Code refactoring and cleanup for 1.0.0 release (#204)

* Migrated modules:
  - Relocated metaschema-model-common to metaschema-core in folder core.
  - Relocated metaschema-model to metaschema-core in folder core.
    - Moved metaschema submodule to core.
  - Relocated the "metaschema-java-binding" and "metaschema-java-codegen" modules to the databind module.
  - Moved metaschema-schema-generator to schemagen.
* Cleaned up reports.
* Ensured generated resources are included for site generation.
* Cleaned up some unneeded generics in the implementation.
* Added many Javadoc comments.
* Relocated unit tests to match new package structure.
* Added a new mock model builder (MockedModelTestSupport) to facilitate creation of unit tests around using a mocked Metaschema model.
* Setup JPMS module-info for the core module.
* Some Maven dependency cleanup, including removing unused dependencies.
  - Removed dependency on JAXB.
* Removed aggregate javadoc.
* Eliminated a significant number of compile, PMD, CPD duplications, and Spotbugs warnings.
* Cleaned up some unused/unneeded classes and methods.
* Improved some logging messages.
* Use treeless Git clones on GHA builds
* Updating to latest oss-maven release.
* Core changes:
  - Added `true()` and `false()` metapath function.
  - Refactored error handling for step-related Metapath expressions to ensure the provided context node item is non-null and a document. This also lays ground work for null node contexts in Metapath expressions that do not require a focused node.
  - Refactored code to remove the IRequiredValue* interfaces.
  - Migrated node item classes to a new package.
  - Refactored INodeItem handling to implement the following correct behaviors:
    - IDocumentNodeItem instances will never have a value (i.e. getValue == null)
    - Root metapaths (i.e. `/`) must be executed against an IDocumentNodeItem or an error should be raised.
  - Refactored node item implementation to provide better interface segregation and to limit class responsibility.
  - Refactored Metapath focus to allow for Metapath evaluations against no focus, as well as cases where the focus is not a node item.
  - Improved memory footprint for Axis expressions, which now use static objects for evaluation. Refactored the Step and ParentItem ASTs to use the new Axis support.
  - Added support for function namespaces.
  - Removed collapsible per usnistgov/metaschema#354.
  - Moved property info factory to static method on IModelPropertyInfo.
  - Adjusted IDataTypeHandler creation to avoid extra method callbacks.
  - Reduced unnecessary overridden methods.
  - Removed the need for specific root assembly model interfaces and classes.
  - Renamed IMetaschema to IModule to be more consistent with terminology.
Deleted unused submodule.
  - For index constraints, enhanced index key miss error reporting to include the key data that missed.
  - Added new String initializer for IAnyAtomicItem.
* Databind changes:
  - Refactored JSON reader and writer to use common instance logic. The collection of instances are now lazy generated and cached, improving read and write performance for commonly accessed Metaschema-based JSON objects.
  - Refactored XML parsing, extracting XML parsing logic into the XmlParser class. This resulted in a cleaner set of bound definition/property classes. Also optimized deserialization to return the Object value directly, instead of first creating an unneeded node item.
  - Refactored JSON parsing, extracting JSON parsing logic into the MetaschemaJsonParser class. This resulted in a cleaner set of bound definition/property classes that no contain no parsing code.
  - Renamed XmlParser to MetaschemaXmlReader, MetaschemaJsonParser to MetaschemaJsonReader, and MetaschemaXmlGenerator to MetaschemaXmlWriter.
  - Cleaned up some collapse unit testing files.
  - Implemented XML problem handler for parsing. Further code cleanup and refactoring of XML parsing code.
  - Implemented the JSON problem handler. Resolved #131.
  - Refactored JSON parser tests.
  - Refactored input stream handling. Input streams should now be properly closed.
  - Adjusted problem handlers to use interface defaults and a common implementation of default handling for missing instances.
  - Refactored binding context to allow for dynamic class generation, compilation, and loading. Removed DynamicBindingContext.java, which is no longer needed.
  - Adjusted YAML parser configuration to set a higher default codepoint limit.
  - Refactored code generation, moving code generation methods into a dedicated class.
  - Refactored code generation production classes to simplify and reduce the number of classes.
* Schema generation changes:
  - Refactored XML and JSON generation by moving generation code into format specific classes (i.e. MetaschemaJsonWriter, MetaschemaXmlWriter).
  - Improved XML schema generation testing.
* Metaschema Maven plugin changes:
  - Adjusted generate sources mojo default phase to a more reasonable value (generate-sources).

Author: david-waltermire

.github/workflows/build.yml

@@ -27,7 +27,7 @@ jobs:
     - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608
       with:
         submodules: recursive
-        fetch-depth: 0
+        filter: tree:0
     # -------------------------
     # Java Environment Setup
     # -------------------------
@@ -79,6 +79,11 @@ jobs:
     - name: Perform CodeQL Analysis
       if: github.event_name == 'push'
       uses: github/codeql-action/analyze@6a28655e3dcb49cb0840ea372fd6d17733edd8a4
+    - name: Upload CodeQL SARIF file
+      uses: github/codeql-action/upload-sarif@a09933a12a80f87b87005513f0abb1494c27a716
+      if: (github.event_name == 'push' || github.event_name == 'workflow_dispatch') && github.ref_name == 'develop'
+      with:
+        token: ${{ secrets.COMMIT_TOKEN }}
     - name: Test Website
       run: |
         # this needs to be run as a second build to ensure source is fully generated by the previous step

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
     - uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608
       with:
         submodules: recursive
-        fetch-depth: 0
+        filter: tree:0
     # -------------------------
     # Java
     # -------------------------

.gitmodules

@@ -1,4 +1,7 @@
-[submodule "metaschema"]
-	path = metaschema-model/metaschema
-	url = https://github.com/usnistgov/metaschema
-	branch = master
+[submodule "core/core/metaschema"]
+	path = core/metaschema
+	url = https://github.com/usnistgov/metaschema.git
+	branch = main
+[submodule "core/qt3tests"]
+	path = core/qt3tests
+	url = https://github.com/w3c/qt3tests.git

.mvn/maven-build-cache-config.xml

@@ -13,4 +13,13 @@
       </discovery>
     </multiModule>
   </configuration>
+  <executionControl>
+    <runAlways>
+      <plugins>
+        <!-- the two following plugins are needed to add sources to the source list -->
+        <plugin groupId="org.antlr" artifactId="antlr4-maven-plugin"/>
+        <plugin groupId="org.codehaus.mojo" artifactId="build-helper-maven-plugin"/>
+      </plugins>
+    </runAlways>
+  </executionControl>
 </cache>

cli-processor/pom.xml

@@ -20,7 +20,7 @@
 	<dependencies>
 		<dependency>
 			<groupId>gov.nist.secauto.metaschema</groupId>
-			<artifactId>metaschema-model-common</artifactId>
+			<artifactId>metaschema-core</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>com.github.spotbugs</groupId>
@@ -43,7 +43,7 @@
 		</dependency>
 		<dependency>
 			<groupId>com.google.auto.service</groupId>
-			<artifactId>auto-service</artifactId>
+			<artifactId>auto-service-annotations</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
@@ -53,17 +53,6 @@
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-jul</artifactId>
 		</dependency>
-
-		<dependency>
-			<groupId>org.junit.jupiter</groupId>
-			<artifactId>junit-jupiter-api</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>org.junit.jupiter</groupId>
-			<artifactId>junit-jupiter-engine</artifactId>
-			<scope>test</scope>
-		</dependency>
 	</dependencies>
 	<build>
 		<plugins>

cli-processor/src/main/java/gov/nist/secauto/metaschema/cli/processor/CLIProcessor.java

@@ -32,8 +32,8 @@
 import gov.nist.secauto.metaschema.cli.processor.command.ExtraArgument;
 import gov.nist.secauto.metaschema.cli.processor.command.ICommand;
 import gov.nist.secauto.metaschema.cli.processor.command.ICommandExecutor;
-import gov.nist.secauto.metaschema.model.common.util.IVersionInfo;
-import gov.nist.secauto.metaschema.model.common.util.ObjectUtils;
+import gov.nist.secauto.metaschema.core.util.IVersionInfo;
+import gov.nist.secauto.metaschema.core.util.ObjectUtils;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -183,7 +183,8 @@ private ExitStatus parseCommand(String... args) {
     CallingContext callingContext = new CallingContext(commandArgs);
 
     ExitStatus status;
-    // the first two arguments should be the <command> and <operation>, where <type> is the object type
+    // the first two arguments should be the <command> and <operation>, where <type>
+    // is the object type
     // the <operation> is performed against.
     if (commandArgs.isEmpty()) {
       status = ExitCode.INVALID_COMMAND.exit();
@@ -205,9 +206,9 @@ private static void handleNoColor() {
     AnsiConsole.systemUninstall();
   }
 
+  @SuppressWarnings("resource")
   public static void handleQuiet() {
-    @SuppressWarnings("resource") LoggerContext ctx = (LoggerContext) LogManager.getContext(false); // NOPMD not
-                                                                                                    // closable here
+    LoggerContext ctx = (LoggerContext) LogManager.getContext(false); // NOPMD not closable here
     Configuration config = ctx.getConfiguration();
     LoggerConfig loggerConfig = config.getLoggerConfig(LogManager.ROOT_LOGGER_NAME);
     Level oldLevel = loggerConfig.getLevel();
@@ -240,7 +241,8 @@ protected void showVersion() {
   // @SuppressWarnings("null")
   // @NonNull
   // public String[] getArgArray() {
-  // return Stream.concat(options.stream(), extraArgs.stream()).toArray(size -> new String[size]);
+  // return Stream.concat(options.stream(), extraArgs.stream()).toArray(size ->
+  // new String[size]);
   // }
 
   public class CallingContext {
@@ -367,7 +369,8 @@ public ExitStatus processCommand() {
         retval = ExitCode.OK.exit();
         // } else {
         // retval = handleInvalidCommand(commandResult, options,
-        // "Invalid command arguments: " + cmdLine.getArgList().stream().collect(Collectors.joining(" ")));
+        // "Invalid command arguments: " +
+        // cmdLine.getArgList().stream().collect(Collectors.joining(" ")));
       }
 
       if (retval == null) {
@@ -578,9 +581,10 @@ public void showHelp() {
       AnsiPrintStream out = AnsiConsole.out();
       int terminalWidth = Math.max(out.getTerminalWidth(), 40);
 
-      @SuppressWarnings("resource") PrintWriter writer = new PrintWriter(out, true, StandardCharsets.UTF_8); // NOPMD -
-                                                                                                             // not
-                                                                                                             // owned
+      @SuppressWarnings("resource") PrintWriter writer = new PrintWriter( // NOPMD not owned
+          out,
+          true,
+          StandardCharsets.UTF_8);
       formatter.printHelp(
           writer,
           terminalWidth,

cli-processor/src/main/java/gov/nist/secauto/metaschema/cli/processor/ExitCode.java

@@ -42,7 +42,8 @@ public enum ExitCode {
    */
   IO_ERROR(2),
   /**
-   * A command was requested by name that doesn't exist or required arguments are missing.
+   * A command was requested by name that doesn't exist or required arguments are
+   * missing.
    */
   INVALID_COMMAND(3),
   /**
@@ -58,7 +59,8 @@ public enum ExitCode {
    */
   RUNTIME_ERROR(6),
   /**
-   * The provided argument information for a command fails to match argument use requirements.
+   * The provided argument information for a command fails to match argument use
+   * requirements.
    */
   INVALID_ARGUMENTS(7);
 

cli-processor/src/main/java/gov/nist/secauto/metaschema/cli/processor/InvalidArgumentException.java

@@ -54,7 +54,8 @@ public InvalidArgumentException(String message) {
   }
 
   /**
-   * Return the option requiring an argument that wasn't provided on the command line.
+   * Return the option requiring an argument that wasn't provided on the command
+   * line.
    *
    * @return the related option
    */
@@ -64,7 +65,8 @@ public Option getOption() {
   }
 
   /**
-   * Assign the option requiring an argument that wasn't provided on the command line.
+   * Assign the option requiring an argument that wasn't provided on the command
+   * line.
    *
    * @param option
    *          the option to set

cli-processor/src/main/java/gov/nist/secauto/metaschema/cli/processor/MessageExitStatus.java

@@ -42,7 +42,8 @@ public class MessageExitStatus
    * @param code
    *          the exit code to use.
    * @param messageArguments
-   *          the arguments that can be passed to a formatted string to generate the message
+   *          the arguments that can be passed to a formatted string to generate
+   *          the message
    */
   public MessageExitStatus(@NonNull ExitCode code, @NonNull Object... messageArguments) {
     super(code);

cli-processor/src/main/java/gov/nist/secauto/metaschema/cli/processor/command/AbstractCommandExecutor.java

@@ -28,7 +28,7 @@
 
 import gov.nist.secauto.metaschema.cli.processor.CLIProcessor.CallingContext;
 import gov.nist.secauto.metaschema.cli.processor.ExitStatus;
-import gov.nist.secauto.metaschema.model.common.util.ObjectUtils;
+import gov.nist.secauto.metaschema.core.util.ObjectUtils;
 
 import org.apache.commons.cli.CommandLine;
 

cli-processor/src/main/java/gov/nist/secauto/metaschema/cli/processor/command/ICommand.java

@@ -28,7 +28,7 @@
 
 import gov.nist.secauto.metaschema.cli.processor.CLIProcessor.CallingContext;
 import gov.nist.secauto.metaschema.cli.processor.InvalidArgumentException;
-import gov.nist.secauto.metaschema.model.common.util.CollectionUtil;
+import gov.nist.secauto.metaschema.core.util.CollectionUtil;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;

cli-processor/src/main/java/gov/nist/secauto/metaschema/cli/processor/command/ICommandExecutor.java

@@ -52,7 +52,7 @@ public ExitStatus execute() {
   }
 
   @FunctionalInterface
-  public interface ExecutionFunction {
+  interface ExecutionFunction {
     @NonNull
     ExitStatus execute(
         @NonNull CallingContext callingContext,