Fixed some SonarCloud issues from the complete code analysis

src/main/java/de/unijena/cheminf/mortar/configuration/Configuration.java

@@ -0,0 +1,96 @@
+/*
+ * MORTAR - MOlecule fRagmenTAtion fRamework
+ * Copyright (C) 2024  Felix Baensch, Jonas Schaub (felix.baensch@w-hs.de, jonas.schaub@uni-jena.de)
+ *
+ * Source code is available at <https://github.com/FelixBaensch/MORTAR>
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package de.unijena.cheminf.mortar.configuration;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.MissingResourceException;
+import java.util.Properties;
+
+/**
+ * Thread-safe singleton class for reading configuration properties file, e.g. for paths to resource folders.
+ *
+ * @author Jonas Schaub
+ * @version 1.0.0.0
+ */
+public class Configuration implements IConfiguration {
+    /**
+     * Single instance of this class.
+     */
+    private static Configuration instance;
+    //
+    /**
+     * Properties imported and cached from the configuration properties file.
+     */
+    private final Properties properties;
+    //
+    /**
+     * Path to the configuration properties file to read.
+     */
+    private static final String PROPERTIES_FILE_PATH = "de/unijena/cheminf/mortar/configuration/MORTAR_configuration.properties";
+    //
+    /**
+     * Private constructor that creates the single instance.
+     *
+     * @throws IOException if the properties file is not found or if an error occurs when reading from the input stream
+     */
+    private Configuration() throws IOException {
+        this.properties = new Properties();
+        try (InputStream tmpInputStream = this.getClass().getClassLoader().getResourceAsStream(Configuration.PROPERTIES_FILE_PATH)) {
+            if (tmpInputStream != null) {
+                //throws IOException if an error occurs when reading from the input stream
+                this.properties.load(tmpInputStream);
+            } else {
+                //extends IOException
+                throw new FileNotFoundException(String.format("property file '%s' not found in the classpath", Configuration.PROPERTIES_FILE_PATH));
+            }
+        }
+    }
+    //
+    /**
+     * Returns the single instance of this class.
+     *
+     * @return instance of this class
+     * @throws IOException if the properties file is not found or if an error occurs when reading from the input stream
+     */
+    public static synchronized Configuration getInstance() throws IOException {
+        if (Configuration.instance == null) {
+            Configuration.instance = new Configuration();
+        }
+        return Configuration.instance;
+    }
+    //
+    @Override
+    public String getProperty(String aKey) throws MissingResourceException {
+        String tmpProperty = this.properties.getProperty(aKey).trim();
+        if (tmpProperty == null) {
+            throw new MissingResourceException(String.format("Property '%s' not found", aKey), Configuration.class.getName(), aKey);
+        } else {
+            return tmpProperty;
+        }
+    }
+}

src/main/java/de/unijena/cheminf/mortar/configuration/IConfiguration.java

@@ -0,0 +1,45 @@
+/*
+ * MORTAR - MOlecule fRagmenTAtion fRamework
+ * Copyright (C) 2024  Felix Baensch, Jonas Schaub (felix.baensch@w-hs.de, jonas.schaub@uni-jena.de)
+ *
+ * Source code is available at <https://github.com/FelixBaensch/MORTAR>
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package de.unijena.cheminf.mortar.configuration;
+
+import java.util.MissingResourceException;
+
+/**
+ * Interface for classes reading configuration properties files, e.g. for paths to resource folders.
+ *
+ * @author Jonas Schaub
+ * @version 1.0.0.0
+ */
+public interface IConfiguration {
+    /**
+     * Returns the string value associated with the key in the configurations properties file.
+     *
+     * @param aKey key defined in the configuration properties file
+     * @return property value associated with the given key
+     * @throws MissingResourceException if no associated value could be found for the given key
+     */
+    public String getProperty(String aKey) throws MissingResourceException;
+}

src/main/java/de/unijena/cheminf/mortar/controller/AboutViewController.java

@@ -25,12 +25,12 @@
 
 package de.unijena.cheminf.mortar.controller;
 
+import de.unijena.cheminf.mortar.configuration.IConfiguration;
 import de.unijena.cheminf.mortar.gui.util.ExternalTool;
 import de.unijena.cheminf.mortar.gui.util.GuiDefinitions;
 import de.unijena.cheminf.mortar.gui.util.GuiUtil;
 import de.unijena.cheminf.mortar.gui.views.AboutView;
 import de.unijena.cheminf.mortar.message.Message;
-import de.unijena.cheminf.mortar.model.util.BasicDefinitions;
 import de.unijena.cheminf.mortar.model.util.LogUtil;
 
 import javafx.application.Platform;
@@ -59,7 +59,6 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.InputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.util.Objects;
@@ -73,28 +72,27 @@
  * @version 1.0.0.0
  */
 public class AboutViewController {
-
     //<editor-fold desc="private class variables" defaultstate="collapsed">
     /**
      * Main Stage / parent Stage
      */
     private Stage mainStage;
     /**
-     * View to controll
+     * View to control
      */
     private AboutView aboutView;
     /**
      * Stage to show AboutView
      */
     private Stage aboutViewStage;
-    /**
-     * path to xml file which contains information about external tools
-     */
-    private String toolsXmlFileName = "de/unijena/cheminf/mortar/descriptions/tools_description.xml";
     /**
      * ObservableList to show properties of ExternalTools
      */
     private ObservableList<ExternalTool> toolObservableList;
+    /**
+     * Configuration class to read resource file paths from.
+     */
+    private final IConfiguration configuration;
     //</editor-fold>
     //
     //<editor-fold desc="private static final class variables" defaultstate="collapsed">
@@ -105,13 +103,15 @@ public class AboutViewController {
     //</editor-fold>
     //
     /**
-     * Constructor
+     * Constructor.
      *
      * @param aStage Stage
+     * @param aConfiguration configuration class reading from properties file
      */
-    public AboutViewController(Stage aStage){
+    public AboutViewController(Stage aStage, IConfiguration aConfiguration) {
         this.mainStage = aStage;
         this.toolObservableList = FXCollections.observableArrayList();
+        this.configuration = aConfiguration;
         this.showAboutView();
     }
     //
@@ -121,7 +121,7 @@ public AboutViewController(Stage aStage){
      */
     private void showAboutView(){
         if(this.aboutView == null){
-            this.aboutView = new AboutView();
+            this.aboutView = new AboutView(this.configuration);
         }
         this.aboutViewStage = new Stage();
         Scene tmpScene = new Scene(this.aboutView, GuiDefinitions.GUI_MAIN_VIEW_WIDTH_VALUE, GuiDefinitions.GUI_MAIN_VIEW_HEIGHT_VALUE);
@@ -131,8 +131,9 @@ private void showAboutView(){
         this.aboutViewStage.setTitle(Message.get("AboutView.title.text"));
         this.aboutViewStage.setMinHeight(GuiDefinitions.GUI_MAIN_VIEW_HEIGHT_VALUE);
         this.aboutViewStage.setMinWidth(GuiDefinitions.GUI_MAIN_VIEW_WIDTH_VALUE);
-        InputStream tmpImageInputStream = AboutViewController.class.getResourceAsStream("/de/unijena/cheminf/mortar/images/Mortar_Logo_Icon1.png");
-        this.aboutViewStage.getIcons().add(new Image(tmpImageInputStream));
+        String tmpIconURL = this.getClass().getClassLoader().getResource(
+                this.configuration.getProperty("mortar.imagesFolder") + this.configuration.getProperty("mortar.logo.icon.name")).toExternalForm();
+        this.aboutViewStage.getIcons().add(new Image(tmpIconURL));
         Platform.runLater(()->{
             this.addListeners();
             this.getExternalToolInfosFromXml();
@@ -182,7 +183,7 @@ else if (tmpOS.contains("NUX") || tmpOS.contains("NIX") || tmpOS.contains("AIX")
             else
                 throw new SecurityException("OS name " + tmpOS + " unknown.");
         } catch (IOException anException) {
-            LOGGER.log(Level.SEVERE, anException.toString(), anException);
+            AboutViewController.LOGGER.log(Level.SEVERE, anException.toString(), anException);
             throw new SecurityException("Could not open directory path");
         }
     }
@@ -194,9 +195,9 @@ else if (tmpOS.contains("NUX") || tmpOS.contains("NIX") || tmpOS.contains("AIX")
      */
     private void openGitHubRepositoryInDefaultBrowser(){
         try{
-            Desktop.getDesktop().browse(new URI(BasicDefinitions.GITHUB_REPOSITORY_URL));
+            Desktop.getDesktop().browse(new URI(this.configuration.getProperty("mortar.github.repository.url")));
         } catch (IOException | URISyntaxException anException) {
-            LOGGER.log(Level.SEVERE, anException.toString(), anException);
+            AboutViewController.LOGGER.log(Level.SEVERE, anException.toString(), anException);
             throw new SecurityException("Could not open directory path");
         }
     }
@@ -207,14 +208,14 @@ private void openGitHubRepositoryInDefaultBrowser(){
     private void openTutorialInDefaultPdfViewer() {
         //Note: Does not work when started from IDE, only in built version started from JAR
         try {
-            Desktop.getDesktop().open(new File(BasicDefinitions.MORTAR_TUTORIAL_RELATIVE_FILE_PATH));
+            Desktop.getDesktop().open(new File(this.configuration.getProperty("mortar.tutorial.relativeFilePath")));
         } catch (IOException | IllegalArgumentException anException) {
             LOGGER.log(Level.SEVERE, anException.toString(), anException);
             Hyperlink tmpLinkToTutorial = new Hyperlink(Message.get("AboutView.tutorialButton.alert.hyperlink.text"));
-            tmpLinkToTutorial.setTooltip(new Tooltip(BasicDefinitions.MORTAR_TUTORIAL_URL));
+            tmpLinkToTutorial.setTooltip(new Tooltip(this.configuration.getProperty("mortar.tutorial.url")));
             tmpLinkToTutorial.setOnAction(event -> {
                 try {
-                    Desktop.getDesktop().browse(new URI(BasicDefinitions.MORTAR_TUTORIAL_URL));
+                    Desktop.getDesktop().browse(new URI(this.configuration.getProperty("mortar.tutorial.url")));
                 } catch (IOException | URISyntaxException e) {
                     LOGGER.log(Level.SEVERE, anException.toString(), anException);
                     throw new SecurityException("Could not open URI");
@@ -226,7 +227,7 @@ private void openTutorialInDefaultPdfViewer() {
     }
     //
     /**
-     * Reads xml file (tools_description.xml in resources) which contains information about the used external tools
+     * Reads xml file (tools_description.xml in resources) which contains information about the used external tools.
      */
     private void getExternalToolInfosFromXml(){
         DocumentBuilderFactory tmpDocumentBuilderFactory = DocumentBuilderFactory.newInstance();
@@ -235,9 +236,11 @@ private void getExternalToolInfosFromXml(){
             // process XML securely, avoid attacks like XML External Entities (XXE)
             tmpDocumentBuilderFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
             DocumentBuilder tmpDocBuilder = tmpDocumentBuilderFactory.newDocumentBuilder();
-            Document tmpDoc = tmpDocBuilder.parse(getClass().getClassLoader().getResourceAsStream(this.toolsXmlFileName));
-            if(tmpDoc == null){
-                throw new FileNotFoundException("File not found " + this.toolsXmlFileName);
+            Document tmpDoc = tmpDocBuilder.parse(this.getClass().getClassLoader().getResource(
+                    this.configuration.getProperty("mortar.descriptionsFolder")
+                            + this.configuration.getProperty("mortar.tools.description.name")).toExternalForm());
+            if (tmpDoc == null) {
+                throw new FileNotFoundException("Tools description XML file not found.");
             }
             // optional, but recommended
             // http://stackoverflow.com/questions/13786607/normalization-in-dom-parsing-with-java-how-does-it-work

src/main/java/de/unijena/cheminf/mortar/controller/FragmentationSettingsViewController.java

@@ -25,6 +25,7 @@
 
 package de.unijena.cheminf.mortar.controller;
 
+import de.unijena.cheminf.mortar.configuration.IConfiguration;
 import de.unijena.cheminf.mortar.gui.util.GuiDefinitions;
 import de.unijena.cheminf.mortar.gui.views.SettingsView;
 import de.unijena.cheminf.mortar.message.Message;
@@ -38,7 +39,6 @@
 import javafx.stage.Modality;
 import javafx.stage.Stage;
 
-import java.io.InputStream;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.logging.Logger;
@@ -51,7 +51,6 @@
  * @version 1.0.0.0
  */
 public class FragmentationSettingsViewController {
-
     //<editor-fold desc="private and private final class variables">
     /**
      * Main stage object of the application
@@ -77,24 +76,29 @@ public class FragmentationSettingsViewController {
      * Name of the selected fragmentation algorithm
      */
     private String selectedFragmenterName;
+    /**
+     * Configuration class to read resource file paths from.
+     */
+    private final IConfiguration configuration;
     /**
      * Logger
      */
     private static final Logger LOGGER = Logger.getLogger(FragmentationSettingsViewController.class.getName());
     //</editor-fold>
-
     /**
      * Constructor
      *
      * @param aStage Stage
      * @param anArrayOfFragmenters IMoleculeFragmenter[]
      * @param aSelectedFragmenterAlgorithmName String
+     * @param aConfiguration configuration instance to read resource file paths from
      */
-    public FragmentationSettingsViewController(Stage aStage, IMoleculeFragmenter[] anArrayOfFragmenters, String aSelectedFragmenterAlgorithmName){
+    public FragmentationSettingsViewController(Stage aStage, IMoleculeFragmenter[] anArrayOfFragmenters, String aSelectedFragmenterAlgorithmName, IConfiguration aConfiguration){
         this.mainStage = aStage;
         this.recentProperties = new HashMap<>(CollectionUtil.calculateInitialHashCollectionCapacity(anArrayOfFragmenters.length));
         this.fragmenters = anArrayOfFragmenters;
         this.selectedFragmenterName = aSelectedFragmenterAlgorithmName;
+        this.configuration = aConfiguration;
         this.openFragmentationSettingsView();
     }
     //
@@ -113,8 +117,10 @@ private void openFragmentationSettingsView(){
         this.fragmentationSettingsViewStage.setTitle(Message.get("FragmentationSettingsView.title.text"));
         this.fragmentationSettingsViewStage.setMinHeight(GuiDefinitions.GUI_MAIN_VIEW_HEIGHT_VALUE);
         this.fragmentationSettingsViewStage.setMinWidth(GuiDefinitions.GUI_MAIN_VIEW_WIDTH_VALUE);
-        InputStream tmpImageInputStream = FragmentationSettingsViewController.class.getResourceAsStream("/de/unijena/cheminf/mortar/images/Mortar_Logo_Icon1.png");
-        this.fragmentationSettingsViewStage.getIcons().add(new Image(tmpImageInputStream));
+        String tmpIconURL = this.getClass().getClassLoader().getResource(
+                this.configuration.getProperty("mortar.imagesFolder")
+                        + this.configuration.getProperty("mortar.logo.icon.name")).toExternalForm();
+        this.fragmentationSettingsViewStage.getIcons().add(new Image(tmpIconURL));
         //
         this.addListener();
         for (IMoleculeFragmenter tmpFragmenter : this.fragmenters) {
@@ -169,7 +175,7 @@ private void addListener(){
      * @param aFragmenter IMoleculeFragmenter
      * @param aRecentPropertiesMap Map
      */
-    private void setRecentProperties(IMoleculeFragmenter aFragmenter, Map aRecentPropertiesMap){
+    private void setRecentProperties(IMoleculeFragmenter aFragmenter, Map<String, Object> aRecentPropertiesMap){
         for (Property tmpProperty : aFragmenter.settingsProperties()) {
             if(aRecentPropertiesMap.containsKey(tmpProperty.getName())){
                 tmpProperty.setValue(aRecentPropertiesMap.get(tmpProperty.getName()));