Fix formatting and trailing whitespace

Signed-off-by: Daniel Bluhm <bluhmdj@ornl.gov>

org.eclipse.ice.dev/org.eclipse.ice.dev.annotations/src/main/java/org/eclipse/ice/dev/annotations/processors/DataElementAnnotationExtractor.java

@@ -23,7 +23,7 @@ import org.eclipse.ice.dev.annotations.DataField;
 /**
  * Flavor of ICEAnnotationExtractionService that specializes in extracting data
  * from Spec classes with the class level annotation of {@link DataElement}
- * 
+ *
  * @author Michael Walsh
  */
 public class DataElementAnnotationExtractor {
@@ -32,9 +32,14 @@ public class DataElementAnnotationExtractor {
 	 * Annotations to not be transfered from member variables of Spec classes to
 	 * final generated classes
 	 */
-	private static final List<String> nonTransferableAnnotations = Stream.of(DataField.class, DataField.Default.class)
+	private static final List<String> nonTransferableAnnotations =
+		Stream.of(DataField.class, DataField.Default.class)
 			.map(Class::getCanonicalName)
-			.collect(Collectors.collectingAndThen(Collectors.toList(), Collections::unmodifiableList));
+			.collect(
+				Collectors.collectingAndThen(
+					Collectors.toList(), Collections::unmodifiableList
+				)
+			);
 
 	/**
 	 * used for extracting and preparing data for writer generation
@@ -48,12 +53,14 @@ public class DataElementAnnotationExtractor {
 
 	/**
 	 * Constructor that lets you initialize the {@link DataElementAnnotationExtractor} with different
-	 * implementations of {@link ICEAnnotationExtractionService} and {@link WriterGenerator} 
+	 * implementations of {@link ICEAnnotationExtractionService} and {@link WriterGenerator}
 	 * @param annotationExtractionService
 	 * @param writerGenerator
 	 */
-	DataElementAnnotationExtractor(ICEAnnotationExtractionService annotationExtractionService,
-			WriterGenerator writerGenerator) {
+	DataElementAnnotationExtractor(
+		ICEAnnotationExtractionService annotationExtractionService,
+		WriterGenerator writerGenerator
+	) {
 		this.annotationExtractionService = annotationExtractionService;
 		this.writerGenerator = writerGenerator;
 		this.annotationExtractionService.setNonTransferableAnnotations(nonTransferableAnnotations);
@@ -61,22 +68,23 @@ public class DataElementAnnotationExtractor {
 	}
 
 	/**
-	 * For a given request it will extract data from client classes 
+	 * For a given request it will extract data from client classes
 	 * and generate a list of {@link VelocitySourceWriter}
-	 * 
+	 *
 	 * @param request
 	 * @return list of generated SourceWriters
 	 * @throws IOException due to {@link ICEAnnotationExtractionService#extract(AnnotationExtractionRequest)}
 	 */
-	public List<VelocitySourceWriter> generateWriters(AnnotationExtractionRequest request) throws IOException {
+	public List<VelocitySourceWriter> generateWriters(
+		AnnotationExtractionRequest request
+	) throws IOException {
 		AnnotationExtractionResponse response = annotationExtractionService.extract(request);
-		List<VelocitySourceWriter> writerList = writerGenerator.generateWriters(request.getElement(),response);
-		return writerList;
+		return writerGenerator.generateWriters(request.getElement(),response);
 	}
 
 	/**
 	 * For a given request it will generate then execute writers
-	 * 
+	 *
 	 * @param request
 	 * @throws IOException
 	 */
@@ -92,12 +100,11 @@ public class DataElementAnnotationExtractor {
 
 	/**
 	 * Determine if the passed field is a DataField.
-	 * 
+	 *
 	 * @param element to check
 	 * @return whether element is a DataField
 	 */
 	public static boolean isDataField(Element element) {
 		return element.getAnnotation(DataField.class) != null;
 	}
-
 }

org.eclipse.ice.dev/org.eclipse.ice.dev.annotations/src/main/java/org/eclipse/ice/dev/annotations/processors/DataElementImplementationWriter.java

@@ -30,9 +30,6 @@ public class DataElementImplementationWriter extends ImplementationWriter {
 
 	/**
 	 * Location of DataElement template for use with velocity.
-	 *
-	 * Use of Velocity ClasspathResourceLoader means files are discovered relative
-	 * to the src/main/resources folder.
 	 */
 	private static final String IMPL_TEMPLATE = "templates/DataElement.vm";
 
@@ -46,8 +43,10 @@ public class DataElementImplementationWriter extends ImplementationWriter {
 	 * @param generatedFile
 	 */
 	@Builder
-	public DataElementImplementationWriter(String packageName, String interfaceName, String className, Fields fields,
-			Types types, FileObject generatedFile) {
+	public DataElementImplementationWriter(
+        String packageName, String interfaceName, String className, Fields
+        fields, Types types, FileObject generatedFile
+	) {
 		super(packageName, interfaceName, className, fields, types, generatedFile);
 		this.template = IMPL_TEMPLATE;
 	}

org.eclipse.ice.dev/org.eclipse.ice.dev.annotations/src/main/java/org/eclipse/ice/dev/annotations/processors/DataElementInterfaceWriter.java

 /*******************************************************************************
- * Copyright (c) 2020- UT-Battelle, LLC.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
+ * Copyright (c) 2020- UT-Battelle, LLC. All rights reserved. This program and
+ * the accompanying materials are made available under the terms of the Eclipse
+ * Public License v1.0 which accompanies this distribution, and is available at
  * http://www.eclipse.org/legal/epl-v10.html
  *
- * Contributors:
- *    Michael Walsh - Initial implementation
+ * Contributors: Michael Walsh - Initial implementation
  *******************************************************************************/
 package org.eclipse.ice.dev.annotations.processors;
 
@@ -24,7 +22,7 @@ import lombok.NonNull;
 /**
  * Implementation of the VelocitySourceWriter that handles generating the
  * DataElementInterfaceWriter
- * 
+ *
  * @author Michael Walsh
  */
 public class DataElementInterfaceWriter extends InterfaceWriter {
@@ -32,22 +30,24 @@ public class DataElementInterfaceWriter extends InterfaceWriter {
 	/**
 	 * Location of Interface template for use with velocity.
 	 *
-	 * Use of Velocity ClasspathResourceLoader means files are discovered relative
-	 * to the src/main/resources folder.
+	 * Use of Velocity ClasspathResourceLoader means files are discovered
+	 * relative to the src/main/resources folder.
 	 */
 	private static final String TEMPLATE = "templates/ElementInterface.vm";
 
 	/**
 	 * Constructor
-	 * 
+	 *
 	 * @param packageName
 	 * @param interfaceName
 	 * @param fields
 	 * @param generatedFile
 	 */
 	@Builder
-	public DataElementInterfaceWriter(String packageName, String interfaceName, @NonNull Fields fields,
-			Types types, FileObject generatedFile) {
+	public DataElementInterfaceWriter(
+		String packageName, String interfaceName, @NonNull Fields fields,
+		Types types, FileObject generatedFile
+	) {
 		super(packageName, interfaceName, fields, types, generatedFile);
 		this.template = TEMPLATE;
 	}
@@ -77,11 +77,10 @@ public class DataElementInterfaceWriter extends InterfaceWriter {
 
 	/**
 	 * Static method for cleanly fetching an initializer
-	 * 
+	 *
 	 * @return DataElementInterfaceWriter init lambda
 	 */
 	public static BiFunction<FileObject, Map, List<VelocitySourceWriter>> getContextInitializer() {
 		return new DataElementInterfaceWriter().getInitializer();
 	}
-
 }

org.eclipse.ice.dev/org.eclipse.ice.dev.annotations/src/main/java/org/eclipse/ice/dev/annotations/processors/DataElementPersistenceHandlerWriter.java

@@ -24,7 +24,7 @@ import lombok.NonNull;
 /**
  * Implementation of the VelocitySourceWriter that handles generating the
  * DataElementPersistenceHandlerWriter
- * 
+ *
  * @author Michael Walsh
  */
 public class DataElementPersistenceHandlerWriter extends PersistenceHandlerWriter {
@@ -39,7 +39,7 @@ public class DataElementPersistenceHandlerWriter extends PersistenceHandlerWrite
 
 	/**
 	 * Constructor
-	 * 
+	 *
 	 * @param packageName
 	 * @param elementInterface
 	 * @param className
@@ -50,11 +50,15 @@ public class DataElementPersistenceHandlerWriter extends PersistenceHandlerWrite
 	 * @param generatedFile
 	 */
 	@Builder
-	public DataElementPersistenceHandlerWriter(String packageName, String elementInterface, String className,
-			String interfaceName, String implementation, String collection, @NonNull Fields fields,
-			Types types, FileObject generatedFile) {
-		super(packageName, elementInterface, className, interfaceName, implementation, collection, fields,
-				types, generatedFile);
+	public DataElementPersistenceHandlerWriter(
+		String packageName, String elementInterface, String className,
+		String interfaceName, String implementation, String collection,
+		@NonNull Fields fields, Types types, FileObject generatedFile
+	) {
+		super(
+			packageName, elementInterface, className, interfaceName,
+			implementation, collection, fields, types, generatedFile
+		);
 		this.template = PERSISTENCE_HANDLER_TEMPLATE;
 	}
 
@@ -72,26 +76,27 @@ public class DataElementPersistenceHandlerWriter extends PersistenceHandlerWrite
 	 */
 	@Override
 	public BiFunction<FileObject, Map, List<VelocitySourceWriter>> getInitializer() {
-		return (fileObject, context) -> 
-					Arrays.asList(DataElementPersistenceHandlerWriter.builder()
-					.packageName((String) context.get(MetaTemplateProperty.PACKAGE))
-					.className((String) context.get(PersistenceHandlerTemplateProperty.CLASS))
-					.types(((Fields) context.get(MetaTemplateProperty.FIELDS)).getTypes())	.interfaceName((String) context.get(PersistenceHandlerTemplateProperty.INTERFACE))
-					.fields((Fields) context.get(MetaTemplateProperty.FIELDS))
-					.types(((Fields) context.get(MetaTemplateProperty.FIELDS)).getTypes())
-					.elementInterface((String) context.get(PersistenceHandlerTemplateProperty.ELEMENT_INTERFACE))
-					.collection((String) context.get(PersistenceHandlerTemplateProperty.COLLECTION))
-					.implementation((String) context.get(PersistenceHandlerTemplateProperty.IMPLEMENTATION))
-					.generatedFile(fileObject).build());
+		return (fileObject, context) -> Arrays.asList(
+			DataElementPersistenceHandlerWriter.builder()
+				.packageName((String) context.get(MetaTemplateProperty.PACKAGE))
+				.className((String) context.get(PersistenceHandlerTemplateProperty.CLASS))
+				.types(((Fields) context.get(MetaTemplateProperty.FIELDS)).getTypes())
+				.interfaceName((String) context.get(PersistenceHandlerTemplateProperty.INTERFACE))
+				.fields((Fields) context.get(MetaTemplateProperty.FIELDS))
+				.types(((Fields) context.get(MetaTemplateProperty.FIELDS)).getTypes())
+				.elementInterface((String) context.get(PersistenceHandlerTemplateProperty.ELEMENT_INTERFACE))
+				.collection((String) context.get(PersistenceHandlerTemplateProperty.COLLECTION))
+				.implementation((String) context.get(PersistenceHandlerTemplateProperty.IMPLEMENTATION))
+				.generatedFile(fileObject).build()
+		);
 	}
 
 	/**
 	 * Static method for cleanly fetching an initializer
-	 * 
+	 *
 	 * @return DataElementPersistenceHandlerWriter init lambda
 	 */
 	public static BiFunction<FileObject, Map, List<VelocitySourceWriter>> getContextInitializer() {
 		return new DataElementPersistenceHandlerWriter().getInitializer();
 	}
-
 }

org.eclipse.ice.dev/org.eclipse.ice.dev.annotations/src/main/java/org/eclipse/ice/dev/annotations/processors/DataElementProcessor.java

@@ -109,12 +109,9 @@ public class DataElementProcessor extends AbstractProcessor {
 		ICEAnnotationExtractionService extractionService = new ICEAnnotationExtractionService(elementUtils, mapper, env,
 				new DefaultNameGenerator());
 		WriterGenerator writerGenerator = new DataElementWriterGenerator(env);
-		this.extractor = new DataElementAnnotationExtractor(extractionService, writerGenerator);
-
-		// Set up Velocity using the Singleton approach; ClasspathResourceLoader allows
-		// us to load templates from src/main/resources
-		final Properties p = VelocityProperties.get();
-		Velocity.init(p);
+		this.extractor = new DataElementAnnotationExtractor(
+			extractionService, writerGenerator
+		);
 		super.init(env);
 	}
 

org.eclipse.ice.dev/org.eclipse.ice.dev.annotations/src/main/java/org/eclipse/ice/dev/annotations/processors/DataElementWriterGenerator.java

@@ -67,7 +67,9 @@ public class DataElementWriterGenerator extends AbstractWriterGenerator implemen
 	 * implementation, and possibly a persistence handler
 	 */
 	@Override
-	public List<VelocitySourceWriter> generateWriters(Element element, AnnotationExtractionResponse response) {
+	public List<VelocitySourceWriter> generateWriters(
+		Element element, AnnotationExtractionResponse response
+	) {
 		List<VelocitySourceWriter> writers = new ArrayList<>();
 		Map<TemplateProperty, Object> classMetadata = response.getClassMetadata();
 		boolean hasAnnotation = specExtractionHelper.hasAnnotation(element, Persisted.class);

org.eclipse.ice.dev/org.eclipse.ice.dev.annotations/src/main/java/org/eclipse/ice/dev/annotations/processors/ICEAnnotationExtractionService.java

@@ -90,7 +90,7 @@ public class ICEAnnotationExtractionService {
 		this.processingEnv = processingEnv;
 		this.nameGenerator = new DefaultNameGenerator();
 	}
-	
+
 	/**
 	 * Constructor
 	 */
@@ -104,63 +104,78 @@ public class ICEAnnotationExtractionService {
 
 	/**
 	 * Main entry point into the metadata extraction flow
-	 * 
+	 *
 	 * @param request
 	 * @return Extracted metadata
 	 * @throws IOException
 	 */
-	public AnnotationExtractionResponse extract(AnnotationExtractionRequest request) throws IOException {
+	public AnnotationExtractionResponse extract(
+		AnnotationExtractionRequest request
+	) throws IOException {
 		Fields fields = extractFields(request);
 		Map<TemplateProperty, Object> metaData = extractClassMetadata(request, fields);
-		return AnnotationExtractionResponse.builder().fields(fields).classMetadata(metaData).build();
+		return AnnotationExtractionResponse
+			.builder()
+			.fields(fields)
+			.classMetadata(metaData)
+			.build();
 	}
 
 	/**
 	 * Collect fields from Spec class, static default field collection, and json if
 	 * applicable
-	 * 
+	 *
 	 * @param request
 	 * @return Fields of the Spec class
 	 * @throws IOException
 	 */
-	public Fields extractFields(AnnotationExtractionRequest request) throws IOException {
+	public Fields extractFields(
+		AnnotationExtractionRequest request
+	) throws IOException {
 		Fields fields = new Fields();
 		Element element = request.getElement();
 
-		if (request.isIncludeDefaults())
+		if (request.isIncludeDefaults()) {
 			fields.collect(DefaultFields.get());
+		}
+
 		fields.collect(
-				specExtractionHelper.getAllFields(element, elementUtils, fieldFilter, nonTransferableAnnotations)); // get
-																													// all
-																													// members
-																													// with
-																													// given
-																													// filter
-		fields.collect(jsonExtractionHelper.collectFromDataFieldJson(element, processingEnv, mapper));
+			specExtractionHelper.getAllFields(
+				element, elementUtils, fieldFilter, nonTransferableAnnotations
+			)
+		); // get all members with given filter
+		fields.collect(
+			jsonExtractionHelper.collectFromDataFieldJson(
+				element, processingEnv, mapper
+			)
+		);
 		return fields;
 	}
 
 	/**
 	 * Parse, generate, and store class metadata in a map.
-	 * 
+	 *
 	 * @param request
 	 * @param fields
 	 * @return metadata map
 	 */
-	public Map<TemplateProperty, Object> extractClassMetadata(AnnotationExtractionRequest request, Fields fields) {
+	public Map<TemplateProperty, Object> extractClassMetadata(
+		AnnotationExtractionRequest request, Fields fields
+	) {
 		SpecClassMetadata specData = extractSpecData(request, fields);
-		Map<TemplateProperty, Object> context = generateClassMetadata(specData);
-		return context;
+		return generateClassMetadata(specData);
 	}
 
 	/**
 	 * Given seed data extracted from a spec class, this method generates the
 	 * necessary metadata for class generation
-	 * 
+	 *
 	 * @param specData
 	 * @return enum keyed map of extracted and processed class metadata
 	 */
-	protected Map<TemplateProperty, Object> generateClassMetadata(SpecClassMetadata specData) {
+	protected Map<TemplateProperty, Object> generateClassMetadata(
+		SpecClassMetadata specData
+	) {
 		Map<TemplateProperty, Object> context = new HashMap<>();
 
 		generateMetaTemplateData(specData, context);
@@ -170,46 +185,83 @@ public class ICEAnnotation