Merge pull request #89 from KPMP/KPMP-4577_TableCountsIncorrect

KPMP-4577: Do better counting of files

.project

@@ -2,30 +2,32 @@
 <projectDescription>
 	<name>pegasus-data</name>
 	<comment></comment>
-	<projects/>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
-	</natures>
+	<projects>
+	</projects>
 	<buildSpec>
 		<buildCommand>
 			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments/>
+			<arguments>
+			</arguments>
 		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
-			<arguments/>
+			<arguments>
+			</arguments>
 		</buildCommand>
 	</buildSpec>
-	<linkedResources/>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
+	</natures>
 	<filteredResources>
 		<filter>
-			<id>1</id>
+			<id>1686668102644</id>
+			<name></name>
 			<type>30</type>
-			<name/>
 			<matcher>
 				<id>org.eclipse.core.resources.regexFilterMatcher</id>
-				<arguments>node_modules|.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
+				<arguments>node_modules|\.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
 			</matcher>
 		</filter>
 	</filteredResources>

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

@@ -6,9 +6,9 @@
 public class AtlasRepoSummaryResult {
 
 	private List<AtlasRepoSummaryRow> summaryRows;
-	private int totalFiles;
+	private Long totalFiles;
 
-	public AtlasRepoSummaryResult(List<AtlasRepoSummaryRow> summaryRows, int totalFiles) {
+	public AtlasRepoSummaryResult(List<AtlasRepoSummaryRow> summaryRows, Long totalFiles) {
 		this.summaryRows = summaryRows;
 		this.totalFiles = totalFiles;
 
@@ -26,11 +26,11 @@ public void setSummaryRows(List<AtlasRepoSummaryRow> summaryRows) {
 		this.summaryRows = summaryRows;
 	}
 
-	public int getTotalFiles() {
+	public Long getTotalFiles() {
 		return totalFiles;
 	}
 
-	public void setTotalFiles(int totalFiles) {
+	public void setTotalFiles(Long totalFiles) {
 		this.totalFiles = totalFiles;
 	}
 

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

@@ -11,6 +11,7 @@
 import org.kpmp.FullDataTypeEnum;
 import org.kpmp.OmicsTypeEnum;
 import org.kpmp.TissueTypeEnum;
+import org.kpmp.file.ARFileInfoService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -26,18 +27,20 @@ public class DataSummaryService {
 
 	private DataSummaryRepository dataSummaryRepository;
 	private AtlasRepoSummaryRepository repoSummaryRepository;
+	private ARFileInfoService fileInfoService;
 
 	@Autowired
 	public DataSummaryService(DataSummaryRepository dataSummaryRepository,
-			AtlasRepoSummaryRepository repoSummaryRepository) {
+			AtlasRepoSummaryRepository repoSummaryRepository, ARFileInfoService fileInfoService) {
 		this.dataSummaryRepository = dataSummaryRepository;
 		this.repoSummaryRepository = repoSummaryRepository;
+		this.fileInfoService = fileInfoService;
 	}
 
 	public AtlasRepoSummaryResult getAtlasRepoSummary() throws Exception {
 		List<ExperimentalStrategyValue> experimentalStrategies = repoSummaryRepository.findAll();
 		Map<String, AtlasRepoSummaryRow> summaryMap = new HashMap<>();
-		int totalFiles = 0;
+
 		for (ExperimentalStrategyValue experimentalStrategyValue : experimentalStrategies) {
 			String experimentalStrategy = experimentalStrategyValue.getExperimentalStrategy();
 			if (experimentalStrategy.isEmpty()
@@ -50,13 +53,11 @@ public AtlasRepoSummaryResult getAtlasRepoSummary() throws Exception {
 			if (summaryMap.containsKey(experimentalStrategy)) {
 				AtlasRepoSummaryRow atlasRepoSummaryRow = summaryMap.get(experimentalStrategy);
 				setCounts(experimentalStrategyValue, atlasRepoSummaryRow);
-				totalFiles += experimentalStrategyValue.getCount();
 			} else {
 				AtlasRepoSummaryRow row = new AtlasRepoSummaryRow(experimentalStrategy,
 						getLinkInformation(experimentalStrategyValue));
 				setCounts(experimentalStrategyValue, row);
 				summaryMap.put(experimentalStrategy, row);
-				totalFiles += experimentalStrategyValue.getCount();
 			}
 		}
 
@@ -69,7 +70,7 @@ public int compare(AtlasRepoSummaryRow one, AtlasRepoSummaryRow two) {
 			}
 		});
 
-		return new AtlasRepoSummaryResult(results, totalFiles);
+		return new AtlasRepoSummaryResult(results, fileInfoService.getRepositoryTotalFileCount());
 	}
 
 	private AtlasRepoSummaryLinkInformation getLinkInformation(ExperimentalStrategyValue experimentalStrategy) {

src/main/java/org/kpmp/file/ARFileInfo.java

@@ -0,0 +1,57 @@
+package org.kpmp.file;
+
+import javax.persistence.Entity;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+@Entity
+@Table(name = "ar_file_info")
+public class ARFileInfo {
+    @Id
+    private int arFileInfoId;
+    private int fileId;
+    private int releaseVersion;
+    private int releaseSunsetVersion;
+    private int metadataTypeId;
+
+    public int getMetadataTypeId() {
+        return metadataTypeId;
+    }
+
+    public void setMetadataTypeId(int metadataTypeId) {
+        this.metadataTypeId = metadataTypeId;
+    }
+
+    public int getArFileInfoId() {
+        return arFileInfoId;
+    }
+
+    public void setArFileInfoId(int arFileInfoId) {
+        this.arFileInfoId = arFileInfoId;
+    }
+
+    public int getFileId() {
+        return fileId;
+    }
+
+    public void setFileId(int fileId) {
+        this.fileId = fileId;
+    }
+
+    public int getReleaseVersion() {
+        return releaseVersion;
+    }
+
+    public void setReleaseVersion(int releaseVersion) {
+        this.releaseVersion = releaseVersion;
+    }
+
+    public int getReleaseSunsetVersion() {
+        return releaseSunsetVersion;
+    }
+
+    public void setReleaseSunsetVersion(int releaseSunsetVersion) {
+        this.releaseSunsetVersion = releaseSunsetVersion;
+    }
+
+}

src/main/java/org/kpmp/file/ARFileInfoRepository.java

@@ -0,0 +1,14 @@
+package org.kpmp.file;
+
+import org.springframework.cache.annotation.Cacheable;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.CrudRepository;
+import org.springframework.stereotype.Repository;
+
+@Repository
+interface ARFileInfoRepository extends CrudRepository<ARFileInfo, Integer>{
+
+    @Cacheable("totalFileCount")
+	@Query(value = "select count(distinct(file_id)) from ar_file_info where release_sunset_version is null" , nativeQuery = true)
+	Long getTotalFileCount();
+}

src/main/java/org/kpmp/file/ARFileInfoService.java

@@ -0,0 +1,20 @@
+package org.kpmp.file;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ARFileInfoService {
+
+    private ARFileInfoRepository repository;
+
+    @Autowired
+    public ARFileInfoService (ARFileInfoRepository repository) {
+        this.repository = repository;
+    }
+
+    public Long getRepositoryTotalFileCount() {
+        return repository.getTotalFileCount();
+    }
+
+}

src/test/java/org/kpmp/dataSummary/AtlasRepoSummaryResultTest.java

@@ -27,11 +27,11 @@ public void tearDown() throws Exception {
 
 	@Test
 	public void testConstructor() throws Exception {
-		int totalFiles = 5;
+		Long totalFiles = 5l;
 		AtlasRepoSummaryResult constructorTest = new AtlasRepoSummaryResult(summaryRows, totalFiles);
 
 		assertEquals(summaryRows, constructorTest.getSummaryRows());
-		assertEquals(5, constructorTest.getTotalFiles());
+		assertEquals(totalFiles, constructorTest.getTotalFiles());
 
 	}
 
@@ -44,9 +44,10 @@ public void testSetSummaryRows() {
 
 	@Test
 	public void testSetTotalFiles() {
-		result.setTotalFiles(58);
+		Long totalFiles = 58l;
+		result.setTotalFiles(totalFiles);
 
-		assertEquals(58, result.getTotalFiles());
+		assertEquals(totalFiles, result.getTotalFiles());
 	}
 
 }

src/test/java/org/kpmp/dataSummary/DataSummaryServiceTest.java

@@ -12,6 +12,7 @@
 import org.kpmp.DataTypeEnum;
 import org.kpmp.FullDataTypeEnum;
 import org.kpmp.TissueTypeEnum;
+import org.kpmp.file.ARFileInfoService;
 import org.mockito.Mock;
 import org.mockito.MockitoAnnotations;
 
@@ -21,11 +22,13 @@ public class DataSummaryServiceTest {
 	private DataSummaryRepository dataSummaryRepository;
 	@Mock
 	private AtlasRepoSummaryRepository atlasRepoSummaryRepository;
+	@Mock
+	private ARFileInfoService fileInfoService;
 
 	@Before
 	public void setUp() throws Exception {
 		MockitoAnnotations.openMocks(this);
-		dataSummaryService = new DataSummaryService(dataSummaryRepository, atlasRepoSummaryRepository);
+		dataSummaryService = new DataSummaryService(dataSummaryRepository, atlasRepoSummaryRepository, fileInfoService);
 	}
 
 	@After
@@ -71,6 +74,7 @@ public void testGetAtlasRepoSummary() throws Exception {
 		List<ExperimentalStrategyValue> strategyValues = Arrays.asList(clinicalData, biomarker1, biomarker2, other1,
 				other2);
 		when(atlasRepoSummaryRepository.findAll()).thenReturn(strategyValues);
+		when(fileInfoService.getRepositoryTotalFileCount()).thenReturn(36l);
 
 		AtlasRepoSummaryResult result = dataSummaryService.getAtlasRepoSummary();
 		List<AtlasRepoSummaryRow> summaryRows = result.getSummaryRows();
@@ -90,7 +94,7 @@ public void testGetAtlasRepoSummary() throws Exception {
 		assertEquals(10, summaryRows.get(2).getOpenCount());
 		assertEquals(new AtlasRepoSummaryLinkInformation("experimental_strategy", "strategy1"),
 				summaryRows.get(2).getLinkInformation());
-		assertEquals(36, result.getTotalFiles());
+		assertEquals(new Long(36), result.getTotalFiles());
 
 	}
 

src/test/java/org/kpmp/file/ARFileInfoServiceTest.java

@@ -0,0 +1,36 @@
+package org.kpmp.file;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.when;
+
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.mockito.Mock;
+import org.mockito.MockitoAnnotations;
+
+public class ARFileInfoServiceTest {
+
+    @Mock
+    ARFileInfoRepository fileInfoRepository;
+    private ARFileInfoService service;
+
+    @BeforeEach
+	public void setUp() throws Exception {
+		MockitoAnnotations.openMocks(this);
+		service = new ARFileInfoService(fileInfoRepository);
+	}
+
+    @AfterEach
+    public void tearDown() throws Exception {
+
+        MockitoAnnotations.openMocks(this).close();
+        service = null;
+    }
+
+    @Test
+    void testGetRepositoryTotalFileCount() {
+        when(fileInfoRepository.getTotalFileCount()).thenReturn(2l);
+        assertEquals(new Long(2), service.getRepositoryTotalFileCount());
+    }
+}

src/test/java/org/kpmp/file/ARFileInfoTest.java

@@ -0,0 +1,54 @@
+package org.kpmp.file;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+public class ARFileInfoTest {
+
+    private ARFileInfo fileInfo;
+
+    @BeforeEach
+    public void setUp() throws Exception {
+        fileInfo = new ARFileInfo();
+    }
+
+    @AfterEach
+    public void tearDown() throws Exception {
+        fileInfo = null;
+    }
+
+    @Test
+    public void testSetArFileInfoId() {
+        fileInfo.setArFileInfoId(4);
+        assertEquals(4, fileInfo.getArFileInfoId());
+    }
+
+    @Test
+    public void testSetFileId() {
+        fileInfo.setFileId(12);
+        assertEquals(12, fileInfo.getFileId());
+    }
+
+    @Test
+    public void testSetReleaseVersion() {
+        fileInfo.setReleaseVersion(4);
+        assertEquals(4, fileInfo.getReleaseVersion());
+    }
+
+    @Test
+    public void testSetReleaseSunsetVersion() {
+        fileInfo.setReleaseSunsetVersion(45);
+        assertEquals(45, fileInfo.getReleaseSunsetVersion());
+    }
+
+    @Test
+    public void testSetMetadataTypeId() {
+        fileInfo.setMetadataTypeId(66);
+        assertEquals(66, fileInfo.getMetadataTypeId());
+    }
+}
+
+