Merge pull request #96 from KPMP/KPMP-4545_total_files_count

KPMP-4545: updated query and resolved test nullptr exceptions

src/main/java/org/kpmp/dataSummary/DataSummaryRepository.java

@@ -51,7 +51,7 @@ public interface DataSummaryRepository extends CrudRepository<DataSummaryValue,
 	String getParticipantIDString(@Param("redcap_id") String redcapId);
 
 	@Cacheable("participantTotalFileCount")
-	@Query(value = "SELECT count(*) FROM file_participant fp JOIN ar_file_info ar ON fp.file_id = ar.file_id "
+	@Query(value = "SELECT count(DISTINCT fp.file_id) FROM file_participant fp JOIN ar_file_info ar ON fp.file_id = ar.file_id "
 				+ "WHERE fp.participant_id= :participant_id AND ar.release_sunset_version IS NULL", nativeQuery = true)
 	Integer getParticipantTotalFileCount(@Param("participant_id") String participantId);
 

src/test/java/org/kpmp/autocomplete/AutocompleteServiceTest.java

@@ -1,6 +1,6 @@
 package org.kpmp.autocomplete;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.when;
 
 import java.io.IOException;
@@ -12,6 +12,8 @@
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.TestInstance.Lifecycle;
 import org.kpmp.cellType.CellType;
 import org.kpmp.cellType.CellTypeRepository;
 import org.kpmp.cellType.CellTypeSynonym;
@@ -20,6 +22,7 @@
 import org.mockito.Mock;
 import org.mockito.MockitoAnnotations;
 
+@TestInstance(Lifecycle.PER_CLASS)
 class AutocompleteServiceTest {
 
 	private AutocompleteService autocompleteService;
@@ -31,7 +34,7 @@ class AutocompleteServiceTest {
 	private CellTypeRepository cellTypeRepository;
 
 	@BeforeEach
-	void setUp() {
+	void setUp() throws Exception {
 		MockitoAnnotations.openMocks(this);
 		autocompleteService = new AutocompleteService(geneService, cellTypeRepository);
 	}
@@ -92,42 +95,52 @@ void testConvertCellTypesToAutocompleteResultsRemovesDuplicatesForCellTypeResult
 		List<CellType> cellTypes = new ArrayList<>();
 		cellTypes.add(ct1);
 		cellTypes.add(ct2);
+		List<CellType> regions = new ArrayList<>();
+		List<CellType> subregions = new ArrayList<>();
 
 		assertEquals(ct1, ct2);
 		List<AutocompleteResult> autocompleteResults = autocompleteService
-				.convertCellTypesToAutocompleteResults(cellTypes, null, null);
+				.convertCellTypesToAutocompleteResults(cellTypes, regions, subregions);
 		assertEquals(1, autocompleteResults.size());
 	}
 
 	@Test
 	void testConvertCellTypesToAutocompleteResultsRemovesDuplicatesForStructureRegionResults() throws Exception {
 		CellType ct1 = new CellType();
+		ct1.setCellType("abc");
 		ct1.setStructureRegion("same name");
 		CellType ct2 = new CellType();
+		ct2.setCellType("abc");
 		ct2.setStructureRegion("same name");
 		List<CellType> regions = new ArrayList<>();
 		regions.add(ct1);
 		regions.add(ct2);
+		List<CellType> subregions = new ArrayList<>();
+		List<CellType> cellTypes = new ArrayList<>();
 
 		assertEquals(ct1, ct2);
-		List<AutocompleteResult> autocompleteResults = autocompleteService.convertCellTypesToAutocompleteResults(null,
-				regions, null);
+		List<AutocompleteResult> autocompleteResults = autocompleteService.convertCellTypesToAutocompleteResults(cellTypes,
+				regions, subregions);
 		assertEquals(1, autocompleteResults.size());
 	}
 
 	@Test
 	void testConvertCellTypesToAutocompleteResultsRemovesDuplicatesForStructureSubregionResults() throws Exception {
 		CellType ct1 = new CellType();
+		ct1.setCellType("abc");
 		ct1.setStructureSubregion("same name");
 		CellType ct2 = new CellType();
+		ct2.setCellType("abc");
 		ct2.setStructureSubregion("same name");
 		List<CellType> subregions = new ArrayList<>();
 		subregions.add(ct1);
 		subregions.add(ct2);
+		List<CellType> regions = new ArrayList<>();
+		List<CellType> cellTypes = new ArrayList<>();
 
 		assertEquals(ct1, ct2);
-		List<AutocompleteResult> autocompleteResults = autocompleteService.convertCellTypesToAutocompleteResults(null,
-				null, subregions);
+		List<AutocompleteResult> autocompleteResults = autocompleteService.convertCellTypesToAutocompleteResults(cellTypes,
+				regions, subregions);
 		assertEquals(1, autocompleteResults.size());
 	}
 

src/test/java/org/kpmp/geneExpressionSummary/RTParticipantValueTest.java

@@ -1,21 +1,24 @@
 package org.kpmp.geneExpressionSummary;
 
-import org.junit.After;
-import org.junit.Before;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.TestInstance.Lifecycle;
 
 import static org.junit.jupiter.api.Assertions.*;
 
+@TestInstance(Lifecycle.PER_CLASS)
 class RTParticipantValueTest {
 
     RTParticipantValue rtParticipantValue;
 
-    @Before
+    @BeforeAll
     public void setUp() throws Exception {
         rtParticipantValue = new RTParticipantValue();
     }
 
-    @After
+    @AfterAll
     public void tearDown() throws Exception {
         rtParticipantValue = null;
     }

src/test/java/org/kpmp/participant/ParticipantSummaryDatasetTest.java

@@ -1,21 +1,23 @@
 package org.kpmp.participant;
 
-import org.junit.After;
-import org.junit.Before;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.TestInstance.Lifecycle;
 
 import static org.junit.jupiter.api.Assertions.*;
 
+@TestInstance(Lifecycle.PER_CLASS)
 class ParticipantSummaryDatasetTest {
     ParticipantSummaryDataset participantSummaryDataset;
 
-    @Before
-
+    @BeforeAll
     public void setUp() throws Exception {
-        participantSummaryDataset = new ParticipantSummaryDataset();
+        this.participantSummaryDataset = new ParticipantSummaryDataset();
     }
 
-    @After
+    @AfterAll
     public void tearDown() throws Exception {
         participantSummaryDataset = null;
     }