style: Fix more Sonar issues

cli/src/main/java/org/jboss/sbomer/cli/CLI.java

@@ -59,7 +59,7 @@ public class CLI implements QuarkusApplication {
 
     @Override
     @ActivateRequestContext
-    public int run(String... args) throws Exception {
+    public int run(String... args) {
         CommandLine commandLine = new CommandLine(this, factory).setExecutionExceptionHandler(new ExceptionHandler())
                 .setExecutionStrategy(new RunOnlyCallable())
                 .setCommandName("sbomerctl");

cli/src/main/java/org/jboss/sbomer/cli/ExceptionHandler.java

@@ -17,7 +17,6 @@
  */
 package org.jboss.sbomer.cli;
 
-import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Map;

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/adjuster/SyftImageAdjuster.java

@@ -215,7 +215,7 @@ private void filterComponents(List<Component> components) {
      * </p>
      *
      * <p>
-     * At the same time it cleans up the main compontn available in the {@link Metadata#getComponent()}.
+     * At the same time it cleans up the main component available in the {@link Metadata#getComponent()}.
      * </p>
      *
      * @param bom
@@ -293,11 +293,11 @@ private void adjustProperties(Bom bom) {
      *
      * <p>
      * Adjusts any values in the main component as well as for each component found in the component list (recursively).
-     * See {@link SyftImageAdjuster#adjustPublisher(List)}.
+     * See {@link SyftImageAdjuster#adjustPublisher(Bom)}.
      * </p>
      *
      * @param bom The manifest to adjust the properties of.
-     * @see SyftImageAdjuster#adjustPublisher(List)
+     * @see SyftImageAdjuster#adjustPublisher(Bom)
      */
     private void adjustPublisher(Bom bom) {
         log.info("Adjusting manifest publisher...");
@@ -331,12 +331,12 @@ private void adjustComponentPublisher(Component component) {
      * Based on the metadata we got the output of Skopeo ({@code skopeo.json} file), adjust main component's purl and
      * name.
      *
-     * @param component
+     * @param bom
      * @param workDir
      */
     private void adjustNameAndPurl(Bom bom, Path workDir) {
-        String tag = null;
-        ContainerImageInspectOutput inspectData = null;
+        String tag;
+        ContainerImageInspectOutput inspectData;
         final Component mainComponent = bom.getMetadata().getComponent();
 
         try {
@@ -378,6 +378,7 @@ private void adjustNameAndPurl(Bom bom, Path workDir) {
             }
         }
 
+        // FIXME: This can be null here
         String[] nameParts = name.split(("/"));
 
         TreeMap<String, String> qualifiers = new TreeMap<>();
@@ -493,12 +494,12 @@ private void adjustProperties(List<Property> properties) {
             boolean supportedProp = ALLOWED_PROPERTY_PREFIXES.stream()
                     .anyMatch(prefix -> prop.getName().startsWith(prefix));
 
-            if (!supportedProp) {
-                // log.debug(
-                // "Property '{}' with value '{}' is not on the supported properties list, removing...",
-                // prop.getName(),
-                // prop.getValue());
-            }
+            // if (!supportedProp) {
+            // log.debug(
+            // "Property '{}' with value '{}' is not on the supported properties list, removing...",
+            // prop.getName(),
+            // prop.getValue());
+            // }
 
             return !supportedProp;
         });
@@ -580,16 +581,15 @@ private String doCleanupPurl(String purl) throws MalformedPackageURLException {
 
         // If we removed any qualifiers, we need to rebuild the purl
         if (qualifiers.entrySet().removeIf(q -> !q.getKey().equals("arch") && !q.getKey().equals("epoch"))) {
-            String updatedPurl = new PackageURL(
+
+            // log.debug("Updating purl to: '{}'", updatedPurl);
+            return new PackageURL(
                     packageURL.getType(),
                     packageURL.getNamespace(),
                     packageURL.getName(),
                     packageURL.getVersion(),
                     qualifiers,
                     packageURL.getSubpath()).canonicalize();
-
-            // log.debug("Updating purl to: '{}'", updatedPurl);
-            return updatedPurl;
         }
         return packageURL.toString();
     }

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/AbstractGenerateCommand.java

@@ -123,7 +123,7 @@ protected String toolVersion() {
     }
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         // Make sure there is no context
         MDCUtils.removeContext();
         MDCUtils.addBuildContext(parent.getBuildId());
@@ -313,7 +313,7 @@ protected void doClone(String url, String tag, Path path, boolean force) {
         }
 
         log.info("Cloning the repository to {}...", path);
-        try (Git git = Git.cloneRepository()
+        try (Git ignored = Git.cloneRepository()
                 .setDirectory(path.toFile())
                 .setURI(url)
                 .setBranch(tag)
@@ -333,7 +333,7 @@ protected void doClone(String url, String tag, Path path, boolean force) {
 
         // Please note that this ignores the block size of a particular storage,
         // and because of this, the number can be different compared to when
-        // an utility like `du` is being used to determine the size.
+        // a utility like `du` is being used to determine the size.
         log.info("Directory size: {} MB", String.format("%.02f", (float) dirSize(path) / 1024));
     }
 

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/AbstractGenerateOperationCommand.java

@@ -65,7 +65,7 @@ public abstract class AbstractGenerateOperationCommand implements Callable<Integ
     protected abstract GeneratorType generatorType();
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         // Make sure there is no context
         MDCUtils.removeContext();
 

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/AbstractGradleGenerateCommand.java

@@ -23,9 +23,9 @@
 import picocli.CommandLine.Option;
 import picocli.CommandLine.ScopeType;
 
+@Getter
 public abstract class AbstractGradleGenerateCommand extends AbstractGenerateCommand {
 
-    @Getter
     @Option(
             names = { "--init-script" },
             description = "Path to Gradle init script file that should be used for this run instead of the default one",

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/AbstractMavenGenerateCommand.java

@@ -23,9 +23,9 @@
 import picocli.CommandLine.Option;
 import picocli.CommandLine.ScopeType;
 
+@Getter
 public abstract class AbstractMavenGenerateCommand extends AbstractGenerateCommand {
 
-    @Getter
     @Option(
             names = { "-s", "--settings" },
             description = "Path to Maven settings.xml file that should be used for this run instead of the default one",

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/AbstractProcessCommand.java

@@ -37,7 +37,7 @@ public abstract class AbstractProcessCommand implements Callable<Integer> {
     protected PncService pncService;
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         try {
             // Make sure there is no context.
             MDCUtils.removeContext();
@@ -67,7 +67,7 @@ public Integer call() throws Exception {
     protected abstract ProcessorType getImplementationType();
 
     /**
-     * Optionally adds a MDC context. The {@link MDCUtils} class can be used for this purpose.
+     * Optionally adds an MDC context. The {@link MDCUtils} class can be used for this purpose.
      */
     protected void addContext() {
 

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/CycloneDxGenerateOperationCommand.java

@@ -128,7 +128,7 @@ protected Path doGenerate() {
                 config);
 
         // Get some metadata about the operation
-        String productName = "";
+        String productName;
         String productMilestone = "";
         DeliverableAnalyzerOperation operation = pncService.getDeliverableAnalyzerOperation(config.getOperationId());
         if (operation.getProductMilestone() != null) {
@@ -254,8 +254,9 @@ protected Path doGenerate() {
         }
 
         // Find the parent to set the correct hierarchy, default to the main root dependency
-        for (String key : pathToDependencies.keySet()) {
-            Dependency dependency = pathToDependencies.get(key);
+        for (Map.Entry<String, Dependency> entry : pathToDependencies.entrySet()) {
+            String key = entry.getKey();
+            Dependency dependency = entry.getValue();
             Optional<Dependency> maybeParent = findClosestParent(pathToDependencies, key);
             Dependency parent = maybeParent.orElse(mainDependency);
             parent.addDependency(dependency);

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/GenerateCommand.java

@@ -24,6 +24,7 @@
 import picocli.CommandLine.Option;
 import picocli.CommandLine.ScopeType;
 
+@Getter
 @Command(
         mixinStandardHelpOptions = true,
         name = "generate",
@@ -33,18 +34,15 @@
                 GradleCycloneDxGenerateCommand.class, NodejsCycloneDxGenerateCommand.class })
 public class GenerateCommand {
 
-    @Getter
     @Option(names = { "-b", "--build-id" }, description = "Build identifier to generate the SBOM for", required = true)
     String buildId;
 
-    @Getter
     @Option(
             names = { "-f", "--force" },
             description = "If the workdir directory should be cleaned up in case it already exists. Default: ${DEFAULT-VALUE}",
             scope = ScopeType.INHERIT)
     boolean force = false;
 
-    @Getter
     @Option(
             names = { "--workdir" },
             defaultValue = "workdir",
@@ -54,7 +52,6 @@ public class GenerateCommand {
             scope = ScopeType.INHERIT)
     Path workdir;
 
-    @Getter
     @Option(
             names = { "-o", "--output" },
             defaultValue = "bom.json",

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/GenerateOperationCommand.java

@@ -24,6 +24,7 @@
 import picocli.CommandLine.Option;
 import picocli.CommandLine.ScopeType;
 
+@Getter
 @Command(
         mixinStandardHelpOptions = true,
         name = "generate-operation",
@@ -32,7 +33,6 @@
         subcommands = { CycloneDxGenerateOperationCommand.class })
 public class GenerateOperationCommand {
 
-    @Getter
     @Option(
             names = { "-c", "--config", },
             paramLabel = "FILE",
@@ -41,28 +41,24 @@ public class GenerateOperationCommand {
             scope = ScopeType.INHERIT)
     Path configPath;
 
-    @Getter
     @Option(
             names = { "--index" },
             description = "Index to select the product configuration passed in the --config option. Starts from 0. If not provided SBOM will be generated for every product in the config serially.",
             scope = ScopeType.INHERIT)
     Integer index;
 
-    @Getter
     @Option(
             names = { "-op", "--operation-id" },
             description = "Operation identifier to generate the SBOM for",
             required = true)
     String operationId;
 
-    @Getter
     @Option(
             names = { "-f", "--force" },
             description = "If the workdir directory should be cleaned up in case it already exists. Default: ${DEFAULT-VALUE}",
             scope = ScopeType.INHERIT)
     boolean force = false;
 
-    @Getter
     @Option(
             names = { "--workdir" },
             defaultValue = "workdir",
@@ -72,7 +68,6 @@ public class GenerateOperationCommand {
             scope = ScopeType.INHERIT)
     Path workdir;
 
-    @Getter
     @Option(
             names = { "-o", "--output" },
             defaultValue = "bom.json",

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/GradleCycloneDxGenerateCommand.java

@@ -91,7 +91,7 @@ protected GeneratorType generatorType() {
     }
 
     private void configureProcessEnvironmentVariable(String buildCmdOptions, Map<String, String> environment) {
-        // If there is an hint about the major Gradle version required, use it.
+        // If there is a hint about the major Gradle version required, use it.
         Optional<Integer> gradleMajorVersion = extractGradleMajorVersion(buildCmdOptions);
         if (gradleMajorVersion.isEmpty() || gradleMajorVersion.get() >= 5) {
             environment.put(GRADLE_PLUGIN_VERSION_ENV_VARIABLE, toolVersion());

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/ProcessCommand.java

@@ -21,6 +21,7 @@
 import picocli.CommandLine.Command;
 import picocli.CommandLine.ParentCommand;
 
+@Getter
 @Command(
         mixinStandardHelpOptions = true,
         name = "process",
@@ -30,7 +31,6 @@
         subcommandsRepeatable = true)
 public class ProcessCommand {
 
-    @Getter
     @ParentCommand
     AbstractGenerateCommand parent;
 

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/adjust/AbstractAdjustCommand.java

@@ -35,7 +35,7 @@ public abstract class AbstractAdjustCommand implements Callable<Integer> {
     AdjustCommand parent;
 
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
         try {
             // Make sure there is no context.
             MDCUtils.removeContext();
@@ -60,7 +60,7 @@ public Integer call() throws Exception {
     }
 
     /**
-     * Optionally adds a MDC context. The {@link MDCUtils} class can be used for this purpose.
+     * Optionally adds an MDC context. The {@link MDCUtils} class can be used for this purpose.
      */
     protected void addContext() {
 

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/adjust/AdjustCommand.java

@@ -26,6 +26,7 @@
 import picocli.CommandLine.Option;
 import picocli.CommandLine.ScopeType;
 
+@Getter
 @Command(
         mixinStandardHelpOptions = true,
         name = "adjust",
@@ -34,7 +35,6 @@
         subcommandsRepeatable = true)
 public class AdjustCommand {
 
-    @Getter
     @Option(
             names = { "-p", "--path" },
             required = true,
@@ -44,7 +44,6 @@ public class AdjustCommand {
             scope = ScopeType.INHERIT)
     Path path;
 
-    @Getter
     @Option(
             names = { "-o", "--output" },
             defaultValue = "bom.json",

cli/src/main/java/org/jboss/sbomer/cli/feature/sbom/command/auto/GenerateCommand.java

@@ -85,7 +85,7 @@ public class GenerateCommand implements Callable<Integer> {
      *         generation process did not finish successfully
      */
     @Override
-    public Integer call() throws Exception {
+    public Integer call() {
 
         if (configPath == null) {
             log.info("Configuration path is null, cannot do any generation.");