#13771 - Corrections to epipulse export queries & mappings

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

@@ -62,12 +62,15 @@ public static String mapSampleMaterialToEpipulseCode(SampleMaterial sampleMateri
 			return "NASALSWAB";
 		case THROAT_SWAB:
 		case RECTAL_SWAB:
+		case CLINICAL_SAMPLE:
 		case OTHER:
 			return "OTH";
 		case SALIVA:
 			return "SALOR"; // Saliva/oral fluid
 		case EDTA_WHOLE_BLOOD:
 			return "EDTA"; // EDTA whole blood
+		case DRY_BLOOD:
+			return "DRYBLOSP"; // Dry blood spot
 		default:
 			return null;
 		}
@@ -234,10 +237,10 @@ public static String mapClusterTypeToEpipulseCode(ClusterType clusterType) {
 	 * Maps SORMAS CaseImportedStatus enum to EpiPulse imported status codes.
 	 * <p>
 	 * EpiPulse Reference Values:
-	 * - AUTOCH = Autochthonous (not imported case)
+	 * - NOTIMP = Not imported case
 	 * - IMP = Imported case
-	 * - IMPR = Import-related case
-	 * - UNK = Unknown importation status
+	 * - IMPREL = Import-related case
+	 * - IMPUNK = Unknown importation status
 	 *
 	 * @param importedStatus
 	 *            SORMAS case imported status enum
@@ -252,11 +255,11 @@ public static String mapCaseImportedStatusToEpipulseCode(CaseImportedStatus impo
 		case IMPORTED_CASE:
 			return "IMP";
 		case IMPORT_RELATED_CASE:
-			return "IMPR";
+			return "IMPREL";
 		case UNKNOWN_IMPORTATION_STATUS:
-			return "UNK";
+			return "IMPUNK";
 		case NOT_IMPORTED_CASE:
-			return "AUTOCH";
+			return "NOTIMP";
 		default:
 			return null;
 		}
@@ -279,6 +282,8 @@ public static String mapCaseImportedStatusToEpipulseCode(CaseImportedStatus impo
 	 *            Diarrhea symptom state
 	 * @param otitisMedia
 	 *            Otitis media symptom state
+	 * @param pneumonia
+	 *            Pneumonia (clinical or radiologic) symptom state
 	 * @param otherComplications
 	 *            Other complications symptom state
 	 * @return List of EpiPulse complication codes (empty list returns "NONE" in CSV)
@@ -287,6 +292,7 @@ public static List<String> mapSymptomsToComplicationCodes(
 		SymptomState acuteEncephalitis,
 		SymptomState diarrhea,
 		SymptomState otitisMedia,
+		SymptomState pneumonia,
 		SymptomState otherComplications) {
 
 		List<String> complications = new ArrayList<>();
@@ -300,11 +306,13 @@ public static List<String> mapSymptomsToComplicationCodes(
 		if (otitisMedia == SymptomState.YES) {
 			complications.add("OME");
 		}
+		if (pneumonia == SymptomState.YES) {
+			complications.add("PNEU");
+		}
 		if (otherComplications == SymptomState.YES) {
 			complications.add("OTH");
 		}
 
-		// Note: PNEU (pneumonia) not currently available in SORMAS Symptoms for MEAS
 		// If no complications found, empty list will result in "NONE" in CSV
 
 		return complications;

sormas-api/src/test/java/de/symeda/sormas/api/epipulse/EpipulseLaboratoryMapperTest.java

@@ -0,0 +1,77 @@
+package de.symeda.sormas.api.epipulse;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
+
+import org.junit.jupiter.api.Test;
+
+import de.symeda.sormas.api.sample.SampleMaterial;
+
+public class EpipulseLaboratoryMapperTest {
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_DryBlood() {
+		assertEquals("DRYBLOSP", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.DRY_BLOOD));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_Blood() {
+		assertEquals("SER", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.BLOOD));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_Sera() {
+		assertEquals("SER", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.SERA));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_Urine() {
+		assertEquals("URINE", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.URINE));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_NasalSwab() {
+		assertEquals("NASALSWAB", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.NASAL_SWAB));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_ThroatSwab() {
+		assertEquals("OTH", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.THROAT_SWAB));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_RectalSwab() {
+		assertEquals("OTH", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.RECTAL_SWAB));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_ClinicalSample() {
+		assertEquals("OTH", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.CLINICAL_SAMPLE));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_Other() {
+		assertEquals("OTH", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.OTHER));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_Saliva() {
+		assertEquals("SALOR", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.SALIVA));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_EdtaWholeBlood() {
+		assertEquals("EDTA", EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.EDTA_WHOLE_BLOOD));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_UnmappedMaterial() {
+		assertNull(EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.CEREBROSPINAL_FLUID));
+		assertNull(EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(SampleMaterial.STOOL));
+	}
+
+	@Test
+	public void testMapSampleMaterialToEpipulseCode_Null() {
+		assertNull(EpipulseLaboratoryMapper.mapSampleMaterialToEpipulseCode(null));
+	}
+}

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

@@ -182,7 +182,7 @@ public String buildPathogenTestsCte() {
 			   "                                                                           pathogentest.testtype," +
 			   "                                                                           pathogentest.testresult" +
 			   "                                                                 ), '#'" +
-			   "                                                                 ORDER BY pathogentest.testdatetime DESC) AS all_pathogen_tests_from_latest" +
+			   "                                                                 ORDER BY COALESCE(pathogentest.testdatetime, pathogentest.reportdate, pathogentest.creationdate) DESC) AS all_pathogen_tests_from_latest" +
 			   "                                               FROM pathogentest" +
 			   "                                                        INNER JOIN case_all_samples_from_latest" +
 			   "                                                                   ON pathogentest.sample_id = ANY" +

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

@@ -222,7 +222,7 @@ private String buildPneuSerotypingDataCte() {
 			   "                                AND s.deleted = false " +
 			   "                                AND pt.testtype IN ('SEROGROUPING', 'GENOTYPING', 'WHOLE_GENOME_SEQUENCING') " +
 			   "                                AND pt.typingid IS NOT NULL " +
-			   "                              ORDER BY pt.testdatetime DESC " +
+			   "                              ORDER BY COALESCE(pt.testdatetime, pt.reportdate, pt.creationdate) DESC NULLS LAST, pt.id DESC " +
 			   "                              LIMIT 1) as serotype " +
 			   "                      FROM filtered_cases c)";
 		//@formatter:on
@@ -240,7 +240,7 @@ private String buildPneuPathogenDetectionMethodCte() {
 			   "                                   WHERE s.associatedcase_id = c.id " +
 			   "                                     AND s.deleted = false " +
 			   "                                     AND pt.testresultverified = true " +
-			   "                                   ORDER BY pt.testdatetime DESC " +
+			   "                                   ORDER BY COALESCE(pt.testdatetime, pt.reportdate, pt.creationdate) DESC NULLS LAST, pt.id DESC " +
 			   "                                   LIMIT 1) as detection_method " +
 			   "                           FROM filtered_cases c)";
 		//@formatter:on
@@ -341,7 +341,7 @@ private String buildPneuAstDataCte() {
 			   "    LEFT JOIN pathogentest pt ON pt.sample_id = s.id " +
 			   "        AND pt.testtype = 'ANTIBIOTIC_SUSCEPTIBILITY' " +
 			   "    LEFT JOIN drugsusceptibility ds ON pt.drugsusceptibility_id = ds.id " +
-			   "    ORDER BY c.id, pt.testdatetime DESC" +
+			   "    ORDER BY c.id, COALESCE(pt.testdatetime, pt.reportdate, pt.creationdate) DESC NULLS LAST, pt.id DESC" +
 			   ")";
 		//@formatter:on
 	}

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

@@ -136,19 +136,21 @@ protected void mapDiseaseSpecificFields(EpipulseDiseaseExportEntryDto dto, Objec
 			}
 		}
 
-		// Complications mapping (4 fields)
+		// Complications mapping (5 fields)
 		String acuteEncephalitisRaw = (String) row[++index];
 		String diarrheaRaw = (String) row[++index];
 		String otitisMediaRaw = (String) row[++index];
+		String pneumoniaRaw = (String) row[++index];
 		String otherComplicationsRaw = (String) row[++index];
 
 		SymptomState acuteEncephalitis = parseSymptomState(acuteEncephalitisRaw);
 		SymptomState diarrhea = parseSymptomState(diarrheaRaw);
 		SymptomState otitisMedia = parseSymptomState(otitisMediaRaw);
+		SymptomState pneumonia = parseSymptomState(pneumoniaRaw);
 		SymptomState otherComplications = parseSymptomState(otherComplicationsRaw);
 
 		dto.setComplicationDiagnosis(
-			EpipulseLaboratoryMapper.mapSymptomsToComplicationCodes(acuteEncephalitis, diarrhea, otitisMedia, otherComplications));
+			EpipulseLaboratoryMapper.mapSymptomsToComplicationCodes(acuteEncephalitis, diarrhea, otitisMedia, pneumonia, otherComplications));
 
 		// Clinical criteria status
 		String clinicalConfirmationRaw = (String) row[++index];
@@ -218,18 +220,22 @@ 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 (SELECT DISTINCT s_vir.id, s_vir.associatedcase_id, s_vir.samplematerial " +
+			   "                LEFT JOIN (SELECT DISTINCT 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 " +
+			   "                             AND s_vir.associatedcase_id IN (SELECT id FROM filtered_cases)) s2 " +
 			   "                          ON s2.associatedcase_id = c.id " +
-			   "                LEFT JOIN (SELECT DISTINCT s_sero.id, s_sero.associatedcase_id, s_sero.samplematerial " +
+			   "                LEFT JOIN (SELECT DISTINCT s_sero.associatedcase_id, s_sero.samplematerial " +
 			   "                           FROM samples s_sero " +
-			   "                           JOIN pathogentest pt_sero ON pt_sero.sample_id = s_sero.id " +
+			   "                           LEFT JOIN pathogentest pt_sero ON pt_sero.sample_id = s_sero.id " +
+			   "                               AND pt_sero.testtype IN ('IGG_SERUM_ANTIBODY', 'IGM_SERUM_ANTIBODY') " +
 			   "                           WHERE s_sero.deleted = false " +
-			   "                             AND pt_sero.testtype IN ('IGG_SERUM_ANTIBODY', 'IGM_SERUM_ANTIBODY', 'SEROLOGY')) s3 " +
+			   "                             AND s_sero.samplematerial IS NOT NULL " +
+			   "                             AND s_sero.associatedcase_id IN (SELECT id FROM filtered_cases) " +
+			   "                             AND (pt_sero.id IS NOT NULL OR NOT EXISTS ( " +
+			   "                                 SELECT 1 FROM pathogentest pt_any WHERE pt_any.sample_id = s_sero.id " +
+			   "                             ))) s3 " +
 			   "                          ON s3.associatedcase_id = c.id " +
 			   "                GROUP BY c.id)";
 		//@formatter:on
@@ -238,29 +244,27 @@ private String buildSampleDataCte() {
 	private String buildVirusDetectionDataCte() {
 		//@formatter:off
 		return "virus_detection_data AS (SELECT c.id as case_id," +
-			   "                                 MIN(pt.testdatetime) as lab_result_date," +
+			   "                                 MIN(COALESCE(pt.testdatetime, pt.reportdate, pt.creationdate)) as lab_result_date," +
 			   "                                 (SELECT pt2.testresult " +
 			   "                                  FROM samples s2 " +
 			   "                                  JOIN pathogentest pt2 ON pt2.sample_id = s2.id " +
 			   "                                  WHERE s2.associatedcase_id = c.id " +
 			   "                                    AND s2.deleted = false " +
-			   "                                    AND pt2.testtype IN ('PCR_RT_PCR', 'CULTURE', 'ISOLATION', 'DIRECT_FLUORESCENT_ANTIBODY', 'INDIRECT_FLUORESCENT_ANTIBODY') " +
-			   "                                    AND pt2.testresultverified = true " +
-			   "                                  ORDER BY pt2.testdatetime ASC " +
+			   "                                    AND pt2.testtype IN ('PCR_RT_PCR', 'CULTURE', 'ISOLATION', 'DIRECT_FLUORESCENT_ANTIBODY', 'INDIRECT_FLUORESCENT_ANTIBODY', 'SEQUENCING', 'GENOTYPING') " +
+			   "                                  ORDER BY pt2.testresultverified DESC, COALESCE(pt2.testdatetime, pt2.reportdate, pt2.creationdate) ASC " +
 			   "                                  LIMIT 1) as virus_detection_result," +
 			   "                                 (SELECT COALESCE(pt3.typingid, pt3.genotyperesult) " +
 			   "                                  FROM samples s3 " +
 			   "                                  JOIN pathogentest pt3 ON pt3.sample_id = s3.id " +
 			   "                                  WHERE s3.associatedcase_id = c.id " +
 			   "                                    AND s3.deleted = false " +
 			   "                                    AND (pt3.typingid IS NOT NULL OR pt3.genotyperesult IS NOT NULL) " +
-			   "                                  ORDER BY pt3.testdatetime ASC " +
+			   "                                  ORDER BY COALESCE(pt3.testdatetime, pt3.reportdate, pt3.creationdate) ASC " +
 			   "                                  LIMIT 1) as genotype_raw " +
 			   "                          FROM filtered_cases c " +
 			   "                          LEFT JOIN samples s ON s.associatedcase_id = c.id AND s.deleted = false " +
 			   "                          LEFT JOIN pathogentest pt ON pt.sample_id = s.id " +
-			   "                              AND pt.testtype IN ('PCR_RT_PCR', 'CULTURE', 'ISOLATION', 'DIRECT_FLUORESCENT_ANTIBODY', 'INDIRECT_FLUORESCENT_ANTIBODY') " +
-			   "                              AND pt.testresultverified = true " +
+			   "                              AND pt.testtype IN ('PCR_RT_PCR', 'CULTURE', 'ISOLATION', 'DIRECT_FLUORESCENT_ANTIBODY', 'INDIRECT_FLUORESCENT_ANTIBODY', 'SEQUENCING', 'GENOTYPING') " +
 			   "                          GROUP BY c.id)";
 		//@formatter:on
 	}
@@ -277,7 +281,7 @@ private String buildIggSerologyDataCte() {
 			   "                               WHERE s_igg.associatedcase_id = c.id " +
 			   "                                 AND s_igg.deleted = false " +
 			   "                                 AND pt_igg.testtype = 'IGG_SERUM_ANTIBODY' " +
-			   "                               ORDER BY pt_igg.testdatetime ASC " +
+			   "                               ORDER BY COALESCE(pt_igg.testdatetime, pt_igg.reportdate, pt_igg.creationdate) ASC " +
 			   "                               LIMIT 1) as igg_result " +
 			   "                      FROM filtered_cases c)";
 		//@formatter:on
@@ -292,7 +296,7 @@ private String buildIgmSerologyDataCte() {
 			   "                               WHERE s_igm.associatedcase_id = c.id " +
 			   "                                 AND s_igm.deleted = false " +
 			   "                                 AND pt_igm.testtype = 'IGM_SERUM_ANTIBODY' " +
-			   "                               ORDER BY pt_igm.testdatetime ASC " +
+			   "                               ORDER BY COALESCE(pt_igm.testdatetime, pt_igm.reportdate, pt_igm.creationdate) ASC " +
 			   "                               LIMIT 1) as igm_result " +
 			   "                      FROM filtered_cases c)";
 		//@formatter:on
@@ -337,6 +341,7 @@ private String buildComplicationsDataCte() {
 			   "                              s.acuteencephalitis," +
 			   "                              s.diarrhea," +
 			   "                              s.otitismedia," +
+			   "                              s.pneumoniaclinicalorradiologic," +
 			   "                              s.othercomplications " +
 			   "                       FROM filtered_cases c " +
 			   "                       LEFT JOIN symptoms s ON c.symptoms_id = s.id)";
@@ -366,6 +371,7 @@ private String buildMeaslesSelectClause() {
 		      .append("       comp.acuteencephalitis,")
 		      .append("       comp.diarrhea,")
 		      .append("       comp.otitismedia,")
+		      .append("       comp.pneumoniaclinicalorradiologic,")
 		      .append("       comp.othercomplications,")
 		      .append("       c.clinicalconfirmation,")
 		      .append("       el.infection_locations,")

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

@@ -253,7 +253,7 @@ private String buildMeniSerogroupCte() {
 			   "              AND s.deleted = false " +
 			   "              AND pt.testtype IN ('SEROGROUPING', 'SLIDE_AGGLUTINATION') " +
 			   "              AND pt.typingid IS NOT NULL " +
-			   "            ORDER BY pt.testdatetime DESC " +
+			   "            ORDER BY COALESCE(pt.testdatetime, pt.reportdate, pt.creationdate) DESC NULLS LAST, pt.id DESC " +
 			   "            LIMIT 1) as serogroup " +
 			   "    FROM filtered_cases c" +
 			   ")";
@@ -419,7 +419,7 @@ private String buildMeniAstDataCte() {
 			   "    LEFT JOIN pathogentest pt ON pt.sample_id = s.id " +
 			   "        AND pt.testtype = 'ANTIBIOTIC_SUSCEPTIBILITY' " +
 			   "    LEFT JOIN drugsusceptibility ds ON pt.drugsusceptibility_id = ds.id " +
-			   "    ORDER BY c.id, pt.testdatetime DESC" +
+			   "    ORDER BY c.id, COALESCE(pt.testdatetime, pt.reportdate, pt.creationdate) DESC NULLS LAST, pt.id DESC" +
 			   ")";
 		//@formatter:on
 	}