#13771 - Add Epipulse export functionality for Measles disease

Author: roldy

sormas-api/src/main/java/de/symeda/sormas/api/epipulse/EpipulseLaboratoryMapper.java

@@ -69,7 +69,7 @@ public static String mapSampleMaterialToEpipulseCode(SampleMaterial sampleMateri
 		case EDTA_WHOLE_BLOOD:
 			return "EDTA"; // EDTA whole blood
 		default:
-			return "OTH";
+			return null;
 		}
 	}
 
@@ -129,8 +129,8 @@ public static String normalizeGenotypeForEpipulse(String genotypeText) {
 		}
 
 		// Try to parse formats like "A", "B1", "D10", etc. and add MEASV_ prefix
-		// This matches a single uppercase letter optionally followed by digits
-		if (normalized.matches("^[A-Z]\\d*$")) {
+		// Measles genotypes are limited (e.g., A, B1-3, C1-2, D1-11, E, F, G1-3, H1-2)
+		if (normalized.matches("^(A|B[1-3]|C[1-2]|D(1[0-1]|[1-9])|E|F|G[1-3]|H[1-2])$")) {
 			return "MEASV_" + normalized;
 		}
 
@@ -301,6 +301,9 @@ public static List<String> mapSymptomsToComplicationCodes(
 	 * @return true if clinically confirmed, false otherwise
 	 */
 	public static Boolean deriveClinicalCriteriaStatus(YesNoUnknown clinicalConfirmation) {
+		if (clinicalConfirmation == null || clinicalConfirmation == YesNoUnknown.UNKNOWN) {
+			return null;
+		}
 		return clinicalConfirmation == YesNoUnknown.YES;
 	}
 }

sormas-backend/src/main/java/de/symeda/sormas/backend/epipulse/EpipulseCsvExportOrchestrator.java

@@ -94,16 +94,15 @@ public void orchestrateExport(String uuid, ExportFunction exportFunction, CsvExp
 				return;
 			}
 
-			if (epipulseExport.getStatus() != EpipulseExportStatus.PENDING) {
-				logger.error("EpipulseExport with uuid " + uuid + " is not in status PENDING");
+			// Atomic status claim: try to update from PENDING to IN_PROGRESS
+			boolean claimed = diseaseExportService.tryClaimExportForProcessing(uuid);
+			if (!claimed) {
+				logger.info("Export {} not claimed - either already processing or not in PENDING status", uuid);
 				return;
 			}
 
 			shouldUpdateStatus = true;
 
-			// Update status to IN_PROGRESS
-			diseaseExportService.updateStatusForBackgroundProcess(uuid, EpipulseExportStatus.IN_PROGRESS, null, null, null);
-
 			// Load configuration
 			EpipulseExportDto exportDto = epipulseExportEjb.toEpipulseExportDto(epipulseExport);
 			String serverCountryCode = configFacadeEjb.getCountryCode();

sormas-backend/src/main/java/de/symeda/sormas/backend/epipulse/EpipulseDiseaseExportService.java

@@ -67,6 +67,39 @@ public EpipulseDiseaseExportResult exportMeaslesCaseBased(EpipulseExportDto expo
 		return measlesExportStrategy.export(exportDto, serverCountryLocale, serverCountryName);
 	}
 
+	@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
+	public boolean tryClaimExportForProcessing(String exportUuid) {
+		try {
+			String sql = "UPDATE epipulse_export SET " +
+				"status = :newStatus, " +
+				"status_change_date = now(), " +
+				"changedate = now() " +
+				"WHERE uuid = :uuid AND status = :expectedStatus";
+
+			int updated = em.createNativeQuery(sql)
+				.setParameter("newStatus", EpipulseExportStatus.IN_PROGRESS.name())
+				.setParameter("uuid", exportUuid)
+				.setParameter("expectedStatus", EpipulseExportStatus.PENDING.name())
+				.executeUpdate();
+
+			em.flush();
+
+			if (updated > 0) {
+				logger.info("Successfully claimed export {} for processing", exportUuid);
+				return true;
+			} else {
+				logger.info("Export {} already claimed by another process or not in PENDING status", exportUuid);
+				return false;
+			}
+
+		} catch (Exception e) {
+			logger.error("Failed to claim export {} for processing: {}", exportUuid, e.getMessage(), e);
+			return false;
+		} finally {
+			em.clear();
+		}
+	}
+
 	@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
 	public void updateStatusForBackgroundProcess(
 		String exportUuid,

sormas-backend/src/main/java/de/symeda/sormas/backend/epipulse/strategy/MeaslesExportStrategy.java

@@ -223,7 +223,13 @@ private String buildSampleDataCte() {
 			   "                       STRING_AGG(DISTINCT CAST(s3.samplematerial AS text), ',' ORDER BY CAST(s3.samplematerial AS text)) as specimen_types_serology " +
 			   "                FROM filtered_cases c " +
 			   "                LEFT JOIN samples s ON s.associatedcase_id = c.id AND s.deleted = false " +
-			   "                LEFT JOIN samples s2 ON s2.associatedcase_id = c.id AND s2.deleted = false AND s2.samplematerial IS NOT NULL " +
+			   "                LEFT JOIN (SELECT DISTINCT s_vir.id, s_vir.associatedcase_id, s_vir.samplematerial " +
+			   "                           FROM samples s_vir " +
+			   "                           JOIN pathogentest pt_vir ON pt_vir.sample_id = s_vir.id " +
+			   "                           WHERE s_vir.deleted = false " +
+			   "                             AND s_vir.samplematerial IS NOT NULL " +
+			   "                             AND pt_vir.testtype IN ('PCR_RT_PCR', 'CULTURE', 'ISOLATION', 'DIRECT_FLUORESCENT_ANTIBODY', 'INDIRECT_FLUORESCENT_ANTIBODY')) s2 " +
+			   "                          ON s2.associatedcase_id = c.id " +
 			   "                LEFT JOIN (SELECT DISTINCT s_sero.id, s_sero.associatedcase_id, s_sero.samplematerial " +
 			   "                           FROM samples s_sero " +
 			   "                           JOIN pathogentest pt_sero ON pt_sero.sample_id = s_sero.id " +
@@ -316,13 +322,14 @@ private String buildExposureLocationsCte() {
 			   "                                  CASE " +
 			   "                                      WHEN co.defaultname IS NOT NULL THEN co.defaultname " +
 			   "                                      WHEN l.city IS NOT NULL THEN l.city " +
-			   "                                      ELSE l.details " +
+			   "                                      WHEN l.details IS NOT NULL THEN l.details " +
+			   "                                      ELSE 'Unknown' " +
 			   "                                  END, " +
 			   "                                  '; ' " +
 			   "                                  ORDER BY e.startdate DESC" +
 			   "                              ) as infection_locations " +
 			   "                       FROM exposures e " +
-			   "                       JOIN location l ON e.location_id = l.id " +
+			   "                       LEFT JOIN location l ON e.location_id = l.id " +
 			   "                       LEFT JOIN country co ON l.country_id = co.id " +
 			   "                       WHERE e.epidata_id IN (SELECT epidata_id FROM filtered_cases WHERE epidata_id IS NOT NULL) " +
 			   "                       GROUP BY e.epidata_id), ";