Use StandardCharsets instead of charset names

src/main/java/edu/harvard/iq/dataverse/DataCitation.java

@@ -15,6 +15,7 @@
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.io.Writer;
+import java.nio.charset.StandardCharsets;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
@@ -253,7 +254,7 @@ public String toBibtexString() {
 
     public void writeAsBibtexCitation(OutputStream os) throws IOException {
         // Use UTF-8
-        Writer out = new BufferedWriter(new OutputStreamWriter(os, "utf-8"));
+        Writer out = new BufferedWriter(new OutputStreamWriter(os, StandardCharsets.UTF_8));
         if(getFileTitle() !=null && isDirect()) {
             out.write("@incollection{");
         } else {
@@ -317,7 +318,7 @@ public String toRISString() {
 
     public void writeAsRISCitation(OutputStream os) throws IOException {
         // Use UTF-8
-        Writer out = new BufferedWriter(new OutputStreamWriter(os, "utf-8"));
+        Writer out = new BufferedWriter(new OutputStreamWriter(os, StandardCharsets.UTF_8));
         out.write("Provider: " + publisher + "\r\n");
         out.write("Content: text/plain; charset=\"utf-8\"" + "\r\n");
         // Using type "DATA" - see https://github.com/IQSS/dataverse/issues/4816

src/main/java/edu/harvard/iq/dataverse/Shib.java

@@ -19,6 +19,7 @@
 import org.apache.commons.lang3.StringUtils;
 
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.sql.Timestamp;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -458,9 +459,9 @@ private String getRequiredValueFromAssertion(String key) throws Exception {
         if (attributeValue.isEmpty()) {
             throw new Exception(key + " was empty");
         }
-		if(systemConfig.isShibAttributeCharacterSetConversionEnabled()) {
-			attributeValue= new String( attributeValue.getBytes("ISO-8859-1"), "UTF-8");
-		}
+        if (systemConfig.isShibAttributeCharacterSetConversionEnabled()) {
+            attributeValue= new String( attributeValue.getBytes(StandardCharsets.ISO_8859_1), StandardCharsets.UTF_8);
+        }
         String trimmedValue = attributeValue.trim();
         logger.fine("The SAML assertion for \"" + key + "\" (required) was \"" + attributeValue + "\" and was trimmed to \"" + trimmedValue + "\".");
         return trimmedValue;

src/main/java/edu/harvard/iq/dataverse/api/Admin.java

@@ -65,6 +65,7 @@
 
 import java.io.InputStream;
 import java.io.StringReader;
+import java.nio.charset.StandardCharsets;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.logging.Level;
@@ -1153,7 +1154,7 @@ public void write(OutputStream os) throws IOException,
                         os.write(",\n".getBytes());
                     }
 
-                    os.write(output.build().toString().getBytes("UTF8"));
+                    os.write(output.build().toString().getBytes(StandardCharsets.UTF_8));
 
                     if (!wroteObject) {
                         wroteObject = true;
@@ -1267,7 +1268,7 @@ public void write(OutputStream os) throws IOException,
                         os.write(",\n".getBytes());
                     }
 
-                    os.write(output.build().toString().getBytes("UTF8"));
+                    os.write(output.build().toString().getBytes(StandardCharsets.UTF_8));
 
                     if (!wroteObject) {
                         wroteObject = true;

src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/PasswordEncryption.java

@@ -1,6 +1,6 @@
 package edu.harvard.iq.dataverse.authorization.providers.builtin;
 
-import java.io.UnsupportedEncodingException;
+import java.nio.charset.StandardCharsets;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import org.apache.commons.lang3.RandomStringUtils;
@@ -36,13 +36,13 @@ public interface Algorithm {
         public String encrypt(String plainText) {
             try {
                 MessageDigest md = MessageDigest.getInstance("SHA");
-                md.update(plainText.getBytes("UTF-8"));
+                md.update(plainText.getBytes(StandardCharsets.UTF_8));
                 byte[] raw = md.digest();
                 //String hash = Base64.encodeToString(raw, true);
                 String hash = Base64.getEncoder().encodeToString(raw);
                 return hash;
 
-            } catch (NoSuchAlgorithmException | UnsupportedEncodingException e) {
+            } catch (NoSuchAlgorithmException e) {
                 throw new RuntimeException(e);
             }
         }

src/main/java/edu/harvard/iq/dataverse/dataaccess/TabularSubsetGenerator.java

@@ -20,30 +20,16 @@
 
 package edu.harvard.iq.dataverse.dataaccess;
 
-import edu.harvard.iq.dataverse.DataFile;
-import edu.harvard.iq.dataverse.datavariable.DataVariable;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Scanner;
-import java.util.Set;
-import java.math.BigDecimal;
-import java.math.MathContext;
-import java.math.RoundingMode;
-import java.nio.ByteBuffer;
-import java.nio.channels.FileChannel;
-import java.nio.file.Paths;
-import java.nio.file.StandardOpenOption;
 import java.util.logging.Logger;
 import java.util.regex.Matcher;
 

src/main/java/edu/harvard/iq/dataverse/dataset/DatasetUtil.java

@@ -17,12 +17,11 @@
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
 import java.nio.channels.FileChannel;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.*;
@@ -281,7 +280,7 @@ public static Dataset persistDatasetLogoToStorageAndCreateThumbnails(Dataset dat
         try {
             tmpFile = FileUtil.inputStreamToFile(inputStream);
         } catch (IOException ex) {
-        	logger.severe(ex.getMessage());
+        	logger.severe("FileUtil.inputStreamToFile failed for tmpFile: " + ex.getMessage());
         }
 
         StorageIO<Dataset> dataAccess = null;
@@ -307,7 +306,7 @@ public static Dataset persistDatasetLogoToStorageAndCreateThumbnails(Dataset dat
             fullSizeImage = ImageIO.read(tmpFile);
         } catch (IOException ex) {
         	IOUtils.closeQuietly(inputStream);
-            logger.severe(ex.getMessage());
+            logger.severe("ImageIO.read failed for tmpFile: " + ex.getMessage());
             return null;
         }
         if (fullSizeImage == null) {
@@ -318,33 +317,22 @@ public static Dataset persistDatasetLogoToStorageAndCreateThumbnails(Dataset dat
         int width = fullSizeImage.getWidth();
         int height = fullSizeImage.getHeight();
         FileChannel src = null;
-        try {
-            src = new FileInputStream(tmpFile).getChannel();
-        } catch (FileNotFoundException ex) {
-        	IOUtils.closeQuietly(inputStream);
-            logger.severe(ex.getMessage());
-            return null;
-        }
         FileChannel dest = null;
-        try {
-            dest = new FileOutputStream(tmpFile).getChannel();
-        } catch (FileNotFoundException ex) {
-        	IOUtils.closeQuietly(inputStream);
-            logger.severe(ex.getMessage());
-            return null;
-        }
-        try {
+        try (FileInputStream fis = new FileInputStream(tmpFile); FileOutputStream fos = new FileOutputStream(tmpFile)) {
+            src = fis.getChannel();
+            dest = fos.getChannel();
             dest.transferFrom(src, 0, src.size());
         } catch (IOException ex) {
-            logger.severe(ex.getMessage());
+        	IOUtils.closeQuietly(inputStream);
+            logger.severe("Error occurred during transfer using FileChannels: " + ex.getMessage());
             return null;
         }
         File tmpFileForResize = null;
         try {
         	//The stream was used around line 274 above, so this creates an empty file (OK since all it is used for is getting a path, but not reusing it here would make it easier to close it above.)
             tmpFileForResize = FileUtil.inputStreamToFile(inputStream);
         } catch (IOException ex) {
-            logger.severe(ex.getMessage());
+            logger.severe("FileUtil.inputStreamToFile failed for tmpFileForResize: " + ex.getMessage());
             return null;
         } finally {
         	IOUtils.closeQuietly(inputStream);
@@ -409,14 +397,8 @@ public static InputStream getThumbnailAsInputStream(Dataset dataset, int size) {
             String base64Image = datasetThumbnail.getBase64image();
             String leadingStringToRemove = FileUtil.DATA_URI_SCHEME;
             String encodedImg = base64Image.substring(leadingStringToRemove.length());
-            byte[] decodedImg = null;
-            try {
-                decodedImg = Base64.getDecoder().decode(encodedImg.getBytes("UTF-8"));
-                logger.fine("returning this many bytes for  " + "dataset id: " + dataset.getId() + ", persistentId: " + dataset.getIdentifier() + " :" + decodedImg.length);
-            } catch (UnsupportedEncodingException ex) {
-                logger.info("dataset thumbnail could not be decoded for dataset id " + dataset.getId() + ": " + ex);
-                return null;
-            }
+            byte[] decodedImg = Base64.getDecoder().decode(encodedImg.getBytes(StandardCharsets.UTF_8));
+            logger.fine("returning this many bytes for  " + "dataset id: " + dataset.getId() + ", persistentId: " + dataset.getIdentifier() + " :" + decodedImg.length);
             ByteArrayInputStream nonDefaultDatasetThumbnail = new ByteArrayInputStream(decodedImg);
             logger.fine("For dataset id " + dataset.getId() + " a thumbnail was found and is being returned.");
             return nonDefaultDatasetThumbnail;
@@ -627,7 +609,7 @@ public static boolean validateDatasetMetadataExternally(Dataset ds, String execu
 
         try {
             File tempFile = File.createTempFile("datasetMetadataCheck", ".tmp");
-            FileUtils.writeStringToFile(tempFile, jsonMetadata);
+            FileUtils.writeStringToFile(tempFile, jsonMetadata, StandardCharsets.UTF_8);
 
             // run the external executable: 
             String[] params = { executable, tempFile.getAbsolutePath() };

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DuraCloudSubmitToArchiveCommand.java

@@ -5,7 +5,6 @@
 import edu.harvard.iq.dataverse.DatasetLock.Reason;
 import edu.harvard.iq.dataverse.authorization.Permission;
 import edu.harvard.iq.dataverse.authorization.users.ApiToken;
-import edu.harvard.iq.dataverse.engine.command.Command;
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
 import edu.harvard.iq.dataverse.workflow.step.Failure;
@@ -14,7 +13,7 @@
 import java.io.IOException;
 import java.io.PipedInputStream;
 import java.io.PipedOutputStream;
-import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.security.DigestInputStream;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
@@ -32,7 +31,7 @@
 import org.duracloud.error.ContentStoreException;
 
 @RequiredPermissions(Permission.PublishDataset)
-public class DuraCloudSubmitToArchiveCommand extends AbstractSubmitToArchiveCommand implements Command<DatasetVersion> {
+public class DuraCloudSubmitToArchiveCommand extends AbstractSubmitToArchiveCommand {
 
     private static final Logger logger = Logger.getLogger(DuraCloudSubmitToArchiveCommand.class.getName());
     private static final String DEFAULT_PORT = "443";
@@ -117,7 +116,7 @@ public WorkflowStepResult performArchiveSubmission(DatasetVersion dv, ApiToken t
                             public void run() {
                                 try (PipedOutputStream dataciteOut = new PipedOutputStream(dataciteIn)) {
 
-                                    dataciteOut.write(dataciteXml.getBytes(Charset.forName("utf-8")));
+                                    dataciteOut.write(dataciteXml.getBytes(StandardCharsets.UTF_8));
                                     dataciteOut.close();
                                     success=true;
                                 } catch (Exception e) {

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GoogleCloudSubmitToArchiveCommand.java

@@ -11,7 +11,6 @@
 import edu.harvard.iq.dataverse.DatasetVersion;
 import edu.harvard.iq.dataverse.authorization.Permission;
 import edu.harvard.iq.dataverse.authorization.users.ApiToken;
-import edu.harvard.iq.dataverse.engine.command.Command;
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
 import edu.harvard.iq.dataverse.settings.JvmSettings;
@@ -26,14 +25,14 @@
 import java.io.IOException;
 import java.io.PipedInputStream;
 import java.io.PipedOutputStream;
-import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.security.DigestInputStream;
 import java.security.MessageDigest;
 import java.util.Map;
 import java.util.logging.Logger;
 
 @RequiredPermissions(Permission.PublishDataset)
-public class GoogleCloudSubmitToArchiveCommand extends AbstractSubmitToArchiveCommand implements Command<DatasetVersion> {
+public class GoogleCloudSubmitToArchiveCommand extends AbstractSubmitToArchiveCommand {
 
     private static final Logger logger = Logger.getLogger(GoogleCloudSubmitToArchiveCommand.class.getName());
     private static final String GOOGLECLOUD_BUCKET = ":GoogleCloudBucket";
@@ -82,7 +81,7 @@ public WorkflowStepResult performArchiveSubmission(DatasetVersion dv, ApiToken t
                             public void run() {
                                 try (PipedOutputStream dataciteOut = new PipedOutputStream(dataciteIn)) {
 
-                                    dataciteOut.write(dataciteXml.getBytes(Charset.forName("utf-8")));
+                                    dataciteOut.write(dataciteXml.getBytes(StandardCharsets.UTF_8));
                                     dataciteOut.close();
                                     success = true;
                                 } catch (Exception e) {

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/S3SubmitToArchiveCommand.java

@@ -5,7 +5,6 @@
 import edu.harvard.iq.dataverse.DatasetLock.Reason;
 import edu.harvard.iq.dataverse.authorization.Permission;
 import edu.harvard.iq.dataverse.authorization.users.ApiToken;
-import edu.harvard.iq.dataverse.engine.command.Command;
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
 import edu.harvard.iq.dataverse.util.bagit.BagGenerator;
@@ -17,6 +16,7 @@
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.FileInputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Map;
 import java.util.logging.Logger;
 
@@ -41,7 +41,7 @@
 import com.amazonaws.services.s3.transfer.TransferManagerBuilder;
 
 @RequiredPermissions(Permission.PublishDataset)
-public class S3SubmitToArchiveCommand extends AbstractSubmitToArchiveCommand implements Command<DatasetVersion> {
+public class S3SubmitToArchiveCommand extends AbstractSubmitToArchiveCommand {
 
     private static final Logger logger = Logger.getLogger(S3SubmitToArchiveCommand.class.getName());
     private static final String S3_CONFIG = ":S3ArchiverConfig";
@@ -86,7 +86,7 @@ public WorkflowStepResult performArchiveSubmission(DatasetVersion dv, ApiToken t
 
                     spaceName = getSpaceName(dataset);
                     String dataciteXml = getDataCiteXml(dv);
-                    try (ByteArrayInputStream dataciteIn = new ByteArrayInputStream(dataciteXml.getBytes("UTF-8"))) {
+                    try (ByteArrayInputStream dataciteIn = new ByteArrayInputStream(dataciteXml.getBytes(StandardCharsets.UTF_8))) {
                         // Add datacite.xml file
                         ObjectMetadata om = new ObjectMetadata();
                         om.setContentLength(dataciteIn.available());

src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java

@@ -7,10 +7,10 @@
 import io.gdcc.spi.export.Exporter;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Locale;
 import java.util.Optional;
 
-import jakarta.json.JsonObject;
 import jakarta.ws.rs.core.MediaType;
 
 
@@ -35,7 +35,7 @@ public String getDisplayName(Locale locale) {
     @Override
     public void exportDataset(ExportDataProvider dataProvider, OutputStream outputStream) throws ExportException {
         try{
-            outputStream.write(dataProvider.getDatasetJson().toString().getBytes("UTF8"));
+            outputStream.write(dataProvider.getDatasetJson().toString().getBytes(StandardCharsets.UTF_8));
             outputStream.flush();
         } catch (Exception e){
             throw new ExportException("Unknown exception caught during JSON export.");

src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java

@@ -7,11 +7,11 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Locale;
 import java.util.Optional;
 import java.util.logging.Logger;
 
-import jakarta.json.JsonObject;
 import jakarta.ws.rs.core.MediaType;
 
 @AutoService(Exporter.class)
@@ -25,7 +25,7 @@ public class OAI_OREExporter implements Exporter {
     public void exportDataset(ExportDataProvider dataProvider, OutputStream outputStream)
             throws ExportException {
         try {
-            outputStream.write(dataProvider.getDatasetORE().toString().getBytes("UTF8"));
+            outputStream.write(dataProvider.getDatasetORE().toString().getBytes(StandardCharsets.UTF_8));
             outputStream.flush();
         } catch (Exception e) {
             logger.severe(e.getMessage());

src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java

@@ -7,6 +7,7 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Locale;
 import java.util.logging.Logger;
 import jakarta.ws.rs.core.MediaType;
@@ -75,7 +76,7 @@ public class SchemaDotOrgExporter implements Exporter {
     @Override
     public void exportDataset(ExportDataProvider dataProvider, OutputStream outputStream) throws ExportException {
         try {
-            outputStream.write(dataProvider.getDatasetSchemaDotOrg().toString().getBytes("UTF8"));
+            outputStream.write(dataProvider.getDatasetSchemaDotOrg().toString().getBytes(StandardCharsets.UTF_8));
         } catch (IOException ex) {
             logger.info("IOException calling outputStream.write: " + ex);
         }