Renable elasticsearch tests (#3850)

* Renable elasticsearch tests

Limit elasticsearch container to 512MB instead of the default 4GB.

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/NumericParamRangeUtil.java

@@ -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;

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

@@ -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);

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HeaderPassthroughOptionTest.java

@@ -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 final String ourConceptsFileName = "target/concepts.csv";
-	private static File myConceptsFile = new File(myConceptsFileName);
+	private static final String ourHierarchyFileName = "target/hierarchy.csv";
-	private static final String myHierarchyFileName = "target/hierarchy.csv";
-	private static File myHierarchyFile = new File(myHierarchyFileName);
 	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();
+		int filenameCounter = ourFilenameCounter.incrementAndGet();
-		String[] args = new String[] {
+		writeConceptAndHierarchyFiles(filenameCounter);
+
+		String[] args = new String[]{
 			"-v", FHIR_VERSION,
 			"-m", "SNAPSHOT",
 			"-t", "http://localhost:" + myPort,
 			"-u", "http://foo",
-			"-d", myConceptsFileName,
+			"-d", getConceptFilename(filenameCounter),
-			"-d", myHierarchyFileName,
+			"-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", getConceptFilename(filenameCounter),
-			"-d", myHierarchyFileName,
+			"-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", getConceptFilename(filenameCounter),
-			"-d", myHierarchyFileName,
+			"-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 {
+	private static void writeConceptAndHierarchyFiles(int theFilenameCounter) throws IOException {
-		if (!myConceptsFile.exists()) {
+		File conceptsFile = new File(getConceptFilename(theFilenameCounter));
-			try (FileWriter w = new FileWriter(myConceptsFile, false)) {
+		File hierarchyFile = new File(getHierarchyFilename(theFilenameCounter));
-				w.append("CODE,DISPLAY\n");
-				w.append("ANIMALS,Animals\n");
-				w.append("CATS,Cats\n");
-				w.append("DOGS,Dogs\n");
-			}
-		}
 
-		if (!myHierarchyFile.exists()) {
+		ourLog.info("Writing {}", conceptsFile.getAbsolutePath());
-			try (FileWriter w = new FileWriter(myHierarchyFile, false)) {
+		try (FileWriter w = new FileWriter(conceptsFile, false)) {
-				w.append("PARENT,CHILD\n");
+			w.append("CODE,DISPLAY\n");
-				w.append("ANIMALS,CATS\n");
+			w.append("ANIMALS,Animals\n");
-				w.append("ANIMALS,DOGS\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 {

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

@@ -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."

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

@@ -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) {
+	public void addFilesToJob(String theBiJobId, List<BulkImportJobFileJson> theFiles) {
-		ourLog.info("Adding {} files to bulk import job: {}", theFiles.size(), theJobId);
+		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)
+			.findByJobId(theBiJobId)
-			.orElseThrow(() -> new InvalidRequestException("Unknown job ID: " + theJobId));
+			.orElseThrow(() -> new InvalidRequestException("Unknown bijob id: " + theBiJobId));
 		return job;
 	}
 
 	@Override
 	@Transactional
-	public void markJobAsReadyForActivation(String theJobId) {
+	public void markJobAsReadyForActivation(String theBiJobId) {
-		ourLog.info("Activating bulk import job {}", theJobId);
+		ourLog.info("Activating bulk import bijob {}", theBiJobId);
 
-		BulkImportJobEntity job = findJobByJobId(theJobId);
+		BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
-		ValidateUtil.isTrueOrThrowInvalidRequest(job.getStatus() == BulkImportJobStatusEnum.STAGING, "Bulk import job %s can not be activated in status: %s", theJobId, job.getStatus());
+		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) {
+	public void setJobToStatus(String theBiJobId, BulkImportJobStatusEnum theStatus) {
-		setJobToStatus(theJobId, theStatus, null);
+		setJobToStatus(theBiJobId, theStatus, null);
 	}
 
 	@Override
-	public void setJobToStatus(String theJobId, BulkImportJobStatusEnum theStatus, String theStatusMessage) {
+	public void setJobToStatus(String theBiJobId, BulkImportJobStatusEnum theStatus, String theStatusMessage) {
-		BulkImportJobEntity job = findJobByJobId(theJobId);
+		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) {
+	public BulkImportJobJson fetchJob(String theBiJobId) {
-		BulkImportJobEntity job = findJobByJobId(theJobId);
+		BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
 		return job.toJson();
 	}
 
         @Override
-        public JobInfo getJobStatus(String theJobId) {
+        public JobInfo getJobStatus(String theBiJobId) {
-                BulkImportJobEntity theJob = findJobByJobId(theJobId);
+                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) {
+	public BulkImportJobFileJson fetchFile(String theBiJobId, int theFileIndex) {
-		BulkImportJobEntity job = findJobByJobId(theJobId);
+		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) {
+	public String getFileDescription(String theBiJobId, int theFileIndex) {
-		BulkImportJobEntity job = findJobByJobId(theJobId);
+		BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
 
 		return myJobFileDao.findFileDescriptionForJob(job, theFileIndex).orElse("");
 	}
 
 	@Override
 	@Transactional
-	public void deleteJobFiles(String theJobId) {
+	public void deleteJobFiles(String theBiJobId) {
-		BulkImportJobEntity job = findJobByJobId(theJobId);
+		BulkImportJobEntity job = findJobByBiJobId(theBiJobId);
-		List<Long> files = myJobFileDao.findAllIdsForJob(theJobId);
+		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();
 	}

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

@@ -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;
 	}
 

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

@@ -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?

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

@@ -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;
 

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

@@ -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")

hapi-fhir-jpaserver-elastic-test-utilities/pom.xml

@@ -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>
 

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

@@ -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
+		int httpPort = myElasticsearchContainer.getMappedPort(9200);//9200 is the HTTP port
-		String host = elasticContainer().getHost();
+		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;
-	}
 }

hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticHSearch.java

@@ -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 {
+}

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

@@ -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);
+		Patient pt = new Patient();
-			myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
+		pt.addName().setFamily("Lastn").addGiven("Arthur");
-			// turn off the setting enabled earlier
+		patient0Id = myPatientDao.create(pt, mockSrd()).getId().toUnqualifiedVersionless();
-			myDaoConfig.setAdvancedHSearchIndexing(false);
+		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();
 

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

@@ -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 {
 

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

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

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

@@ -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);

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

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

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

@@ -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

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

@@ -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 = {
+// wipmb hierarchy for context
-	TestR4Config.class,
+@ContextHierarchy({
-	TestHSearchAddInConfig.Elasticsearch.class,
+	@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class),
-	DaoTestDataBuilder.Config.class,
+	@ContextConfiguration(classes = {
-	TestDaoSearch.Config.class
+		DaoTestDataBuilder.Config.class,
+		TestDaoSearch.Config.class
+	})
 })
 @DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
 @TestExecutionListeners(listeners = {

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

@@ -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";

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

@@ -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 = {
+@ContextHierarchy({
-	TestR4Config.class,
+	@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class),
-	TestHSearchAddInConfig.Elasticsearch.class,
+	@ContextConfiguration(classes = {
-	DaoTestDataBuilder.Config.class,
+		DaoTestDataBuilder.Config.class,
-	TestDaoSearch.Config.class
+		TestDaoSearch.Config.class
+	})
 })
 @Disabled
 public class HSearchSandboxTest extends BaseJpaTest {

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

@@ -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 {
+	public void testDeleteObservation() throws IOException {
-		indexSingleObservation();
+		indexMultipleObservations();
 		SearchParameterMap searchParameterMap = new SearchParameterMap();
-		searchParameterMap.setLastNMax(10);
+		searchParameterMap.setLastNMax(100);
-		List<ObservationJson> persistedObservationEntities = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
+		List<ObservationJson> observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
-		assertEquals(1, persistedObservationEntities.size());
+		assertEquals(100, observationDocuments.size());
-		ObservationJson persistedObservationEntity = persistedObservationEntities.get(0);
+		// Check that fifth observation for fifth patient has been indexed.
-		assertEquals(SINGLE_SUBJECT_ID, persistedObservationEntity.getSubject());
+		ObservationJson observation = elasticsearchSvc.getObservationDocument("55");
-		assertEquals(SINGLE_OBSERVATION_PID, persistedObservationEntity.getIdentifier());
+		assertNotNull(observation);
-		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 = new SearchParameterMap();
-		ReferenceParam subjectParam = new ReferenceParam("Patient", "", SINGLE_SUBJECT_ID);
+		searchParameterMap.add(Observation.SP_SUBJECT, multiSubjectParams);
-		searchParameterMap.add(Observation.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().addOr(subjectParam)));
+		searchParameterMap.setLastNMax(10);
-		TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE);
+		List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
-		searchParameterMap.add(Observation.SP_CATEGORY, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(categoryParam)));
+		assertEquals(100, observationIdsOnly.size());
-		TokenParam codeParam = new TokenParam(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE);
+		assertTrue(observationIdsOnly.contains("55"));
-		searchParameterMap.add(Observation.SP_CODE, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(codeParam)));
-		searchParameterMap.setLastNMax(3);
 
-		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 {
+	public void testIndexObservationSingle() throws IOException {
-		indexMultipleObservations();
+		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);
+		List<ObservationJson> persistedObservationEntities = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
-		assertEquals(100, observationIdsOnly.size());
+		assertEquals(1, persistedObservationEntities.size());
-		assertTrue(observationIdsOnly.contains("55"));
+		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.
+		String observationCodeNormalizedId = persistedObservationEntity.getCode_concept_id();
-		ResourceTable entity = new ResourceTable();
-		entity.setId(55L);
-		entity.setResourceType("Observation");
-		entity.setVersion(0L);
 
-		testObservationPersist.deleteObservationIndex(entity);
+		// List<CodeJson> persistedObservationCodes = elasticsearchSvc.queryAllIndexedObservationCodesForTest();
-		elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
+		// 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);
+		ReferenceParam subjectParam = new ReferenceParam("Patient", "", SINGLE_SUBJECT_ID);
-		observationDocuments = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx);
+		searchParameterMap.add(Observation.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().addOr(subjectParam)));
-		assertEquals(99, observationDocuments.size());
+		TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE);
-		observation = elasticsearchSvc.getObservationDocument("55");
+		searchParameterMap.add(Observation.SP_CATEGORY, new TokenAndListParam().addAnd(new TokenOrListParam().addOr(categoryParam)));
-		assertNull(observation);
+		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);
+		List<String> observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 100);
-		assertEquals(99, observationIdsOnly.size());
-		assertTrue(!observationIdsOnly.contains("55"));
 
+		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());
-
-	}
 
 }

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

@@ -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);
 

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

@@ -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 = {
+@ContextHierarchy({
-	TestR4Config.class,
+	@ContextConfiguration(classes = TestR4ConfigWithElasticHSearch.class),
-	TestHSearchAddInConfig.Elasticsearch.class,
+	@ContextConfiguration(classes = {
-	DaoTestDataBuilder.Config.class
+		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;

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

@@ -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));
-	}
-
-}

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

@@ -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;

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

@@ -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;

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

@@ -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 {
 

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

@@ -1,7 +1,6 @@
 package ca.uhn.fhir.jpa.term;
 
-import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
+import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticHSearch;
-import ca.uhn.fhir.jpa.test.config.TestR4Config;
 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 {
 
 }

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

@@ -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));
 	}
 

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

@@ -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);
+			int elasticsearchPort = myElasticsearchContainer.getMappedPort(9200);
-			String host = elasticContainer().getHost();
+			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;
+		}
 
 	}
 }

hapi-fhir-jpaserver-test-utilities/src/main/resources/logback-test.xml

@@ -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" additivity="false" level="TRACE"/>
-	<logger name="org.hibernate.search" level="TRACE"/>
+	<logger name="org.hibernate.search.query" additivity="false" level="TRACE"/>
-	<logger name="org.hibernate.search.query" level="TRACE"/>
+	<logger name="org.hibernate.search.elasticsearch.request" additivity="false" level="TRACE"/>
-	<logger name="org.hibernate.search.elasticsearch.request" 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"/>  -->

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

@@ -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());
 		}
 	}
 

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

@@ -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();

hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchFtTest.java

@@ -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)));
 
 	}

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

@@ -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;

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

@@ -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;

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

@@ -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;

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

@@ -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;

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

@@ -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;

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

@@ -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;
 	}

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

@@ -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);
 			}

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

@@ -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;
 

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

@@ -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;

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

@@ -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;

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

@@ -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);

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

@@ -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 {

pom.xml

@@ -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>