndexing finished. lastn {} advancedHSearchIndexing {}", myDaoConfig.isLastNEnabled(), myDaoConfig.isAdvancedHSearchIndexing());
}
@AfterEach

16
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java
View File

@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.dao.IHSearchEventListener;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
@ -26,8 +27,6 @@ import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.test.util.TestHSearchEventDispatcher;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
@ -91,6 +90,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.ContextHierarchy;
import org.springframework.test.context.TestContext;
import org.springframework.test.context.TestExecutionListeners;
import org.springframework.test.context.junit.jupiter.SpringExtension;
@ -136,11 +136,13 @@ import static org.mockito.Mockito.when;
@ExtendWith(SpringExtension.class)
@ExtendWith(MockitoExtension.class)
@RequiresDocker
@ContextConfiguration(classes = {
TestR4Config.class,
TestHSearchAddInConfig.Elasticsearch.class,
DaoTestDataBuilder.Config.class,
TestDaoSearch.Config.class
// wipmb hierarchy for context
@ContextHierarchy({
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class),
@ContextConfiguration(classes = {
DaoTestDataBuilder.Config.class,
TestDaoSearch.Config.class
})
})
@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
@TestExecutionListeners(listeners = {

5
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyElasticsearchIT.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -14,8 +15,6 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@ -51,7 +50,7 @@ import static org.mockito.Mockito.when;
@ExtendWith(SpringExtension.class)
@RequiresDocker
@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.Elasticsearch.class})
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class)
public class FhirResourceDaoR4TerminologyElasticsearchIT extends BaseJpaTest {
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";

15
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/HSearchSandboxTest.java
View File

@ -5,12 +5,11 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityParam;
@ -39,6 +38,7 @@ import org.junit.jupiter.api.extension.ExtendWith;
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.ContextHierarchy;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.transaction.PlatformTransactionManager;
@ -58,11 +58,12 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
*/
@ExtendWith(SpringExtension.class)
@RequiresDocker
@ContextConfiguration(classes = {
TestR4Config.class,
TestHSearchAddInConfig.Elasticsearch.class,
DaoTestDataBuilder.Config.class,
TestDaoSearch.Config.class
@ContextHierarchy({
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class),
@ContextConfiguration(classes = {
DaoTestDataBuilder.Config.class,
TestDaoSearch.Config.class
})
})
@Disabled
public class HSearchSandboxTest extends BaseJpaTest {

254
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/PersistObservationIndexedSearchParamLastNR4IT.java
View File

@ -3,14 +3,13 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
@ -63,7 +62,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
@ExtendWith(SpringExtension.class)
@RequiresDocker
@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.Elasticsearch.class})
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class PersistObservationIndexedSearchParamLastNR4IT {
@ -105,50 +104,50 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
myDaoConfig.setLastNEnabled(new DaoConfig().isLastNEnabled());
}
@Order(3)
@Order(0)
@Test
public void testIndexObservationSingle() throws IOException {
indexSingleObservation();
public void testDeleteObservation() throws IOException {
indexMultipleObservations();
SearchParameterMap searchParameterMap = new SearchParameterMap();
searchParameterMap.setLastNMax(10);
List<ObservationJson> persistedObservationEntities = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
assertEquals(1, persistedObservationEntities.size());
ObservationJson persistedObservationEntity = persistedObservationEntities.get(0);
assertEquals(SINGLE_SUBJECT_ID, persistedObservationEntity.getSubject());
assertEquals(SINGLE_OBSERVATION_PID, persistedObservationEntity.getIdentifier());
assertEquals(SINGLE_EFFECTIVEDTM, persistedObservationEntity.getEffectiveDtm());
String observationCodeNormalizedId = persistedObservationEntity.getCode_concept_id();
// List<CodeJson> persistedObservationCodes = elasticsearchSvc.queryAllIndexedObservationCodesForTest();
// assertEquals(1, persistedObservationCodes.size());
// Check that we can retrieve code by hash value.
String codeSystemHash = persistedObservationEntity.getCode_coding_code_system_hash();
CodeJson persistedObservationCode = elasticsearchSvc.getObservationCodeDocument(codeSystemHash, null);
assertNotNull(persistedObservationCode);
assertEquals(observationCodeNormalizedId, persistedObservationCode.getCodeableConceptId());
assertEquals(SINGLE_OBSERVATION_CODE_TEXT, persistedObservationCode.getCodeableConceptText());
// Also confirm that we can retrieve code by text value.
persistedObservationCode = elasticsearchSvc.getObservationCodeDocument(null, SINGLE_OBSERVATION_CODE_TEXT);
assertNotNull(persistedObservationCode);
searchParameterMap.setLastNMax(100);
List<ObservationJson> observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
assertEquals(100, observationDocuments.size());
// Check that fifth observation for fifth patient has been indexed.
ObservationJson observation = elasticsearchSvc.getObservationDocument("55");
assertNotNull(observation);
searchParameterMap = new SearchParameterMap();
ReferenceParam subjectParam = new ReferenceParam("Patient", "", SINGLE_SUBJECT_ID);
searchParameterMap.add(Observation.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().addOr(subjectParam)));
TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE);
searchParameterMap.add(Observation.SP_CATEGORY, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(categoryParam)));
TokenParam codeParam = new TokenParam(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE);
searchParameterMap.add(Observation.SP_CODE, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(codeParam)));
searchParameterMap.setLastNMax(3);
searchParameterMap.add(Observation.SP_SUBJECT, multiSubjectParams);
searchParameterMap.setLastNMax(10);
List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(100, observationIdsOnly.size());
assertTrue(observationIdsOnly.contains("55"));
List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 100);
// Delete fifth observation for fifth patient.
ResourceTable entity = new ResourceTable();
entity.setId(55L);
entity.setResourceType("Observation");
entity.setVersion(0L);
testObservationPersist.deleteObservationIndex(entity);
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
// Confirm that observation was deleted.
searchParameterMap = new SearchParameterMap();
searchParameterMap.setLastNMax(100);
observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
assertEquals(99, observationDocuments.size());
observation = elasticsearchSvc.getObservationDocument("55");
assertNull(observation);
observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(99, observationIdsOnly.size());
assertTrue(!observationIdsOnly.contains("55"));
assertEquals(1, observationIdsOnly.size());
assertEquals(SINGLE_OBSERVATION_PID, observationIdsOnly.get(0));
}
private void indexSingleObservation() throws IOException {
Observation myObservation = new Observation();
@ -206,6 +205,63 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
return codeableConceptField;
}
@Order(1)
@Test
public void testSampleBundleInTransaction() throws IOException {
FhirContext myFhirCtx = FhirContext.forR4Cached();
PathMatchingResourcePatternResolver provider = new PathMatchingResourcePatternResolver();
final Resource[] bundleResources = provider.getResources("lastntestbundle.json");
assertEquals(1, bundleResources.length);
AtomicInteger index = new AtomicInteger();
Arrays.stream(bundleResources).forEach(
resource -> {
index.incrementAndGet();
InputStream resIs = null;
String nextBundleString;
try {
resIs = resource.getInputStream();
nextBundleString = IOUtils.toString(resIs, Charsets.UTF_8);
} catch (IOException e) {
return;
} finally {
try {
if (resIs != null) {
resIs.close();
}
} catch (final IOException ioe) {
// ignore
}
}
IParser parser = myFhirCtx.newJsonParser();
Bundle bundle = parser.parseResource(Bundle.class, nextBundleString);
myDao.transaction(null, bundle);
}
);
elasticsearchSvc.refreshIndex("*");
SearchParameterMap searchParameterMap = new SearchParameterMap();
// execute Observation ID search - Composite Aggregation
searchParameterMap.setLastNMax(1);
List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(20, observationIdsOnly.size());
searchParameterMap.setLastNMax(3);
observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(38, observationIdsOnly.size());
}
@Order(2)
@Test
public void testIndexObservationMultiple() throws IOException {
@ -309,46 +365,48 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
}
@Order(0)
@Order(3)
@Test
public void testDeleteObservation() throws IOException {
indexMultipleObservations();
public void testIndexObservationSingle() throws IOException {
indexSingleObservation();
SearchParameterMap searchParameterMap = new SearchParameterMap();
searchParameterMap.setLastNMax(100);
List<ObservationJson> observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
assertEquals(100, observationDocuments.size());
// Check that fifth observation for fifth patient has been indexed.
ObservationJson observation = elasticsearchSvc.getObservationDocument("55");
assertNotNull(observation);
searchParameterMap = new SearchParameterMap();
searchParameterMap.add(Observation.SP_SUBJECT, multiSubjectParams);
searchParameterMap.setLastNMax(10);
List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(100, observationIdsOnly.size());
assertTrue(observationIdsOnly.contains("55"));
List<ObservationJson> persistedObservationEntities = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
assertEquals(1, persistedObservationEntities.size());
ObservationJson persistedObservationEntity = persistedObservationEntities.get(0);
assertEquals(SINGLE_SUBJECT_ID, persistedObservationEntity.getSubject());
assertEquals(SINGLE_OBSERVATION_PID, persistedObservationEntity.getIdentifier());
assertEquals(SINGLE_EFFECTIVEDTM, persistedObservationEntity.getEffectiveDtm());
// Delete fifth observation for fifth patient.
ResourceTable entity = new ResourceTable();
entity.setId(55L);
entity.setResourceType("Observation");
entity.setVersion(0L);
String observationCodeNormalizedId = persistedObservationEntity.getCode_concept_id();
testObservationPersist.deleteObservationIndex(entity);
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
// List<CodeJson> persistedObservationCodes = elasticsearchSvc.queryAllIndexedObservationCodesForTest();
// assertEquals(1, persistedObservationCodes.size());
// Check that we can retrieve code by hash value.
String codeSystemHash = persistedObservationEntity.getCode_coding_code_system_hash();
CodeJson persistedObservationCode = elasticsearchSvc.getObservationCodeDocument(codeSystemHash, null);
assertNotNull(persistedObservationCode);
assertEquals(observationCodeNormalizedId, persistedObservationCode.getCodeableConceptId());
assertEquals(SINGLE_OBSERVATION_CODE_TEXT, persistedObservationCode.getCodeableConceptText());
// Also confirm that we can retrieve code by text value.
persistedObservationCode = elasticsearchSvc.getObservationCodeDocument(null, SINGLE_OBSERVATION_CODE_TEXT);
assertNotNull(persistedObservationCode);
// Confirm that observation was deleted.
searchParameterMap = new SearchParameterMap();
searchParameterMap.setLastNMax(100);
observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
assertEquals(99, observationDocuments.size());
observation = elasticsearchSvc.getObservationDocument("55");
assertNull(observation);
ReferenceParam subjectParam = new ReferenceParam("Patient", "", SINGLE_SUBJECT_ID);
searchParameterMap.add(Observation.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().addOr(subjectParam)));
TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE);
searchParameterMap.add(Observation.SP_CATEGORY, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(categoryParam)));
TokenParam codeParam = new TokenParam(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE);
searchParameterMap.add(Observation.SP_CODE, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(codeParam)));
searchParameterMap.setLastNMax(3);
observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(99, observationIdsOnly.size());
assertTrue(!observationIdsOnly.contains("55"));
List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 100);
assertEquals(1, observationIdsOnly.size());
assertEquals(SINGLE_OBSERVATION_PID, observationIdsOnly.get(0));
}
@Order(4)
@ -412,61 +470,5 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
}
@Order(1)
@Test
public void testSampleBundleInTransaction() throws IOException {
FhirContext myFhirCtx = FhirContext.forR4Cached();
PathMatchingResourcePatternResolver provider = new PathMatchingResourcePatternResolver();
final Resource[] bundleResources;
bundleResources = provider.getResources("lastntestbundle.json");
AtomicInteger index = new AtomicInteger();
Arrays.stream(bundleResources).forEach(
resource -> {
index.incrementAndGet();
InputStream resIs = null;
String nextBundleString;
try {
resIs = resource.getInputStream();
nextBundleString = IOUtils.toString(resIs, Charsets.UTF_8);
} catch (IOException e) {
return;
} finally {
try {
if (resIs != null) {
resIs.close();
}
} catch (final IOException ioe) {
// ignore
}
}
IParser parser = myFhirCtx.newJsonParser();
Bundle bundle = parser.parseResource(Bundle.class, nextBundleString);
myDao.transaction(null, bundle);
}
);
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
SearchParameterMap searchParameterMap = new SearchParameterMap();
// execute Observation ID search - Composite Aggregation
searchParameterMap.setLastNMax(1);
List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(20, observationIdsOnly.size());
searchParameterMap.setLastNMax(3);
observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
assertEquals(38, observationIdsOnly.size());
}
}

4
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ElasticTest.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.test.utilities.docker.RequiresDocker;
import org.apache.commons.io.IOUtils;
@ -50,7 +50,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
@ExtendWith(SpringExtension.class)
@RequiresDocker
@ContextConfiguration(classes = TestHSearchAddInConfig.Elasticsearch.class)
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class)
public class ResourceProviderR4ElasticTest extends BaseResourceProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderR4ElasticTest.class);

22
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/search/autocomplete/TokenAutocompleteElasticsearchIT.java
View File

@ -6,12 +6,12 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.storage.test.DaoTestDataBuilder;
@ -26,12 +26,14 @@ import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Observation;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
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.ContextHierarchy;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
@ -49,10 +51,12 @@ import static org.hamcrest.Matchers.not;
@ExtendWith(SpringExtension.class)
@RequiresDocker
@ContextConfiguration(classes = {
TestR4Config.class,
TestHSearchAddInConfig.Elasticsearch.class,
DaoTestDataBuilder.Config.class
@ContextHierarchy({
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class),
@ContextConfiguration(classes = {
DaoTestDataBuilder.Config.class,
TestDaoSearch.Config.class
})
})
public class TokenAutocompleteElasticsearchIT extends BaseJpaTest {
public static final Coding erythrocyte_by_volume = new Coding("http://loinc.org", "789-8", "Erythrocytes [#/volume] in Blood by Automated count");
@ -96,6 +100,12 @@ public class TokenAutocompleteElasticsearchIT extends BaseJpaTest {
myDaoConfig.setAdvancedHSearchIndexing(true);
}
@AfterEach
void resetConfig() {
DaoConfig defaultConfig = new DaoConfig();
myDaoConfig.setAdvancedHSearchIndexing(defaultConfig.isAdvancedHSearchIndexing());
}
@Override
protected FhirContext getFhirContext() {
return myFhirCtx;

21
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/search/elastic/TestElasticsearchContainerHelper.java
View File

@ -1,21 +0,0 @@
package ca.uhn.fhir.jpa.search.elastic;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
import java.time.Duration;
import static java.time.temporal.ChronoUnit.SECONDS;
public class TestElasticsearchContainerHelper {
public static final String ELASTICSEARCH_VERSION = "7.16.3";
public static final String ELASTICSEARCH_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTICSEARCH_VERSION;
public static ElasticsearchContainer getEmbeddedElasticSearch() {
return new ElasticsearchContainer(ELASTICSEARCH_IMAGE)
.withStartupTimeout(Duration.of(300, SECONDS));
}
}

2
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsIT.java
View File

@ -2,10 +2,10 @@ package ca.uhn.fhir.jpa.search.lastn;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.search.elastic.TestElasticsearchContainerHelper;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.config.TestElasticsearchContainerHelper;
import ca.uhn.fhir.rest.param.DateAndListParam;
import ca.uhn.fhir.rest.param.DateOrListParam;
import ca.uhn.fhir.rest.param.DateParam;

2
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcSingleObservationIT.java
View File

@ -3,10 +3,10 @@ package ca.uhn.fhir.jpa.search.lastn;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
import ca.uhn.fhir.jpa.search.elastic.TestElasticsearchContainerHelper;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.test.config.TestElasticsearchContainerHelper;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;

5
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java
View File

@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -19,8 +20,6 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.test.BaseJpaTest;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -56,7 +55,7 @@ import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.Elasticsearch.class})
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class)
@RequiresDocker
public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {

5
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetHSearchExpansionR4ElasticIT.java
View File

@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
import ca.uhn.fhir.jpa.test.config.TestR4Config;
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
@ -10,7 +9,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
* This class runs all parent class tests using Elasticsearch configuration
*/
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {TestR4Config.class, TestHSearchAddInConfig.Elasticsearch.class})
@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class)
public class ValueSetHSearchExpansionR4ElasticIT extends AbstractValueSetHSearchExpansionR4Test {
}

0
hapi-fhir-jpaserver-test-utilities/src/test/resources/lastntestbundle.json → hapi-fhir-jpaserver-elastic-test-utilities/src/test/resources/lastntestbundle.json
View File

4
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestElasticsearchContainerHelper.java
View File

@ -35,6 +35,10 @@ public class TestElasticsearchContainerHelper {
public static ElasticsearchContainer getEmbeddedElasticSearch() {
return new ElasticsearchContainer(ELASTICSEARCH_IMAGE)
// the default is 4GB which is too much for our little tests
.withEnv("ES_JAVA_OPTS", "-Xms512m -Xmx512m")
// turn off security warnings
.withEnv("xpack.security.enabled", "false")
.withStartupTimeout(Duration.of(300, SECONDS));
}

32
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/config/TestHSearchAddInConfig.java
View File

@ -37,8 +37,10 @@ import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
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.context.annotation.Import;
import org.springframework.context.annotation.Primary;
import org.testcontainers.elasticsearch.ElasticsearchContainer;
@ -177,7 +179,11 @@ public class TestHSearchAddInConfig {
* Make sure you add {@link RequiresDocker} annotation to any uses.
*/
@Configuration
@Import(PooledElasticsearchContainerConfig.class)
public static class Elasticsearch {
@Autowired
ElasticsearchContainer myElasticsearchContainer;
@Bean
@Primary // override the default
IHSearchConfigurer hibernateSearchConfigurer(ElasticsearchContainer theContainer) {
@ -208,18 +214,6 @@ public class TestHSearchAddInConfig {
return new TestHSearchEventDispatcher();
}
@Bean
public ElasticsearchContainer elasticContainer() {
ElasticsearchContainer embeddedElasticSearch = TestElasticsearchContainerHelper.getEmbeddedElasticSearch();
embeddedElasticSearch.start();
return embeddedElasticSearch;
}
@PreDestroy
public void stop() {
elasticContainer().stop();
}
@Bean
public PartitionSettings partitionSettings() {
return new PartitionSettings();
@ -227,8 +221,8 @@ public class TestHSearchAddInConfig {
@Bean()
public ElasticsearchSvcImpl myElasticsearchSvc() {
int elasticsearchPort = elasticContainer().getMappedPort(9200);
String host = elasticContainer().getHost();
int elasticsearchPort = myElasticsearchContainer.getMappedPort(9200);
String host = myElasticsearchContainer.getHost();
return new ElasticsearchSvcImpl("http", host + ":" + elasticsearchPort, null, null);
}
@ -236,6 +230,16 @@ public class TestHSearchAddInConfig {
public void stopEsClient() throws IOException {
myElasticsearchSvc().close();
}
}
@Configuration
public static class PooledElasticsearchContainerConfig {
@Bean
public ElasticsearchContainer elasticContainer() {
ElasticsearchContainer embeddedElasticSearch = TestElasticsearchContainerHelper.getEmbeddedElasticSearch();
embeddedElasticSearch.start();
return embeddedElasticSearch;
}
}
}

9
hapi-fhir-jpaserver-test-utilities/src/test/resources/logback-test.xml → hapi-fhir-jpaserver-test-utilities/src/main/resources/logback-test.xml
View File

@ -49,13 +49,14 @@
<appender-ref ref="STDOUT" />
</logger>
<logger name="org.elasticsearch.client" additivity="true" level="trace"/>
<!--
<logger name="ca.uhn.fhir.jpa.model.search" additivity="false" level="debug"/>
<logger name="org.elasticsearch.client" additivity="true" level="trace"/>
<logger name="org.hibernate.search.elasticsearch.request" additivity="false" level="trace"/>
<logger name="org.hibernate.search" level="TRACE"/>
<logger name="org.hibernate.search.query" level="TRACE"/>
<logger name="org.hibernate.search.elasticsearch.request" level="TRACE"/>
<logger name="org.hibernate.search" additivity="false" level="TRACE"/>
<logger name="org.hibernate.search.query" additivity="false" level="TRACE"/>
<logger name="org.hibernate.search.elasticsearch.request" additivity="false" level="TRACE"/>
-->
<!-- See https://docs.jboss.org/hibernate/stable/search/reference/en-US/html_single/#backend-lucene-io-writer-infostream for lucene logging
<logger name="org.hibernate.search.backend.lucene.infostream" level="TRACE"/> -->

6
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportSvcImplTest.java
View File

@ -8,9 +8,9 @@ import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobDao;
import ca.uhn.fhir.jpa.dao.data.IBulkImportJobFileDao;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.BulkImportJobEntity;
import ca.uhn.fhir.jpa.entity.BulkImportJobFileEntity;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import com.google.common.collect.Lists;
@ -99,7 +99,7 @@ public class BulkDataImportSvcImplTest extends BaseJpaR4Test {
try {
mySvc.addFilesToJob("ABCDEFG", Lists.newArrayList(file3));
} catch (InvalidRequestException e) {
assertEquals("Unknown job ID: ABCDEFG", e.getMessage());
assertEquals("Unknown bijob id: ABCDEFG", e.getMessage());
}
}
@ -119,7 +119,7 @@ public class BulkDataImportSvcImplTest extends BaseJpaR4Test {
try {
mySvc.addFilesToJob("ABCDEFG", Lists.newArrayList(file3));
} catch (InvalidRequestException e) {
assertEquals(Msg.code(1769) + "Job ABCDEFG has status RUNNING and can not be added to", e.getMessage());
assertEquals(Msg.code(1769) + "bijob id ABCDEFG has status RUNNING and can not be added to", e.getMessage());
}
}

5
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ComboUniqueParamTest.java
View File

@ -35,6 +35,7 @@ import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.SearchParameter;
import org.hl7.fhir.r4.model.ServiceRequest;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Tag;
import org.junit.jupiter.api.Test;
import org.springframework.transaction.TransactionStatus;
@ -65,6 +66,10 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ComboUniqueParamTest.class);
@AfterEach
public void purgeUniqueIndexes() {
myResourceIndexedCompositeStringUniqueDao.deleteAll();
}
private void createUniqueBirthdateAndGenderSps() {
SearchParameter sp = new SearchParameter();

18
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchFtTest.java → hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchFtTest.java
View File

@ -243,16 +243,16 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, null, null, mockSrd()));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, null, null, null, mockSrd()));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, devId1)));
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obstext1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, null, param, null, mockSrd()));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, null, param, null, null, mockSrd()));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, devId1)));
request = mock(HttpServletRequest.class);
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, null, null, null, mockSrd()));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, null, null, null, null, mockSrd()));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId2, devId1)));
/*
@ -268,7 +268,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, null, null, mockSrd()));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, null, null, null, mockSrd()));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId4, devId1)));
/*
@ -284,7 +284,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, null, null, mockSrd()));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, null, param, null, null, null, mockSrd()));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId4)));
}
@ -335,11 +335,11 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, mockSrd(), null));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, null, mockSrd(), null));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, devId1)));
request = mock(HttpServletRequest.class);
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, null, null, null, mockSrd(), null));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, null, null, null, null, mockSrd(), null));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId1, obsId2, devId1, ptId2, obsId3)));
/*
@ -355,7 +355,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, mockSrd(), null));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, null, mockSrd(), null));
assertThat(actual, containsInAnyOrder(toValues(ptId1, ptId2, obsId1, obsId4, devId1)));
/*
@ -371,7 +371,7 @@ public class FhirResourceDaoR4SearchFtTest extends BaseJpaR4Test {
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, mockSrd(), null));
actual = toUnqualifiedVersionlessIdValues(myPatientDao.patientTypeEverything(request, null, null, null, null, param, null, null, null, mockSrd(), null));
assertThat(actual, containsInAnyOrder(toValues(ptId1, obsId4)));
}

20
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/importpull/BulkImportParameterValidator.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.importpull;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* 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.batch2.api.IJobParametersValidator;
import ca.uhn.fhir.batch2.importpull.models.Batch2BulkImportPullJobParameters;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;

20
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/importpull/BulkImportPullConfig.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.importpull;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* 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.batch2.importpull.models.Batch2BulkImportPullJobParameters;
import ca.uhn.fhir.batch2.importpull.models.BulkImportFilePartitionResult;
import ca.uhn.fhir.batch2.importpull.models.BulkImportRecord;

20
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/importpull/FetchPartitionedFilesStep.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.importpull;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* 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.batch2.api.IFirstJobStepWorker;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;

20
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/importpull/ReadInResourcesFromFileStep.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.importpull;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* 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.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;

20
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/importpull/WriteBundleForImportStep.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.jobs.importpull;
/*-
* #%L
* hapi-fhir-storage-batch2-jobs
* %%
* 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.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.ILastJobStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;

4
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/BaseDataSink.java
View File

@ -62,6 +62,10 @@ abstract class BaseDataSink<PT extends IModelJson, IT extends IModelJson, OT ext
return myJobWorkCursor.isFirstStep && getWorkChunkCount() == 0;
}
public boolean hasExactlyOneChunk() {
return getWorkChunkCount() == 1;
}
public JobDefinitionStep<PT,IT,OT> getTargetStep() {
return myJobWorkCursor.currentStep;
}

2
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/JobStepExecutor.java
View File

@ -101,7 +101,7 @@ public class JobStepExecutor<PT extends IModelJson, IT extends IModelJson, OT ex
jobInstance.setJobDefinition(myDefinition);
JobInstanceProgressCalculator calculator = new JobInstanceProgressCalculator(myJobPersistence, jobInstance, new JobChunkProgressAccumulator());
calculator.calculateAndStoreInstanceProgress();
} else {
} else if (theDataSink.hasExactlyOneChunk()) {
JobWorkNotification workNotification = new JobWorkNotification(jobInstance, myCursor.nextStep.getStepId(), ((JobDataSink<PT,IT,OT>) theDataSink).getOnlyChunkId());
myBatchJobSender.sendWorkChannelMessage(workNotification);
}

20
hapi-fhir-storage/src/main/java/ca/uhn/fhir/batch2/importpull/models/Batch2BulkImportPullJobParameters.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.importpull.models;
/*-
* #%L
* HAPI FHIR Storage 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.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;

20
hapi-fhir-storage/src/main/java/ca/uhn/fhir/batch2/importpull/models/BulkImportFilePartitionResult.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.importpull.models;
/*-
* #%L
* HAPI FHIR Storage 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.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;

20
hapi-fhir-storage/src/main/java/ca/uhn/fhir/batch2/importpull/models/BulkImportRecord.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.batch2.importpull.models;
/*-
* #%L
* HAPI FHIR Storage 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.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;

8
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoPatient.java
View File

@ -35,14 +35,6 @@ import javax.servlet.http.HttpServletRequest;
public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirResourceDao<T> {
default IBundleProvider patientInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdate, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, StringAndListParam theFilter, RequestDetails theRequestDetails){
return patientInstanceEverything(theServletRequest, theId, theCount, theOffset, theLastUpdate, theSort, theContent, theNarrative, theFilter, new StringAndListParam(), theRequestDetails);
}
default IBundleProvider patientTypeEverything(HttpServletRequest theServletRequest, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdated, SortSpec theSortSpec, StringAndListParam theContent, StringAndListParam theNarrative, StringAndListParam theFilter, RequestDetails theRequestDetails, TokenOrListParam theId){
return patientTypeEverything(theServletRequest, theCount, theOffset, theLastUpdated, theSortSpec, theContent, theNarrative, theFilter, new StringAndListParam(), theRequestDetails, theId);
}
IBundleProvider patientInstanceEverything(HttpServletRequest theServletRequest, IIdType theId, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdate, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative, StringAndListParam theFilter, StringAndListParam theTypes, RequestDetails theRequestDetails);
IBundleProvider patientTypeEverything(HttpServletRequest theServletRequest, IPrimitiveType<Integer> theCount, IPrimitiveType<Integer> theOffset, DateRangeParam theLastUpdated, SortSpec theSortSpec, StringAndListParam theContent, StringAndListParam theNarrative, StringAndListParam theFilter, StringAndListParam theTypes, RequestDetails theRequestDetails, TokenOrListParam theId);

20
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/model/ActivateJobResult.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.bulk.imprt.model;
/*-
* #%L
* HAPI FHIR Storage 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 javax.annotation.Nullable;
public class ActivateJobResult {

2
pom.xml
View File

@ -2791,9 +2791,7 @@
<module>hapi-fhir-docs</module>
<module>hapi-fhir-test-utilities</module>
<module>hapi-fhir-jpaserver-test-utilities</module>
<!-- TODO KHS temporarily disable these tests because they are blocking ci
<module>hapi-fhir-jpaserver-elastic-test-utilities</module>
-->
<module>hapi-tinder-plugin</module>
<module>hapi-tinder-test</module>
<module>hapi-fhir-client</module>