Add constants, fix up some tests

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

@@ -28,7 +28,9 @@ import org.springframework.context.annotation.Import;
 //When you define a new batch job, add it here.
 @Import({
 	CommonBatchJobConfig.class,
-	BulkExportJobConfig.class,})
+	BulkExportJobConfig.class
+})
 public class BatchJobsConfig {
-	//Empty config, as this is just an aggregator for all the various batch jobs defined around the system.
+	public static final String BULK_EXPORT_JOB_NAME = "bulkExportJob";
+	public static final String GROUP_BULK_EXPORT_JOB_NAME = "groupBulkExportJob";
 }

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

@@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.bulk.job;
  * #L%
  */
 
+import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
 import ca.uhn.fhir.jpa.batch.processors.PidToIBaseResourceProcessor;
 import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@@ -46,6 +47,7 @@ import java.util.List;
  */
 @Configuration
 public class BulkExportJobConfig {
+
 	public static final String JOB_UUID_PARAMETER = "jobUUID";
 	public static final String READ_CHUNK_PARAMETER = "readChunkSize";
 	public static final String EXPAND_MDM_PARAMETER = "expandMdm";
@@ -70,7 +72,7 @@ public class BulkExportJobConfig {
 	@Bean
 	@Lazy
 	public Job bulkExportJob() {
-		return myJobBuilderFactory.get("bulkExportJob")
+		return myJobBuilderFactory.get(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
 			.validator(bulkJobParameterValidator())
 			.start(createBulkExportEntityStep())
 			.next(partitionStep())
@@ -81,7 +83,7 @@ public class BulkExportJobConfig {
 	@Bean
 	@Lazy
 	public Job groupBulkExportJob() {
-		return myJobBuilderFactory.get("groupBulkExportJob")
+		return myJobBuilderFactory.get(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
 			.validator(groupBulkJobParameterValidator())
 			.validator(bulkJobParameterValidator())
 			.start(createBulkExportEntityStep())

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/provider/BulkDataExportProvider.java

@@ -189,6 +189,10 @@ public class BulkDataExportProvider {
 		@IdParam IIdType theIdParam,
 		@OperationParam(name = JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theOutputFormat,
 		@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theType,
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_SINCE, min = 0, max = 1, typeName = "instant") IPrimitiveType<Date> theSince,
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_TYPE_FILTER, min = 0, max = 1, typeName = "string") IPrimitiveType<String> theTypeFilter,
+		@OperationParam(name = JpaConstants.PARAM_EXPORT_MDM, min = 0, max = 1, typeName = "boolean") IPrimitiveType<Boolean> theMdm,
+
 		ServletRequestDetails theRequestDetails
 	) {
 
@@ -207,10 +211,20 @@ public class BulkDataExportProvider {
 
 		//TODO GGG eventually, we will support these things. 
 		Set<String> filters = null;
-		Date since = null;
-		boolean theMdm = false;
 
-		IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(outputFormat, resourceTypes, since, filters, theIdParam, theMdm));
+		Date since = null;
+		if (theSince != null) {
+			since = theSince.getValue();
+		}
+
+		boolean mdm = false;
+		if (theMdm != null) {
+			mdm = theMdm.getValue();
+		}
+		if (theTypeFilter != null) {
+			filters = ArrayUtil.commaSeparatedListToCleanSet(theTypeFilter.getValueAsString());
+		}
+		IBulkDataExportSvc.JobInfo outcome = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(outputFormat, resourceTypes, since, filters, theIdParam, mdm));
 
 		String serverBase = getServerBase(theRequestDetails);
 		String pollLocation = serverBase + "/" + JpaConstants.OPERATION_EXPORT_POLL_STATUS + "?" + JpaConstants.PARAM_EXPORT_POLL_STATUS_JOB_ID + "=" + outcome.getJobId();

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

@@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
+import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
 import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
 import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
 import ca.uhn.fhir.jpa.bulk.api.GroupBulkDataExportOptions;
@@ -105,11 +106,11 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 	private IBatchJobSubmitter myJobSubmitter;
 
 	@Autowired
-	@Qualifier("bulkExportJob")
+	@Qualifier(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
 	private org.springframework.batch.core.Job myBulkExportJob;
 
 	@Autowired
-	@Qualifier("groupBulkExportJob")
+	@Qualifier(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
 	private org.springframework.batch.core.Job myGroupBulkExportJob;
 
 	private final int myRetentionPeriod = (int) (2 * DateUtils.MILLIS_PER_HOUR);
@@ -139,8 +140,9 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 
 		String jobUuid = bulkExportJobEntity.getJobId();
 		String theGroupId = getGroupIdIfPresent(bulkExportJobEntity.getRequest());
+		String theMdmExpand= getMdmIfPresent(bulkExportJobEntity.getRequest());
 		try {
-				processJob(jobUuid, theGroupId);
+				processJob(jobUuid, theGroupId, theMdmExpand);
 		} catch (Exception e) {
 			ourLog.error("Failure while preparing bulk export extract", e);
 			myTxTemplate.execute(t -> {
@@ -166,6 +168,16 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 		}
 		return null;
 	}
+	private String getMdmIfPresent(String theRequestString) {
+		Map<String, String[]> stringMap = UrlUtil.parseQueryString(theRequestString);
+		if (stringMap != null) {
+			String[] strings = stringMap.get(JpaConstants.PARAM_EXPORT_MDM);
+			if (strings != null) {
+				return String.join(",", strings);
+			}
+		}
+		return null;
+	}
 
 
 	/**
@@ -215,7 +227,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 
 	}
 
-	private void processJob(String theJobUuid, String theGroupId) {
+	private void processJob(String theJobUuid, String theGroupId, String theExpandMdm) {
 		JobParametersBuilder parameters = new JobParametersBuilder()
 			.addString(BulkExportJobConfig.JOB_UUID_PARAMETER, theJobUuid)
 			.addLong(BulkExportJobConfig.READ_CHUNK_PARAMETER, READ_CHUNK_SIZE);
@@ -225,6 +237,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 		try {
 			if (!StringUtils.isBlank(theGroupId)) {
 				parameters.addString(BulkExportJobConfig.GROUP_ID_PARAMETER, theGroupId);
+				parameters.addString(BulkExportJobConfig.EXPAND_MDM_PARAMETER, theExpandMdm);
 				myJobSubmitter.runJob(myGroupBulkExportJob, parameters.toJobParameters());
 			} else {
 				myJobSubmitter.runJob(myBulkExportJob, parameters.toJobParameters());
@@ -284,8 +297,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
 		if (theBulkDataExportOptions instanceof GroupBulkDataExportOptions) {
 			GroupBulkDataExportOptions groupOptions = (GroupBulkDataExportOptions) theBulkDataExportOptions;
 			requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_GROUP_ID).append("=").append(groupOptions.getGroupId().getValue());
-			//TODO GGG eventually we will support this
+			requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_MDM).append("=").append(groupOptions.isMdm());
-//			requestBuilder.append("&").append(JpaConstants.PARAM_EXPORT_MDM).append("=").append(groupOptions.isMdm());
 		}
 		String request = requestBuilder.toString();
 

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

@@ -49,6 +49,8 @@ import java.util.concurrent.TimeUnit;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.containsString;
+import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.notNullValue;
 import static org.hamcrest.Matchers.nullValue;
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -306,11 +308,14 @@ public class BulkDataExportProviderTest {
 
 		InstantType now = InstantType.now();
 
+
 		Parameters input = new Parameters();
+		StringType obsTypeFilter = new StringType("Observation?code=OBSCODE,DiagnosticReport?code=DRCODE");
 		input.addParameter(JpaConstants.PARAM_EXPORT_OUTPUT_FORMAT, new StringType(Constants.CT_FHIR_NDJSON));
 		input.addParameter(JpaConstants.PARAM_EXPORT_TYPE, new StringType("Observation, DiagnosticReport"));
 		input.addParameter(JpaConstants.PARAM_EXPORT_SINCE, now);
-		input.addParameter(JpaConstants.PARAM_EXPORT_TYPE_FILTER, new StringType("Observation?code=OBSCODE,DiagnosticReport?code=DRCODE"));
+		input.addParameter(JpaConstants.PARAM_EXPORT_MDM, true);
+		input.addParameter(JpaConstants.PARAM_EXPORT_TYPE_FILTER, obsTypeFilter);
 
 		ourLog.info(myCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input));
 
@@ -329,11 +334,9 @@ public class BulkDataExportProviderTest {
 		GroupBulkDataExportOptions options = myGroupBulkDataExportOptionsCaptor.getValue();
 		assertEquals(Constants.CT_FHIR_NDJSON, options.getOutputFormat());
 		assertThat(options.getResourceTypes(), containsInAnyOrder("Observation", "DiagnosticReport"));
-		//TODO GGG eventually, we will support since in group exports
+		assertThat(options.getSince(), notNullValue());
-		assertThat(options.getSince(), nullValue());
+		assertThat(options.getFilters(), notNullValue());
-		//TODO GGG eventually, we will support filters in group exports
-		assertThat(options.getFilters(), nullValue());
 		assertEquals(GROUP_ID, options.getGroupId().getValue());
-		assertFalse(options.isMdm());
+		assertThat(options.isMdm(), is(equalTo(true)));
 	}
 }

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

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.bulk;
 import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
 import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
 import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
 import ca.uhn.fhir.jpa.bulk.api.GroupBulkDataExportOptions;
@@ -89,11 +90,11 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 	private JobExplorer myJobExplorer;
 
 	@Autowired
-	@Qualifier("bulkExportJob")
+	@Qualifier(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
 	private Job myBulkJob;
 
 	@Autowired
-	@Qualifier("groupBulkExportJob")
+	@Qualifier(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
 	private Job myGroupBulkJob;
 
 	private IIdType myPatientGroupId;
@@ -490,7 +491,8 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 	}
 
 	public void awaitAllBulkJobCompletions() {
-		List<JobInstance> bulkExport = myJobExplorer.findJobInstancesByJobName("bulkExportJob", 0, 100);
+		List<JobInstance> bulkExport = myJobExplorer.findJobInstancesByJobName(BatchJobsConfig.BULK_EXPORT_JOB_NAME, 0, 100);
+		bulkExport.addAll(myJobExplorer.findJobInstancesByJobName(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME, 0, 100));
 		if (bulkExport.isEmpty()) {
 			fail("There are no bulk export jobs running!");
 		}
@@ -615,16 +617,11 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
 		// Create a bulk job
 		IBulkDataExportSvc.JobInfo jobDetails = myBulkDataExportSvc.submitJob(new GroupBulkDataExportOptions(null, Sets.newHashSet("Immunization", "Observation"), null, null, myPatientGroupId, true));
 
-		GroupBulkExportJobParametersBuilder paramBuilder = new GroupBulkExportJobParametersBuilder();
+		myBulkDataExportSvc.buildExportFiles();
-		paramBuilder.setGroupId(myPatientGroupId.getIdPart());
+		awaitAllBulkJobCompletions();
-		paramBuilder.setMdm(true);
-		paramBuilder.setJobUUID(jobDetails.getJobId());
-		paramBuilder.setReadChunkSize(10L);
 
-		JobExecution jobExecution = myBatchJobSubmitter.runJob(myGroupBulkJob, paramBuilder.toJobParameters());
-
-		awaitJobCompletion(jobExecution);
 		IBulkDataExportSvc.JobInfo jobInfo = myBulkDataExportSvc.getJobInfoOrThrowResourceNotFound(jobDetails.getJobId());
+		assertEquals("/$export?_outputFormat=application%2Ffhir%2Bndjson&_type=Observation,Immunization&_groupId=" + myPatientGroupId +"&_mdm=true", jobInfo.getRequest());
 
 		assertThat(jobInfo.getStatus(), equalTo(BulkJobStatusEnum.COMPLETE));
 		assertThat(jobInfo.getFiles().size(), equalTo(2));

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java

@@ -190,10 +190,9 @@ public class JpaConstants {
 	public static final Object PARAM_EXPORT_GROUP_ID = "_groupId";
 
 	/**
-	 * TODO GGG eventually we will support this.
 	 * Whether mdm should be performed on group export items to expand the group items to linked items before performing the export
 	 */
-//	public static final String PARAM_EXPORT_MDM = "_mdm";
+	public static final String PARAM_EXPORT_MDM = "_mdm";
 
 	/**
 	 * Parameter for delete to indicate the deleted resources should also be expunged