fixed sonarqube quality issues

src/main/java/edu/kit/provideq/toolbox/maxcut/MaxCutConfiguration.java

@@ -1,6 +1,7 @@
 package edu.kit.provideq.toolbox.maxcut;
 
 import edu.kit.provideq.toolbox.ResourceProvider;
+import edu.kit.provideq.toolbox.exception.MissingExampleException;
 import edu.kit.provideq.toolbox.maxcut.solvers.CirqMaxCutSolver;
 import edu.kit.provideq.toolbox.maxcut.solvers.GamsMaxCutSolver;
 import edu.kit.provideq.toolbox.maxcut.solvers.QiskitMaxCutSolver;
@@ -53,7 +54,7 @@ private Set<Problem<String, String>> loadExampleProblems(ResourceProvider resour
       problem.setInput(resourceProvider.readStream(problemInputStream));
       return Set.of(problem);
     } catch (IOException e) {
-      throw new RuntimeException("Could not load example problems", e);
+      throw new MissingExampleException("Could not load example problems", e);
     }
   }
 }

src/main/java/edu/kit/provideq/toolbox/meta/setting/BooleanState.java

@@ -13,10 +13,10 @@ public BooleanState(String name, String title, boolean state) {
   }
 
   public boolean getState() {
-      return state;
+    return state;
   }
 
   public void setState(boolean state) {
-      this.state = state;
+    this.state = state;
   }
 }

src/main/java/edu/kit/provideq/toolbox/meta/setting/MetaSolverSetting.java

@@ -4,20 +4,37 @@
 
 @JsonDeserialize(using = MetaSolverSettingDeserializer.class)
 public abstract class MetaSolverSetting {
-  public String name;
+  private String name;
+  private MetaSolverSettingType type;
   private String title;
-  public MetaSolverSettingType type;
 
-  public MetaSolverSetting() {
+  protected MetaSolverSetting(String name, String title, MetaSolverSettingType type) {
+    this.setName(name);
+    this.setType(type);
+    this.setTitle(title);
   }
 
-  protected MetaSolverSetting(String name, String title, MetaSolverSettingType type) {
+  public String getTitle() {
+    return title;
+  }
+
+  public String getName() {
+    return name;
+  }
+
+  public void setName(String name) {
     this.name = name;
+  }
+
+  public MetaSolverSettingType getType() {
+    return type;
+  }
+
+  public void setType(MetaSolverSettingType type) {
     this.type = type;
-    this.title = title;
   }
 
-  public String getTitle() {
-      return title;
+  public void setTitle(String title) {
+    this.title = title;
   }
 }

src/main/java/edu/kit/provideq/toolbox/meta/setting/Select.java

@@ -4,9 +4,9 @@
 import javax.annotation.Nullable;
 
 public class Select<T> extends MetaSolverSetting {
-  public List<T> options;
+  private List<T> options;
   @Nullable
-  public T selectedOption;
+  private T selectedOption;
 
   public Select(String name, String title, List<T> options) {
     this(name, title, options, null);
@@ -15,7 +15,24 @@ public Select(String name, String title, List<T> options) {
   public Select(String name, String title, List<T> options, T selectedOption) {
     super(name, title, MetaSolverSettingType.SELECT);
 
+    this.setOptions(options);
+    this.setSelectedOption(selectedOption);
+  }
+
+  public List<T> getOptions() {
+    return options;
+  }
+
+  public void setOptions(List<T> options) {
     this.options = options;
+  }
+
+  @Nullable
+  public T getSelectedOption() {
+    return selectedOption;
+  }
+
+  public void setSelectedOption(@Nullable T selectedOption) {
     this.selectedOption = selectedOption;
   }
 }

src/main/java/edu/kit/provideq/toolbox/process/GamsProcessRunner.java

@@ -1,14 +1,13 @@
 package edu.kit.provideq.toolbox.process;
 
 import edu.kit.provideq.toolbox.meta.ProblemType;
+import java.util.Optional;
 import java.util.UUID;
 import org.apache.logging.log4j.util.Strings;
 import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.context.annotation.Scope;
 import org.springframework.stereotype.Component;
 
-import java.util.Optional;
-
 /**
  * Process runner with input & output post-processing specifically for invoking GAMS.
  */
@@ -55,14 +54,6 @@ public GamsProcessRunner(String directory, String scriptFileName, String... argu
     addProblemFilePathToProcessCommand("--INPUT=\"%s\"");
   }
 
-  @Override
-  public ProcessResult<String> run(ProblemType<?, ?> problemType, UUID solutionId, String problemData) {
-    var result = super.run(problemType, solutionId, problemData);
-
-    var obfuscatedOutput = obfuscateGamsLicense(result.output().get());
-    return new ProcessResult<>(result.success(), Optional.of(obfuscatedOutput), Optional.empty());
-  }
-
   /**
    * Removes GAMS' license output from an output log.
    */
@@ -90,4 +81,13 @@ private static String obfuscateGamsLicense(String output) {
   private static String obfuscateLine(String line) {
     return Strings.repeat("*", line.length());
   }
+
+  @Override
+  public ProcessResult<String> run(ProblemType<?, ?> problemType, UUID solutionId,
+                                   String problemData) {
+    var result = super.run(problemType, solutionId, problemData);
+
+    var obfuscatedOutput = obfuscateGamsLicense(result.output().orElse("no license found"));
+    return new ProcessResult<>(result.success(), Optional.of(obfuscatedOutput), Optional.empty());
+  }
 }

src/main/java/edu/kit/provideq/toolbox/process/ProcessRunner.java

@@ -183,7 +183,7 @@ public <T> ProcessResult<T> run(ProblemType<?, ?> problemType, UUID solutionId,
           .getProblemDirectory(problemType, solutionId)
           .getAbsolutePath();
     } catch (IOException e) {
-      return new ProcessResult<T>(
+      return new ProcessResult<>(
           false,
           Optional.empty(),
           Optional.of(
@@ -202,7 +202,7 @@ public <T> ProcessResult<T> run(ProblemType<?, ?> problemType, UUID solutionId,
     try {
       Files.writeString(problemFilePath, problemData);
     } catch (IOException e) {
-      return new ProcessResult<T>(
+      return new ProcessResult<>(
           false,
           Optional.empty(),
           Optional.of("Error: The problem data couldn't be written to %s:%n%s".formatted(
@@ -244,7 +244,7 @@ public <T> ProcessResult<T> run(ProblemType<?, ?> problemType, UUID solutionId,
 
       processExitCode = process.waitFor();
     } catch (IOException | InterruptedException e) {
-      return new ProcessResult<T>(
+      return new ProcessResult<>(
           false,
           Optional.empty(),
           Optional.of(
@@ -256,7 +256,7 @@ public <T> ProcessResult<T> run(ProblemType<?, ?> problemType, UUID solutionId,
 
     // Return prematurely if the process failed
     if (processExitCode != 0) {
-      return new ProcessResult<T>(
+      return new ProcessResult<>(
           false,
           Optional.empty(),
           Optional.of(
@@ -268,7 +268,7 @@ public <T> ProcessResult<T> run(ProblemType<?, ?> problemType, UUID solutionId,
         reader.read(solutionFile, problemFilePath, Path.of(problemDirectoryPath));
 
     if (!result.success()) {
-      return new ProcessResult<T>(
+      return new ProcessResult<>(
           result.success(),
           result.output(),
           result.errorOutput().isPresent() ? Optional.of(

src/main/java/edu/kit/provideq/toolbox/process/PythonProcessRunner.java

@@ -1,6 +1,5 @@
 package edu.kit.provideq.toolbox.process;
 
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.config.ConfigurableBeanFactory;
 import org.springframework.context.annotation.Scope;
 import org.springframework.stereotype.Component;

src/main/java/edu/kit/provideq/toolbox/qubo/QuboConfiguration.java

@@ -1,6 +1,7 @@
 package edu.kit.provideq.toolbox.qubo;
 
 import edu.kit.provideq.toolbox.ResourceProvider;
+import edu.kit.provideq.toolbox.exception.MissingExampleException;
 import edu.kit.provideq.toolbox.meta.Problem;
 import edu.kit.provideq.toolbox.meta.ProblemManager;
 import edu.kit.provideq.toolbox.meta.ProblemType;
@@ -55,7 +56,7 @@ private Set<Problem<String, String>> loadExampleProblems(ResourceProvider resour
       problem.setInput(resourceProvider.readStream(problemInputStream));
       return Set.of(problem);
     } catch (IOException e) {
-      throw new RuntimeException("Could not load example problems", e);
+      throw new MissingExampleException("Could not load example problems", e);
     }
   }
 }

src/main/java/edu/kit/provideq/toolbox/qubo/solvers/DwaveQuboSolver.java

@@ -16,8 +16,6 @@
  */
 @Component
 public class DwaveQuboSolver extends QuboSolver {
-  private static final String METHOD_SETTING_NAME = "method";
-  private static final String API_TOKEN_SETTING_NAME = "dwave-token";
   private final String quboScriptPath;
   private final ApplicationContext context;
 
@@ -34,37 +32,20 @@ public String getName() {
     return "(D-Wave) Annealing QUBO Solver";
   }
 
-    /*
-    @Override
-    public List<MetaSolverSetting> getSettings() {
-        return List.of(
-            new Select<String>(METHOD_SETTING_NAME, "DWave Annealing Method", List.of("sim", "hybrid", "qbsolv", "direct"), "sim"),
-            new Text(API_TOKEN_SETTING_NAME, "DWave API Token (required for non-sim methods)")
-        );
-    }*/
-
   @Override
   public Mono<Solution<String>> solve(
       String input,
       SubRoutineResolver subRoutineResolver
   ) {
-        /*
-        String dwaveAnnealingMethod = settings.stream()
-            .filter(setting -> setting.name.equals(METHOD_SETTING_NAME))
-            .map(setting -> ((Select<String>) setting))
-            .findFirst()
-            .map(setting -> setting.selectedOption)
-            .orElse("sim");
 
-        Optional<String> dwaveToken = settings.stream()
-            .filter(setting -> setting.name.equals(API_TOKEN_SETTING_NAME))
-            .map(setting -> ((Text) setting))
-            .findFirst()
-            .map(setting -> setting.text);
-        */ //TODO: Add Setting again (currently not part of our model)
+    // there is currently no field where a token can be added by the user
+    // this field is kept because it was used in Lucas implementation and will be added back later
+    Optional<String> dwaveToken = Optional.empty();
 
-    String dwaveAnnealingMethod = "sim"; //TODO: remove this again
-    Optional<String> dwaveToken = Optional.empty(); //TODO: remove this again
+    // this field is only relevant when a dwaveToken is added
+    // (a token is needed to access the d-wave hardware)
+    // options are: sim, hybrid, absolv, direct
+    String dwaveAnnealingMethod = "sim";
 
     var solution = new Solution<String>();
 

src/main/java/edu/kit/provideq/toolbox/sat/SatConfiguration.java

@@ -1,6 +1,7 @@
 package edu.kit.provideq.toolbox.sat;
 
 import edu.kit.provideq.toolbox.ResourceProvider;
+import edu.kit.provideq.toolbox.exception.MissingExampleException;
 import edu.kit.provideq.toolbox.format.cnf.dimacs.DimacsCnfSolution;
 import edu.kit.provideq.toolbox.meta.Problem;
 import edu.kit.provideq.toolbox.meta.ProblemManager;
@@ -51,7 +52,7 @@ private Set<Problem<String, DimacsCnfSolution>> loadExampleProblems(
       problem.setInput(resourceProvider.readStream(problemInputStream));
       return Set.of(problem);
     } catch (IOException e) {
-      throw new RuntimeException("Could not load example problems", e);
+      throw new MissingExampleException("Could not load example problems", e);
     }
   }
 }

src/main/java/edu/kit/provideq/toolbox/tsp/TspConfiguration.java

@@ -8,7 +8,6 @@
 import edu.kit.provideq.toolbox.tsp.solvers.LkhTspSolver;
 import edu.kit.provideq.toolbox.tsp.solvers.QuboTspSolver;
 import java.io.IOException;
-import java.util.Collections;
 import java.util.HashSet;
 import java.util.Objects;
 import java.util.Set;
@@ -41,7 +40,7 @@ ProblemManager<String, String> getTspManager(
 
   private Set<Problem<String, String>> loadExampleProblems(ResourceProvider provider) {
     try {
-      String[] problemNames = new String[]{
+      String[] problemNames = new String[] {
           "att48.tsp", "SmallSampleTSP.tsp", "VerySmallSampleTSP.tsp"
       };