Fix compile warnings in deposit-services

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/RemedialDepositException.java

@@ -24,6 +24,7 @@
  * @author Elliot Metsger ([email protected])
  */
 public class RemedialDepositException extends DepositServiceRuntimeException {
+    private static final long serialVersionUID = 1L;
 
     public RemedialDepositException(PassEntity resource) {
         super(resource);

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/ArchiveOutputStreamFactory.java

@@ -18,6 +18,7 @@
 import java.io.OutputStream;
 import java.util.Map;
 
+import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveOutputStream;
 
 /**
@@ -37,6 +38,7 @@ public interface ArchiveOutputStreamFactory {
      * @param toWrap         the output stream to be wrapped by the returned {@code ArchiveOutputStream}
      * @return the configured {@code ArchiveOutputStream} ready for writing
      */
-    ArchiveOutputStream newInstance(Map<String, Object> packageOptions, OutputStream toWrap);
+    <O extends ArchiveOutputStream<? extends ArchiveEntry>> O newInstance(Map<String, Object> packageOptions,
+                                                                          OutputStream toWrap);
 
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/ArchivingPackageStream.java

@@ -29,6 +29,7 @@
 import java.util.concurrent.TimeUnit;
 import java.util.function.BiConsumer;
 
+import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveOutputStream;
 import org.eclipse.pass.deposit.assembler.PackageOptions.Archive;
 import org.eclipse.pass.deposit.model.DepositSubmission;
@@ -130,7 +131,7 @@ public InputStream open() {
 
         // Wrap the output stream in an ArchiveOutputStream
         // we support zip, tar and tar.gz so far
-        ArchiveOutputStream archiveOut = archiveOutputStreamFactory.newInstance(packageOptions, pipedOut);
+        ArchiveOutputStream<ArchiveEntry> archiveOut = archiveOutputStreamFactory.newInstance(packageOptions, pipedOut);
 
         // Set on the writer, and used to report any exceptions caught by the writer to the reader.  That way a full
         // stack trace of the exception will be reported when it is encountered by the reader

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/CallableStreamWriter.java

@@ -23,6 +23,7 @@
 import java.util.concurrent.Callable;
 import java.util.concurrent.atomic.AtomicBoolean;
 
+import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveOutputStream;
 import org.eclipse.pass.deposit.model.DepositSubmission;
 import org.springframework.core.io.Resource;
@@ -36,7 +37,7 @@ public class CallableStreamWriter<V> implements Callable<V>, StreamWriter {
 
     private StreamWriter delegate;
 
-    private ArchiveOutputStream archiveOut;
+    private ArchiveOutputStream<ArchiveEntry> archiveOut;
 
     private List<DepositFileResource> custodialFiles;
 
@@ -55,7 +56,7 @@ public class CallableStreamWriter<V> implements Callable<V>, StreamWriter {
      * @param custodialFiles
      */
     CallableStreamWriter(StreamWriter delegate,
-                         ArchiveOutputStream archiveOut,
+                         ArchiveOutputStream<ArchiveEntry> archiveOut,
                          List<DepositFileResource> custodialFiles) {
         this.delegate = delegate;
         this.archiveOut = archiveOut;
@@ -73,7 +74,8 @@ public V call() throws Exception {
     }
 
     @Override
-    public void start(List<DepositFileResource> custodialFiles, ArchiveOutputStream archiveOut) throws IOException {
+    public void start(List<DepositFileResource> custodialFiles, ArchiveOutputStream<ArchiveEntry> archiveOut)
+        throws IOException {
         if (alreadyStarted.getAndSet(true) == Boolean.FALSE) {
             delegate.start(custodialFiles, archiveOut);
         } else {
@@ -98,7 +100,7 @@ public void finish(DepositSubmission submission, List<PackageStream.Resource> cu
     }
 
     @Override
-    public void close() throws Exception {
+    public void close() throws IOException {
         if (alreadyClosed.getAndSet(true) == Boolean.FALSE) {
             delegate.close();
         } else {

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/DebuggingArchiveOutputStream.java

@@ -28,11 +28,11 @@
 /**
  * @author Elliot Metsger ([email protected])
  */
-public class DebuggingArchiveOutputStream extends ArchiveOutputStream {
+public class DebuggingArchiveOutputStream extends ArchiveOutputStream<ArchiveEntry> {
 
-    private ArchiveOutputStream delegate;
+    private ArchiveOutputStream<ArchiveEntry> delegate;
 
-    public DebuggingArchiveOutputStream(ArchiveOutputStream delegate) {
+    public DebuggingArchiveOutputStream(ArchiveOutputStream<ArchiveEntry> delegate) {
         this.delegate = delegate;
     }
 
@@ -78,21 +78,6 @@ public void write(int b) throws IOException {
         delegate.write(b);
     }
 
-//    @Override
-//    protected void count(int written) {
-//        delegate.count(written);
-//    }
-//
-//    @Override
-//    protected void count(long written) {
-//        delegate.count(written);
-//    }
-
-    @Override
-    public int getCount() {
-        return delegate.getCount();
-    }
-
     @Override
     public long getBytesWritten() {
         return delegate.getBytesWritten();

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/DebuggingArchiveOutputStreamFactory.java

@@ -18,6 +18,7 @@
 import java.io.OutputStream;
 import java.util.Map;
 
+import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveOutputStream;
 
 /**
@@ -29,8 +30,10 @@ public DebuggingArchiveOutputStreamFactory(Map<String, Object> packageOptions) {
         super(packageOptions);
     }
 
+    @SuppressWarnings("unchecked")
     @Override
-    public ArchiveOutputStream newInstance(Map<String, Object> packageOptions, OutputStream toWrap) {
-        return new DebuggingArchiveOutputStream(super.newInstance(packageOptions, toWrap));
+    public <O extends ArchiveOutputStream<? extends ArchiveEntry>> O newInstance(Map<String, Object> packageOptions,
+                                                                                 OutputStream toWrap) {
+        return (O) new DebuggingArchiveOutputStream(super.newInstance(packageOptions, toWrap));
     }
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/DefaultArchiveOutputStreamFactory.java

@@ -18,6 +18,7 @@
 import java.io.OutputStream;
 import java.util.Map;
 
+import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveOutputStream;
 import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
 import org.apache.commons.compress.archivers.zip.ZipArchiveOutputStream;
@@ -40,38 +41,38 @@ public DefaultArchiveOutputStreamFactory(Map<String, Object> packageOptions) {
         this.packageOptions = packageOptions;
     }
 
+    @SuppressWarnings("unchecked")
     @Override
-    public ArchiveOutputStream newInstance(Map<String, Object> packageOptions, OutputStream toWrap) {
-        // Wrap the output stream in an ArchiveOutputStream
-        // we support zip, tar and tar.gz so far
-        ArchiveOutputStream archiveOut;
+    public <O extends ArchiveOutputStream<? extends ArchiveEntry>> O newInstance(Map<String, Object> packageOptions,
+                                                                                 OutputStream toWrap) {
 
         if (packageOptions.getOrDefault(PackageOptions.Archive.KEY, PackageOptions.Archive.OPTS.NONE) ==
             PackageOptions.Archive.OPTS.TAR) {
             try {
+                TarArchiveOutputStream tarArchiveOutputStream;
                 if (packageOptions.getOrDefault(PackageOptions.Compression.KEY, PackageOptions.Compression.OPTS.NONE)
                     == PackageOptions.Compression.OPTS.GZIP) {
-                    archiveOut = new TarArchiveOutputStream(new GzipCompressorOutputStream(toWrap));
+                    tarArchiveOutputStream = new TarArchiveOutputStream(new GzipCompressorOutputStream(toWrap));
                 } else {
-                    archiveOut = new TarArchiveOutputStream(toWrap);
+                    tarArchiveOutputStream = new TarArchiveOutputStream(toWrap);
                 }
+                return (O) tarArchiveOutputStream;
             } catch (Exception e) {
                 throw new RuntimeException(String.format(ERR_CREATING_ARCHIVE_STREAM, PackageOptions.Archive.OPTS.TAR,
                     e.getMessage()), e);
             }
         } else if (packageOptions.getOrDefault(PackageOptions.Archive.KEY, PackageOptions.Archive.OPTS.NONE) ==
             PackageOptions.Archive.OPTS.ZIP) {
             try {
-                archiveOut = new ZipArchiveOutputStream(toWrap);
+                ZipArchiveOutputStream zipArchiveOutputStream = new ZipArchiveOutputStream(toWrap);
+                return (O) zipArchiveOutputStream;
             } catch (Exception e) {
                 throw new RuntimeException(String.format(ERR_CREATING_ARCHIVE_STREAM, PackageOptions.Archive.OPTS.ZIP,
                     e.getMessage()), e);
             }
         } else {
             throw new RuntimeException(ERR_NO_ARCHIVE_FORMAT);
         }
-
-        return archiveOut;
     }
 
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/DefaultStreamWriterImpl.java

@@ -48,7 +48,7 @@ public class DefaultStreamWriterImpl implements StreamWriter {
     private final List<DepositFileResource> packageFiles;
     private final ResourceBuilderFactory rbf;
     private final DepositSubmission submission;
-    protected ArchiveOutputStream archiveOut;
+    protected ArchiveOutputStream<ArchiveEntry> archiveOut;
     protected Map<String, Object> packageOptions;
     protected PackageProvider packageProvider;
 
@@ -75,7 +75,8 @@ public DefaultStreamWriterImpl(DepositSubmission submission,
     }
 
     @Override
-    public void start(List<DepositFileResource> custodialFiles, ArchiveOutputStream archiveOut) throws IOException {
+    public void start(List<DepositFileResource> custodialFiles, ArchiveOutputStream<ArchiveEntry> archiveOut)
+        throws IOException {
         this.archiveOut = archiveOut;
         List<PackageStream.Resource> assembledResources = new ArrayList<>();
 
@@ -118,7 +119,7 @@ public void start(List<DepositFileResource> custodialFiles, ArchiveOutputStream
     }
 
     @Override
-    public void close() throws Exception {
+    public void close() throws IOException {
         archiveOut.close();
     }
 
@@ -215,7 +216,8 @@ protected ArchiveEntry createEntry(String name, long length) {
      * @param archiveEntryIn the bytes to be written
      * @throws IOException if there is an error encountered writing the bytes
      */
-    private void writeResource(ArchiveOutputStream archiveOut, ArchiveEntry archiveEntry, InputStream archiveEntryIn)
+    private void writeResource(ArchiveOutputStream<ArchiveEntry> archiveOut, ArchiveEntry archiveEntry,
+                               InputStream archiveEntryIn)
         throws IOException {
         archiveOut.putArchiveEntry(archiveEntry);
         int bytesWritten = IOUtils.copy(archiveEntryIn, archiveOut);

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/assembler/StreamWriter.java

@@ -18,6 +18,7 @@
 import java.io.IOException;
 import java.util.List;
 
+import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveOutputStream;
 import org.eclipse.pass.deposit.model.DepositSubmission;
 import org.springframework.core.io.Resource;
@@ -45,7 +46,8 @@ interface StreamWriter extends AutoCloseable {
      * @param archiveOut     the {@code OutputStream} to be written to
      * @throws IOException if there are any errors encountered initializing state
      */
-    void start(List<DepositFileResource> custodialFiles, ArchiveOutputStream archiveOut) throws IOException;
+    void start(List<DepositFileResource> custodialFiles, ArchiveOutputStream<ArchiveEntry> archiveOut)
+        throws IOException;
 
     /**
      * Writes the {@code Resource} and returns metadata describing the {@code custodialFile}.
@@ -70,4 +72,5 @@ interface StreamWriter extends AutoCloseable {
      */
     void finish(DepositSubmission submission, List<PackageStream.Resource> custodialResources) throws IOException;
 
+    void close() throws IOException;
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/builder/DepositSubmissionMapper.java

@@ -91,7 +91,7 @@ public DepositSubmission createDepositSubmission(Submission submissionEntity, Li
         // Prepare for Metadata
         DepositMetadata metadata = new DepositMetadata();
         submission.setMetadata(metadata);
-        submission.setSubmissionMeta(new JsonParser().parse(submissionEntity.getMetadata()).getAsJsonObject());
+        submission.setSubmissionMeta(JsonParser.parseString(submissionEntity.getMetadata()).getAsJsonObject());
         DepositMetadata.Manuscript manuscript = new DepositMetadata.Manuscript();
         metadata.setManuscriptMetadata(manuscript);
         DepositMetadata.Article article = new DepositMetadata.Article();
@@ -328,7 +328,7 @@ private void processPmcMetadata(DepositMetadata metadata, JsonObject submissionD
      * @param metadataStr
      */
     void processMetadata(DepositMetadata depositMetadata, String metadataStr) {
-        JsonObject json = new JsonParser().parse(metadataStr).getAsJsonObject();
+        JsonObject json = JsonParser.parseString(metadataStr).getAsJsonObject();
         processCommonMetadata(depositMetadata, json);
         processPmcMetadata(depositMetadata, json);
         processCrossrefMetadata(depositMetadata, json);

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/config/repository/SpringEnvironmentDeserializer.java

@@ -25,6 +25,7 @@
 import org.springframework.core.env.Environment;
 
 public class SpringEnvironmentDeserializer extends StringDeserializer {
+    private static final long serialVersionUID = 1L;
 
     private Environment env;
 

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/TransportSession.java

@@ -16,6 +16,7 @@
 
 package org.eclipse.pass.deposit.transport;
 
+import java.io.IOException;
 import java.util.Map;
 
 import org.eclipse.pass.deposit.assembler.PackageStream;
@@ -50,4 +51,6 @@ public interface TransportSession extends AutoCloseable {
 
     boolean closed();
 
+    void close() throws IOException;
+
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/devnull/DevNullTransport.java

@@ -15,6 +15,7 @@
  */
 package org.eclipse.pass.deposit.transport.devnull;
 
+import java.io.IOException;
 import java.net.URI;
 import java.util.Map;
 
@@ -120,7 +121,7 @@ public boolean closed() {
         }
 
         @Override
-        public void close() throws Exception {
+        public void close() throws IOException {
             // no-op
         }
 

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/fs/FilesystemTransport.java

@@ -193,7 +193,7 @@ public boolean closed() {
         }
 
         @Override
-        public void close() throws Exception {
+        public void close() throws IOException {
             // no-op
         }
 

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/ftp/FtpTransportSession.java

@@ -137,7 +137,7 @@ public boolean closed() {
     }
 
     @Override
-    public void close() throws Exception {
+    public void close() throws IOException {
         LOG.debug("Closing {}@{}...",
                   this.getClass().getSimpleName(), toHexString(identityHashCode(this)));
         if (transfer != null && !transfer.isDone()) {

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/ftp/FtpUtil.java

@@ -94,7 +94,7 @@ private FtpUtil () {
      * @param clientCommand the command to perform
      * @throws RuntimeException if the command throw a checked exception
      */
-    static void performSilently(ExceptionThrowingVoidCommand clientCommand) {
+    static <T> void performSilently(ExceptionThrowingVoidCommand<T> clientCommand) {
         try {
             clientCommand.perform();
         } catch (Exception e) {

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/inveniordm/InvenioRdmSession.java

@@ -15,6 +15,7 @@
  */
 package org.eclipse.pass.deposit.transport.inveniordm;
 
+import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.util.List;
 import java.util.Map;
@@ -104,7 +105,7 @@ public boolean closed() {
     }
 
     @Override
-    public void close() throws Exception {
+    public void close() throws IOException {
         // no-op resources are closed with try-with-resources
     }
 

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/sftp/SftpTransportSession.java

@@ -148,7 +148,7 @@ public boolean closed() {
     }
 
     @Override
-    public void close() throws Exception {
+    public void close() throws IOException {
         // no-op resources are closed with try-with-resources
     }
 }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/sword2/InvalidCollectionUrl.java

@@ -21,6 +21,7 @@
  * For example, when the Collection URL is no present in the SWORD service document.
  */
 class InvalidCollectionUrl extends RuntimeException {
+    private static final long serialVersionUID = 1L;
 
     InvalidCollectionUrl(String message) {
         super(message);

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/sword2/Sword2TransportSession.java

@@ -192,7 +192,7 @@ public boolean closed() {
     }
 
     @Override
-    public void close() throws Exception {
+    public void close() throws IOException {
         if (this.closed()) {
             return;
         }

pass-deposit-services/deposit-core/src/main/java/org/eclipse/pass/deposit/transport/sword2/SwordErrorMessageWrapper.java

@@ -22,6 +22,7 @@
  * Wraps a {@link SWORDError} for the purpose of providing a non-null response to {@link Throwable#getMessage()}.
  */
 class SwordErrorMessageWrapper extends Exception {
+    private static final long serialVersionUID = 1L;
 
     private SWORDError wrapped;