v2.0.4 changes

config/appConfig.xml

@@ -3,8 +3,8 @@
 <properties>
 <comment>Application configuration</comment>
 <entry key="Application.Name">EFSA TSE data reporting tool</entry> <!-- main title of the application -->
-<entry key="Application.Version">2.0.3</entry> <!-- version of the application that will displayed after the application name -->
-<entry key="Db.MinRequiredVersion">2.0.3</entry> <!-- version of the database needed -->
+<entry key="Application.Version">2.0.4</entry> <!-- version of the application that will displayed after the application name -->
+<entry key="Db.MinRequiredVersion">2.0.4</entry> <!-- version of the database needed -->
 <entry key="Application.Icon">app-icon.png</entry> <!-- application icon (in the icon folder) -->
 
 <entry key="TechnicalSupport.Email">zoonoses_support@efsa.europa.eu</entry> <!-- email which will be used for technical support -->

pom.xml

@@ -41,18 +41,18 @@
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-api</artifactId>
-			<version>[2.17.1,)</version>
+			<version>2.17.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>[2.17.1,)</version>
+			<version>2.17.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.junit.jupiter</groupId>
 			<artifactId>junit-jupiter</artifactId>
 			<scope>test</scope>
-			<version>[5.5.2,)</version>
+			<version>5.5.2</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.derby</groupId>

src/main/java/predefined_results/PredefinedResultList.java

@@ -9,11 +9,9 @@
 import app_config.BooleanValue;
 
 public class PredefinedResultList extends ArrayList<PredefinedResult> {
-
 	private static final Logger LOGGER = LogManager.getLogger(PredefinedResultList.class);
-
 	private static final long serialVersionUID = -6372192676663884532L;
-	
+
 	private static PredefinedResultList predefinedResultsCache;
 
 	/**
@@ -23,16 +21,14 @@ public class PredefinedResultList extends ArrayList<PredefinedResult> {
 	 * @return
 	 */
 	public PredefinedResult get(String recordType, String source, boolean confirmatoryTested, String sampEventAsses) {
-
 		for (PredefinedResult prh : this) {
-
 			String thisRecordType = prh.get(PredefinedResultHeader.RECORD_TYPE);
 			String thisSource = prh.get(PredefinedResultHeader.SOURCE);
 			String thisSampEventAsses = prh.get(PredefinedResultHeader.SAMP_EVENT_ASSES);
 			String thisConfTested = prh.get(PredefinedResultHeader.CONFIRMATORY_EXECUTED);
 
 			boolean confCheck = (BooleanValue.isTrue(thisConfTested) && confirmatoryTested)
-					|| (BooleanValue.isFalse(thisConfTested) && !confirmatoryTested);
+							|| (BooleanValue.isFalse(thisConfTested) && !confirmatoryTested);
 
 			if (isFieldEqual(thisRecordType, recordType)
 					&& isFieldEqual(thisSource, source)
@@ -52,9 +48,8 @@ && isFieldEqual(thisSampEventAsses, sampEventAsses)
 	 * @return
 	 */
 	private static boolean isFieldEqual(String predefResValue, String rowValue) {
-
 		// always match an empty field in the configuration
-		if(predefResValue == null || predefResValue.isEmpty() || predefResValue.equals("null")) {
+		if (predefResValue == null || predefResValue.isEmpty() || predefResValue.equals("null")) {
 			return true;
 		}
 
@@ -72,18 +67,14 @@ private static boolean isFieldEqual(String predefResValue, String rowValue) {
 	 * @throws IOException
 	 */
 	public static PredefinedResultList getAll() {
-
 		// if first time
 		if (predefinedResultsCache == null) {
-
 			predefinedResultsCache = new PredefinedResultList();
 
 			//solve memory leak
 			try (PredefinedResultsReader reader = new PredefinedResultsReader()){
 				reader.readFirstSheet();
-
 				predefinedResultsCache = reader.getResults();
-
 			} catch (IOException e) {
 				LOGGER.error("Cannot retrieve predefined results list", e);
 				e.printStackTrace();

src/main/java/providers/PredefinedResultService.java

@@ -25,11 +25,10 @@
  *
  */
 public class PredefinedResultService {
-
 	private static final Logger LOGGER = LogManager.getLogger(PredefinedResultService.class);
 
-	private ITableDaoService daoService;
-	private IFormulaService formulaService;
+	private final ITableDaoService daoService;
+	private final IFormulaService formulaService;
 
 	public PredefinedResultService(ITableDaoService daoService, IFormulaService formulaService) {
 		this.daoService = daoService;
@@ -43,9 +42,7 @@ public PredefinedResultService(ITableDaoService daoService, IFormulaService form
 	 * @param caseReport
 	 * @throws IOException
 	 */
-	public TableRowList createDefaultResults(Report report, 
-			SummarizedInfo summInfo, CaseReport caseReport) throws IOException {
-
+	public TableRowList createDefaultResults(Report report, SummarizedInfo summInfo, CaseReport caseReport) {
 		TableRowList results = new TableRowList();
 
 		AnalyticalResult r = createDefaultResult(report, summInfo, caseReport, 
@@ -85,39 +82,34 @@ public TableRowList createDefaultResults(Report report,
 	 * @return
 	 * @throws IOException
 	 */
-	public boolean isConfirmatoryTested(String type) throws IOException {
-
-		String confirmatory = "";
-
+	public boolean isConfirmatoryTested(String type) {
+		String column;
 		switch(type) {
-		case CustomStrings.SUMMARIZED_INFO_BSE_TYPE:
-			confirmatory = Relation.getGlobalParent(CustomStrings.PREFERENCES_SHEET, daoService)
-					.getCode(CustomStrings.PREFERENCES_CONFIRMATORY_BSE);
-			break;
-		case CustomStrings.SUMMARIZED_INFO_SCRAPIE_TYPE:
-			confirmatory = Relation.getGlobalParent(CustomStrings.PREFERENCES_SHEET, daoService)
-			.getCode(CustomStrings.PREFERENCES_CONFIRMATORY_SCRAPIE);
-			break;
-		case CustomStrings.SUMMARIZED_INFO_CWD_TYPE:
-			confirmatory = Relation.getGlobalParent(CustomStrings.PREFERENCES_SHEET, daoService)
-			.getCode(CustomStrings.PREFERENCES_CONFIRMATORY_CWD);
-			break;
-		default:
-			break;
+			case CustomStrings.SUMMARIZED_INFO_BSE_TYPE:
+				column = CustomStrings.PREFERENCES_CONFIRMATORY_BSE;
+				break;
+			case CustomStrings.SUMMARIZED_INFO_SCRAPIE_TYPE:
+				column = CustomStrings.PREFERENCES_CONFIRMATORY_SCRAPIE;
+				break;
+			case CustomStrings.SUMMARIZED_INFO_CWD_TYPE:
+				column = CustomStrings.PREFERENCES_CONFIRMATORY_CWD;
+				break;
+			case CustomStrings.SUMMARIZED_INFO_BSEOS_TYPE:
+				column = CustomStrings.PREFERENCES_CONFIRMATORY_BSE_OS;
+				break;
+			default:
+				return false;
 		}
-
-		return !confirmatory.isEmpty();
+		return ! Relation.getGlobalParent(CustomStrings.PREFERENCES_SHEET, daoService)
+					.getCode(column)
+					.isEmpty();
 	}
 
-	public static String getPreferredTestType(String testType) throws IOException {
-
-		return Relation.getGlobalParent(CustomStrings.PREFERENCES_SHEET)
-				.getCode(testType);
+	public static String getPreferredTestType(String testType) {
+		return Relation.getGlobalParent(CustomStrings.PREFERENCES_SHEET).getCode(testType);
 	}
 
-	public static String getPreferredTestType(String recordType, String testType) 
-			throws IOException {
-
+	public static String getPreferredTestType(String recordType, String testType) {
 		String preferredTestType = null;
 
 		switch(testType) {
@@ -135,6 +127,10 @@ public static String getPreferredTestType(String recordType, String testType)
 				preferredTestType = getPreferredTestType( 
 						CustomStrings.PREFERENCES_SCREENING_CWD);
 				break;
+			case CustomStrings.SUMMARIZED_INFO_BSEOS_TYPE:
+					preferredTestType = getPreferredTestType(
+							CustomStrings.PREFERENCES_SCREENING_BSE_OS);
+					break;
 			default:
 				break;
 			}
@@ -153,6 +149,10 @@ public static String getPreferredTestType(String recordType, String testType)
 				preferredTestType = getPreferredTestType( 
 						CustomStrings.PREFERENCES_CONFIRMATORY_CWD);
 				break;
+			case CustomStrings.SUMMARIZED_INFO_BSEOS_TYPE:
+				preferredTestType = getPreferredTestType(
+						CustomStrings.PREFERENCES_CONFIRMATORY_BSE_OS);
+				break;
 			default:
 				break;
 			}
@@ -171,6 +171,10 @@ public static String getPreferredTestType(String recordType, String testType)
 				preferredTestType = getPreferredTestType( 
 						CustomStrings.PREFERENCES_DISCRIMINATORY_CWD);
 				break;
+			case CustomStrings.SUMMARIZED_INFO_BSEOS_TYPE:
+				preferredTestType = getPreferredTestType(
+						CustomStrings.PREFERENCES_DISCRIMINATORY_BSE_OS);
+				break;
 			default:
 				break;
 			}
@@ -185,8 +189,7 @@ public static String getPreferredTestType(String recordType, String testType)
 		return preferredTestType;
 	}
 
-	public PredefinedResult getPredefinedResult(SummarizedInfo summInfo, TableRow caseReport) throws IOException {
-
+	public PredefinedResult getPredefinedResult(SummarizedInfo summInfo, TableRow caseReport) {
 		// put the predefined value for the param code and the result
 		PredefinedResultList predResList = PredefinedResultList.getAll();
 
@@ -208,14 +211,11 @@ public PredefinedResult getPredefinedResult(SummarizedInfo summInfo, TableRow ca
 	 * @param report
 	 * @param summInfo
 	 * @param caseReport
-	 * @param codeCol
 	 * @param testTypeCode
 	 * @throws IOException
 	 */
-	private AnalyticalResult createDefaultResult(Report report, 
-			SummarizedInfo summInfo, TableRow caseReport, 
-			PredefinedResultHeader test, 
-			String testTypeCode) throws IOException {
+	private AnalyticalResult createDefaultResult(Report report, SummarizedInfo summInfo, TableRow caseReport,
+			PredefinedResultHeader test, String testTypeCode) {
 
 		AnalyticalResult resultRow = new AnalyticalResult();
 
@@ -231,7 +231,6 @@ private AnalyticalResult createDefaultResult(Report report,
 		boolean added = addParamAndResult(resultRow, defaultResult, test);
 
 		if (added) {
-
 			// code crack to save the row id for the resId field
 			// otherwise its default value will be corrupted
 			daoService.add(resultRow);
@@ -269,10 +268,7 @@ private AnalyticalResult createDefaultResult(Report report,
 	 * @param codeCol
 	 * @return
 	 */
-	public static boolean addParamAndResult(TableRow result, 
-			PredefinedResult defValues, 
-			PredefinedResultHeader codeCol) {
-
+	private boolean addParamAndResult(TableRow result, PredefinedResult defValues, PredefinedResultHeader codeCol) {
 		String code = defValues.get(codeCol);
 
 		// put the test aim
@@ -284,17 +280,15 @@ public static boolean addParamAndResult(TableRow result,
 		return addParamAndResult(result, code);
 	}
 
-
-
 	/**
 	 * Add param and result. These values are taken from the test code
 	 * which is composed of paramBaseTerm$resultValue
+	 *
 	 * @param result
 	 * @param testCode
 	 * @return
 	 */
 	public static boolean addParamAndResult(TableRow result, String testCode) {
-
 		if (testCode == null)
 			return false;