Partially complete groupbulkexportjob

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processors/PidToIBaseResourceProcessor.java

@@ -58,7 +58,8 @@ public class PidToIBaseResourceProcessor implements ItemProcessor<List<ResourceP
 
 	@Override
 	public List<IBaseResource> process(List<ResourcePersistentId> theResourcePersistentId) {
-
+		String collect = theResourcePersistentId.stream().map(pid -> pid.getId().toString()).collect(Collectors.joining(","));
+		ourLog.info("Processing pids {}" + collect);
 		IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(myResourceType);
 		Class<? extends IBaseResource> resourceTypeClass = myContext.getResourceDefinition(myResourceType).getImplementingClass();
 
@@ -66,7 +67,7 @@ public class PidToIBaseResourceProcessor implements ItemProcessor<List<ResourceP
 		List<IBaseResource> outgoing = new ArrayList<>();
 		sb.loadResourcesByPid(theResourcePersistentId, Collections.emptyList(), outgoing, false, null);
 
-		ourLog.trace("Loaded resources: {}", outgoing.stream().map(t->t.getIdElement().getValue()).collect(Collectors.joining(", ")));
+		ourLog.warn("Loaded resources: {}", outgoing.stream().map(t->t.getIdElement().getValue()).collect(Collectors.joining(", ")));
 
 		return outgoing;
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkItemReader.java

@@ -31,7 +31,6 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
 import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
 import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
 import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
-import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
 import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
@@ -41,27 +40,24 @@ import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.param.DateRangeParam;
 import ca.uhn.fhir.rest.param.HasParam;
-import ca.uhn.fhir.rest.param.ReferenceOrListParam;
-import ca.uhn.fhir.rest.param.ReferenceParam;
-import ca.uhn.fhir.rest.param.StringOrListParam;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.UrlUtil;
 import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.Immunization;
-import org.hl7.fhir.r4.model.Patient;
 import org.slf4j.Logger;
 import org.springframework.batch.item.ItemReader;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 
+import javax.annotation.Nonnull;
+import javax.persistence.EntityManager;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
-import java.util.stream.Collectors;
+import java.util.Set;
 
 public class GroupBulkItemReader implements ItemReader<List<ResourcePersistentId>> {
 	private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
@@ -83,18 +79,12 @@ public class GroupBulkItemReader implements ItemReader<List<ResourcePersistentId
 	private FhirContext myContext;
 	@Autowired
 	private SearchBuilderFactory mySearchBuilderFactory;
+	@Autowired
+	private EntityManager myEntityManager;
 
 	@Autowired
 	private MatchUrlService myMatchUrlService;
 
-	private List<String> getGroupMemberIds() {
-		IFhirResourceDao group = myDaoRegistry.getResourceDao("Group");
-		IBaseResource read = group.read(new IdDt(myGroupId));
-		FhirTerser fhirTerser = myContext.newTerser();
-		List<IBaseReference> values = fhirTerser.getValues(read, "Group.member", IBaseReference.class);
-		return values.stream().map(theIBaseReference -> theIBaseReference.getReferenceElement().getValue()).collect(Collectors.toList());
-	}
-
 	private void loadResourcePids() {
 		Optional<BulkExportJobEntity> jobOpt = myBulkExportJobDao.findByJobId(myJobUUID);
 		if (!jobOpt.isPresent()) {
@@ -102,33 +92,57 @@ public class GroupBulkItemReader implements ItemReader<List<ResourcePersistentId
 			return;
 		}
 		BulkExportJobEntity jobEntity = jobOpt.get();
-		ourLog.info("Bulk export starting generation for batch export job: {}", jobEntity);
+		ourLog.info("Group Bulk export starting generation for batch export job: [{}] with resourceType [{}] and UUID [{}]", jobEntity, myResourceType, myJobUUID);
 
+
+		//Fetch all the pids given the query.
+		ISearchBuilder searchBuilder = getSearchBuilder();
+		SearchParameterMap searchParameterMap = getParameterMap(jobEntity);
+
+		IResultIterator resultIterator = searchBuilder.createQuery(
+			searchParameterMap,
+			new SearchRuntimeDetails(null, myJobUUID),
+			null,
+			RequestPartitionId.allPartitions()
+		);
+
+		List<ResourcePersistentId> myReadPids = new ArrayList<>();
+		while (resultIterator.hasNext()) {
+			myReadPids.add(resultIterator.next());
+		}
+		Set<ResourcePersistentId> resourcePersistentIds = searchBuilder.loadIncludes(myContext, myEntityManager, myReadPids, searchParameterMap.getRevIncludes(), true, searchParameterMap.getLastUpdated(), myJobUUID, null);
+		myPidIterator = resourcePersistentIds.iterator();
+	}
+
+	private ISearchBuilder getSearchBuilder() {
 		IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao("Patient");
-
-		ourLog.info("Bulk export assembling export of type {} for job {}", myResourceType, myJobUUID);
-
 		RuntimeResourceDefinition def = myContext.getResourceDefinition("Patient");
 		Class<? extends IBaseResource> nextTypeClass = def.getImplementingClass();
-		ISearchBuilder sb = mySearchBuilderFactory.newSearchBuilder(dao, myResourceType, nextTypeClass);
+		return mySearchBuilderFactory.newSearchBuilder(dao, "Patient", nextTypeClass);
+	}
 
+	@Nonnull
+	private SearchParameterMap getParameterMap(BulkExportJobEntity jobEntity) {
 		SearchParameterMap spm = new SearchParameterMap();
-		myGroupId = "21";
 		spm.add("_has", new HasParam("Group", "member", "_id", myGroupId));
-		spm.addRevInclude(new Include("Immunization:patient").toLocked());
+		spm.addRevInclude(new Include(lookupRevIncludeParameter(myResourceType)).toLocked());
-
-
-//		SearchParameterMap map = createSearchParameterMapFromTypeFilter(jobEntity, def);
 		if (jobEntity.getSince() != null) {
 			spm.setLastUpdated(new DateRangeParam(jobEntity.getSince(), null));
 		}
 		spm.setLoadSynchronous(true);
-		IResultIterator myResultIterator = sb.createQuery(spm, new SearchRuntimeDetails(null, myJobUUID), null, RequestPartitionId.allPartitions());
+		return spm;
-		List<ResourcePersistentId> myReadPids = new ArrayList<>();
+	}
-		while (myResultIterator.hasNext()) {
+
-			myReadPids.add(myResultIterator.next());
+	private String lookupRevIncludeParameter(String theResourceType) {
+		switch (theResourceType) {
+			case "Immunization":
+				return "Immunization:patient";
+			case "Observation":
+				return "Observation:patient";
+			default:
+				throw new UnsupportedOperationException("You cannot currently do a group bulk export for type " + theResourceType);
+
 		}
-		myPidIterator = myReadPids.iterator();
 	}
 
 	private SearchParameterMap createSearchParameterMapFromTypeFilter(BulkExportJobEntity theJobEntity, RuntimeResourceDefinition theDef) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/ResourceToFileWriter.java

@@ -64,7 +64,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 	private Long myBulkExportCollectionEntityId;
 
 	@Value("#{stepExecutionContext['resourceType']}")
-	private String myReosurceType;
+	private String myResourceType;
 
 	private IFhirResourceDao<IBaseBinary> myBinaryDao;
 
@@ -116,6 +116,8 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 		int count = 0;
 		for (List<IBaseResource> resourceList : theList) {
 			for (IBaseResource nextFileResource : resourceList) {
+				System.out.println("ZOOP");
+				System.out.println(myParser.setPrettyPrint(true).encodeResourceToString(nextFileResource));
 				myParser.encodeResourceToWriter(nextFileResource, myWriter);
 				myWriter.append("\n");
 				count++;
@@ -124,7 +126,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
 
 		Optional<IIdType> createdId = flushToFiles();
 		if (createdId.isPresent()) {
-			ourLog.info("Created {} resources for bulk export file containing {} resources of type {} ", count, createdId.get().toUnqualifiedVersionless().getValue(), myReosurceType);
+			ourLog.info("Created {} resources for bulk export file containing {} resources of type {} ", count, createdId.get().toUnqualifiedVersionless().getValue(), myResourceType);
 		}
 	}
 }

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

@@ -42,6 +42,7 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.UrlUtil;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -64,6 +65,7 @@ import javax.annotation.PostConstruct;
 import javax.transaction.Transactional;
 import java.util.Date;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 import java.util.UUID;
@@ -71,6 +73,7 @@ import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.util.UrlUtil.escapeUrlParam;
 import static ca.uhn.fhir.util.UrlUtil.escapeUrlParams;
+import static org.apache.commons.lang3.StringUtils.contains;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
@@ -102,6 +105,10 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 	@Qualifier("bulkExportJob")
 	private org.springframework.batch.core.Job myBulkExportJob;
 
+	@Autowired
+	@Qualifier("groupBulkExportJob")
+	private org.springframework.batch.core.Job myGroupBulkExportJob;
+
 	private final int myRetentionPeriod = (int) (2 * DateUtils.MILLIS_PER_HOUR);
 
 	/**
@@ -125,10 +132,12 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 			return;
 		}
 
-		String jobUuid = jobToProcessOpt.get().getJobId();
+		BulkExportJobEntity bulkExportJobEntity = jobToProcessOpt.get();
 
+		String jobUuid = bulkExportJobEntity.getJobId();
+		boolean isForGroupExport = containsGroupId(bulkExportJobEntity.getRequest());
 		try {
-			processJob(jobUuid);
+				processJob(jobUuid, isForGroupExport);
 		} catch (Exception e) {
 			ourLog.error("Failure while preparing bulk export extract", e);
 			myTxTemplate.execute(t -> {
@@ -144,6 +153,15 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 		}
 
 	}
+	private boolean containsGroupId(String theRequestString) {
+		Map<String, String[]> stringMap = UrlUtil.parseQueryString(theRequestString);
+		String[] strings = stringMap.get(JpaConstants.PARAM_EXPORT_GROUP_ID);
+		if (strings != null && strings.length > 0) {
+			return true;
+		} else {
+			return false;
+		}
+	}
 
 
 	/**
@@ -193,22 +211,24 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 
 	}
 
-	private void processJob(String theJobUuid) {
+	private void processJob(String theJobUuid, boolean theIsGroupRequest) {
 		JobParameters parameters = new JobParametersBuilder()
 			.addString("jobUUID", theJobUuid)
-			.addLong("readChunkSize", READ_CHUNK_SIZE)
+			.addLong("readChunkSize", READ_CHUNK_SIZE).toJobParameters();
-			.toJobParameters();
 
 		ourLog.info("Submitting bulk export job {} to job scheduler", theJobUuid);
 
 		try {
+			if (theIsGroupRequest) {
+				myJobSubmitter.runJob(myGroupBulkExportJob, parameters);
+			} else {
 				myJobSubmitter.runJob(myBulkExportJob, parameters);
+			}
 		} catch (JobParametersInvalidException theE) {
 			ourLog.error("Unable to start job with UUID: {}, the parameters are invalid. {}", theJobUuid, theE.getMessage());
 		}
 	}
 
-
 	@SuppressWarnings("unchecked")
 	private IFhirResourceDao<IBaseBinary> getBinaryDao() {
 		return myDaoRegistry.getResourceDao("Binary");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java

@@ -65,6 +65,7 @@ import static org.awaitility.Awaitility.await;
 import static org.hamcrest.CoreMatchers.containsString;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.is;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.fail;
@@ -524,7 +525,6 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 
 
 		//Add the UUID to the job
-		//TODO GGG START HERE
 		GroupBulkExportJobParametersBuilder paramBuilder = new GroupBulkExportJobParametersBuilder();
 		paramBuilder.setGroupId(myPatientGroupId.getIdPart());
 		paramBuilder.setJobUUID(jobDetails.getJobId());
@@ -538,7 +538,8 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 		IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
 
 		assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
-		assertThat(jobInfo.getFiles().size(), equalTo(2));
+		assertThat(jobInfo.getFiles().size(), equalTo(1));
+		assertThat(jobInfo.getFiles().get(0).getResourceType(), is(equalTo("Immunization")));
 	}
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4LegacySearchBuilderTest.java

@@ -278,18 +278,18 @@ public class FhirResourceDaoR4LegacySearchBuilderTest extends BaseJpaR4Test {
 
 		Group group = new Group();
 		group.addMember().setEntity(new Reference(patientId));
-		Long daoMethodOutcome = myGroupDao.create(group).getId().getIdPartAsLong();
+		myGroupDao.create(group).getId().getIdPartAsLong();
 
 		Immunization immunization = new Immunization();
 		immunization.setPatient(new Reference(patientId));
 		String immunizationId = myImmunizationDao.create(immunization).getId().toUnqualifiedVersionless().getValue();
 
-		String criteria = "?_has:Group:member:_id="+ daoMethodOutcome + "&_revinclude=Immunization:patient";
+//		String criteria = "?_has:Group:member:_id="+ daoMethodOutcome + "&_revinclude=Immunization:patient";
+		String criteria = "?_revinclude=Immunization:patient";
 		//TODO GGG the matchUrlService _doesnt translate rev includes!
 		SearchParameterMap searchParameterMap = myMatchUrlService.translateMatchUrl(criteria, myFhirCtx.getResourceDefinition(Patient.class));
 		searchParameterMap.addRevInclude(new Include("Immunization:patient").toLocked());
 		searchParameterMap.setLoadSynchronous(true);
-
 		IBundleProvider search = myPatientDao.search(searchParameterMap);
 		List<String> strings = toUnqualifiedVersionlessIdValues(search);
 		assertThat(strings, hasItems(patientId, immunizationId));