Code cleanup and Javadocs

core/src/main/java/gov/nist/secauto/metaschema/core/metapath/item/atomic/UuidItemImpl.java

@@ -8,6 +8,7 @@
 import gov.nist.secauto.metaschema.core.datatype.adapter.MetaschemaDataTypeProvider;
 import gov.nist.secauto.metaschema.core.datatype.adapter.UuidAdapter;
 import gov.nist.secauto.metaschema.core.metapath.item.function.IMapKey;
+import gov.nist.secauto.metaschema.core.util.ObjectUtils;
 
 import java.util.UUID;
 
@@ -38,7 +39,7 @@ public IMapKey asMapKey() {
 
   @Override
   public String asString() {
-    return asUuid().toString();
+    return ObjectUtils.notNull(asUuid().toString());
   }
 
   @Override

core/src/test/java/gov/nist/secauto/metaschema/core/metapath/item/atomic/IUUIDItemTest.java → core/src/test/java/gov/nist/secauto/metaschema/core/metapath/item/atomic/IUuidItemTest.java

@@ -7,6 +7,8 @@
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
+import gov.nist.secauto.metaschema.core.util.ObjectUtils;
+
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
@@ -18,10 +20,10 @@
 
 class IUuidItemTest {
   private static Stream<Arguments> testCompare() { // NOPMD - false positive
-    UUID uuidRandom = UUID.randomUUID();
-    UUID uuid1 = UUID.fromString("4cfa2c52-9345-4012-8055-0bc9ac9b03fa");
-    UUID uuid2 = UUID.fromString("25a6d916-f179-4550-ad2b-7e7cd9df35d2");
-    String uuid2String = uuid2.toString();
+    UUID uuidRandom = ObjectUtils.notNull(UUID.randomUUID());
+    UUID uuid1 = ObjectUtils.notNull(UUID.fromString("4cfa2c52-9345-4012-8055-0bc9ac9b03fa"));
+    UUID uuid2 = ObjectUtils.notNull(UUID.fromString("25a6d916-f179-4550-ad2b-7e7cd9df35d2"));
+    String uuid2String = ObjectUtils.notNull(uuid2.toString());
 
     return Stream.of(
         Arguments.of(IUuidItem.valueOf(uuidRandom), IUuidItem.valueOf(uuidRandom), IIntegerItem.ZERO),

databind/src/main/java/gov/nist/secauto/metaschema/databind/io/IWritingContext.java

@@ -44,7 +44,7 @@ interface ObjectWriter<T extends IFeatureComplexItemValueHandler> {
 
     /**
      * Perform a series of property write operations, starting first with this
-     * operation and followed bu the {@code after} operation.
+     * operation and followed by the {@code after} operation.
      *
      * @param after
      *          the secondary property write operation to perform

databind/src/main/java/gov/nist/secauto/metaschema/databind/io/json/MetaschemaJsonWriter.java

@@ -157,8 +157,10 @@ public void writeItemField(IBoundObject item, IBoundInstanceModelGroupedField in
     writeGroupedModelObject(
         instance,
         item,
-        ((ObjectWriter<IBoundInstanceModelGroupedField>) this::writeDiscriminatorProperty)
-            .andThen(this::writeObjectProperties));
+        (parent, handler) -> {
+          writeDiscriminatorProperty(handler);
+          writeObjectProperties(parent, handler);
+        });
   }
 
   @Override
@@ -184,8 +186,10 @@ public void writeItemAssembly(IBoundObject item, IBoundInstanceModelGroupedAssem
     writeGroupedModelObject(
         instance,
         item,
-        ((ObjectWriter<IBoundInstanceModelGroupedAssembly>) this::writeDiscriminatorProperty)
-            .andThen(this::writeObjectProperties));
+        (parent, handler) -> {
+          writeDiscriminatorProperty(handler);
+          writeObjectProperties(parent, handler);
+        });
   }
 
   @Override
@@ -216,7 +220,6 @@ private void writeScalarItem(@NonNull Object item, @NonNull IFeatureScalarItemVa
   }
 
   private <T extends IBoundInstanceModelGroupedNamed> void writeDiscriminatorProperty(
-      @NonNull Object parentItem,
       @NonNull T instance) throws IOException {
 
     IBoundInstanceModelChoiceGroup choiceGroup = instance.getParentContainer();

databind/src/test/java/gov/nist/secauto/metaschema/databind/codegen/AbstractMetaschemaTest.java

@@ -66,6 +66,7 @@ public static Class<? extends IBoundObject> compileModule(@NonNull Path moduleFi
         .loadClass(rootClassName)));
   }
 
+  @NonNull
   private static <T extends IBoundObject> T read(
       @NonNull Format format,
       @NonNull Path file,

databind/src/test/java/gov/nist/secauto/metaschema/databind/codegen/BasicMetaschemaTest.java

@@ -234,6 +234,7 @@ void testExistsWithVariable() throws IOException, URISyntaxException, Metaschema
   }
 
   @Test
+  @SuppressWarnings("unchecked")
   void codegenTest() throws MetaschemaException, IOException {
     List<IConstraintSet> constraints;
     {

databind/src/test/java/gov/nist/secauto/metaschema/databind/io/json/JsonParserTest.java

@@ -25,7 +25,7 @@ class JsonParserTest
   @Test
   void testIssue308Regression() throws IOException, MetaschemaException {
     ModuleLoader moduleLoader = new ModuleLoader();
-    IMetaschemaModule module
+    IMetaschemaModule<?> module
         = moduleLoader.load(Paths.get("src/test/resources/metaschema/308-choice-regression/metaschema.xml"));
 
     IBindingContext context = IBindingContext.instance();

databind/src/test/java/gov/nist/secauto/metaschema/databind/model/DefaultAssemblyClassBindingTest.java

@@ -11,6 +11,7 @@
 import com.fasterxml.jackson.core.JsonParser;
 
 import gov.nist.secauto.metaschema.core.model.IModule;
+import gov.nist.secauto.metaschema.core.util.ObjectUtils;
 import gov.nist.secauto.metaschema.databind.io.json.MetaschemaJsonReader;
 
 import org.junit.jupiter.api.Test;
@@ -32,7 +33,9 @@ void testMinimalJsonParse() throws JsonParseException, IOException {
       IBoundDefinitionModelAssembly classBinding = getRootAssemblyClassBinding();
 
       try (JsonParser parser = newJsonParser(reader)) {
-        Object value = new MetaschemaJsonReader(parser).readObjectRoot(classBinding, classBinding.getRootJsonName());
+        Object value = new MetaschemaJsonReader(parser).readObjectRoot(
+            classBinding,
+            ObjectUtils.requireNonNull(classBinding.getRootJsonName()));
         assertNotNull(value, "root was null");
       }
     }

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/CLI.java

@@ -21,15 +21,28 @@
 
 @SuppressWarnings("PMD.ShortClassName")
 public final class CLI {
+  /**
+   * The main command line entry point.
+   *
+   * @param args
+   *          the command line arguments
+   */
   public static void main(String[] args) {
     System.exit(runCli(args).getExitCode().getStatusCode());
   }
 
+  /**
+   * Execute a command line.
+   *
+   * @param args
+   *          the command line arguments
+   * @return the execution result
+   */
   @NonNull
   public static ExitStatus runCli(String... args) {
     System.setProperty("java.util.logging.manager", "org.apache.logging.log4j.jul.LogManager");
 
-    Map<String, IVersionInfo> versions = ObjectUtils.notNull(
+    @SuppressWarnings("serial") Map<String, IVersionInfo> versions = ObjectUtils.notNull(
         new LinkedHashMap<>() {
           {
             put(CLIProcessor.COMMAND_VERSION, new MetaschemaJavaVersion());

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/commands/AbstractConvertSubcommand.java

@@ -113,12 +113,25 @@ public void validateOptions(CallingContext callingContext, CommandLine cmdLine)
   protected abstract static class AbstractConversionCommandExecutor
       extends AbstractCommandExecutor {
 
-    public AbstractConversionCommandExecutor(
+    /**
+     * Construct a new command executor.
+     *
+     * @param callingContext
+     *          the context of the command execution
+     * @param commandLine
+     *          the parsed command line details
+     */
+    protected AbstractConversionCommandExecutor(
         @NonNull CallingContext callingContext,
         @NonNull CommandLine commandLine) {
       super(callingContext, commandLine);
     }
 
+    /**
+     * Get the binding context to use for data processing.
+     *
+     * @return the context
+     */
     @NonNull
     protected abstract IBindingContext getBindingContext();
 
@@ -161,9 +174,10 @@ public ExitStatus execute() {
         }
       }
 
-      String sourceName = extraArgs.get(0);
+      String sourceName = ObjectUtils.notNull(extraArgs.get(0));
+      URI cwd = ObjectUtils.notNull(Paths.get("").toAbsolutePath().toUri());
+
       URI source;
-      URI cwd = Paths.get("").toAbsolutePath().toUri();
       try {
         source = UriUtils.toUri(sourceName, cwd);
       } catch (URISyntaxException ex) {
@@ -206,6 +220,22 @@ public ExitStatus execute() {
       return ExitCode.OK.exit();
     }
 
+    /**
+     * Called to perform a content conversion.
+     *
+     * @param source
+     *          the resource to convert
+     * @param toFormat
+     *          the format to convert to
+     * @param writer
+     *          the writer to use to write converted content
+     * @param loader
+     *          the Metaschema loader to use to load the content to convert
+     * @throws FileNotFoundException
+     *           if the requested resource was not found
+     * @throws IOException
+     *           if there was an error reading or writing content
+     */
     protected abstract void handleConversion(
         @NonNull URI source,
         @NonNull Format toFormat,

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/commands/AbstractValidateContentCommand.java

@@ -147,12 +147,31 @@ protected abstract class AbstractValidationCommandExecutor
       extends AbstractCommandExecutor
       implements ISchemaValidationProvider {
 
+    /**
+     * Construct a new command executor.
+     *
+     * @param callingContext
+     *          the context of the command execution
+     * @param commandLine
+     *          the parsed command line details
+     */
     public AbstractValidationCommandExecutor(
         @NonNull CallingContext callingContext,
         @NonNull CommandLine commandLine) {
       super(callingContext, commandLine);
     }
 
+    /**
+     * Get the binding context to use for data processing.
+     *
+     * @param constraintSets
+     *          the constraints to configure in the resulting binding context
+     * @return the context
+     * @throws MetaschemaException
+     *           if a Metaschema error occurred
+     * @throws IOException
+     *           if an error occurred while reading data
+     */
     @NonNull
     protected abstract IBindingContext getBindingContext(@NonNull Set<IConstraintSet> constraintSets)
         throws MetaschemaException, IOException;
@@ -267,7 +286,7 @@ public ExitStatus execute() {
       }
 
       if (cmdLine.hasOption(SARIF_OUTPUT_FILE_OPTION) && LOGGER.isInfoEnabled()) {
-        Path sarifFile = Paths.get(cmdLine.getOptionValue(SARIF_OUTPUT_FILE_OPTION));
+        Path sarifFile = ObjectUtils.notNull(Paths.get(cmdLine.getOptionValue(SARIF_OUTPUT_FILE_OPTION)));
 
         IVersionInfo version
             = getCallingContext().getCLIProcessor().getVersionInfos().get(CLIProcessor.COMMAND_VERSION);

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/commands/GenerateSchemaCommand.java

@@ -137,6 +137,15 @@ public ICommandExecutor newExecutor(CallingContext callingContext, CommandLine c
     return ICommandExecutor.using(callingContext, cmdLine, this::executeCommand);
   }
 
+  /**
+   * Called to execute the schema generation.
+   *
+   * @param callingContext
+   *          the context information for the execution
+   * @param cmdLine
+   *          the parsed command line details
+   * @return the execution result
+   */
   @SuppressWarnings({
       "PMD.OnlyOneReturn", // readability
       "unused"
@@ -188,12 +197,12 @@ protected ExitStatus executeCommand(
       }
     }
 
-    URI input;
-    String inputName = extraArgs.get(0);
-    URI cwd = Paths.get("").toAbsolutePath().toUri();
+    String inputName = ObjectUtils.notNull(extraArgs.get(0));
+    URI cwd = ObjectUtils.notNull(Paths.get("").toAbsolutePath().toUri());
 
+    URI input;
     try {
-      input = UriUtils.toUri(extraArgs.get(0), cwd);
+      input = UriUtils.toUri(inputName, cwd);
     } catch (URISyntaxException ex) {
       return ExitCode.IO_ERROR.exitMessage(
           String.format("Unable to load '%s' as it is not a valid file or URI.", inputName)).withThrowable(ex);

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/commands/ValidateContentUsingModuleCommand.java

@@ -87,18 +87,20 @@ private OscalCommandExecutor(
       super(callingContext, commandLine);
     }
 
+    @NonNull
     private Path getTempDir() throws IOException {
       if (tempDir == null) {
         tempDir = Files.createTempDirectory("validation-");
         tempDir.toFile().deleteOnExit();
       }
+      assert tempDir != null;
       return tempDir;
     }
 
     @NonNull
     private IModule getModule(@NonNull Set<IConstraintSet> constraintSets)
         throws MetaschemaException, IOException {
-      URI cwd = Paths.get("").toAbsolutePath().toUri();
+      URI cwd = ObjectUtils.notNull(Paths.get("").toAbsolutePath().toUri());
 
       if (module == null) {
         try {
@@ -135,7 +137,7 @@ public List<Source> getXmlSchemas(@NonNull URL targetResource) throws IOExceptio
       IMutableConfiguration<SchemaGenerationFeature<?>> configuration = new DefaultConfiguration<>();
       ISchemaGenerator.generateSchema(getModule(), schemaFile, SchemaFormat.XML, configuration);
       return ObjectUtils.requireNonNull(List.of(
-          XmlUtil.getStreamSource(schemaFile.toUri().toURL())));
+          XmlUtil.getStreamSource(ObjectUtils.notNull(schemaFile.toUri().toURL()))));
     }
 
     @Override

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/commands/ValidateModuleCommand.java

@@ -27,8 +27,6 @@
 import gov.nist.secauto.metaschema.schemagen.SchemaGenerationFeature;
 
 import org.apache.commons.cli.CommandLine;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.json.JSONObject;
 
 import java.io.BufferedReader;
@@ -47,7 +45,6 @@
 
 public class ValidateModuleCommand
     extends AbstractValidateContentCommand {
-  private static final Logger LOGGER = LogManager.getLogger(ValidateModuleCommand.class);
   @NonNull
   private static final String COMMAND = "validate";
 

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/commands/metapath/ListFunctionsSubcommand.java

@@ -50,9 +50,17 @@ public ICommandExecutor newExecutor(CallingContext callingContext, CommandLine c
     return ICommandExecutor.using(callingContext, cmdLine, this::executeCommand);
   }
 
+  /**
+   * Execute the list functions command.
+   *
+   * @param callingContext
+   *          the context of the command execution
+   * @param cmdLine
+   *          the parsed command line details
+   * @return the execution result
+   */
   @SuppressWarnings({
-      "PMD.OnlyOneReturn", // readability
-      "unused"
+      "PMD.OnlyOneReturn" // readability
   })
   protected ExitStatus executeCommand(
       @NonNull CallingContext callingContext,

metaschema-cli/src/main/java/gov/nist/secauto/metaschema/cli/commands/metapath/MetapathCommand.java

@@ -11,6 +11,9 @@ public class MetapathCommand
     extends AbstractParentCommand {
   private static final String COMMAND = "metapath";
 
+  /**
+   * Constructor for a new Metapath command.
+   */
   public MetapathCommand() {
     super(true);
     addCommandHandler(new ListFunctionsSubcommand());