fix(ENGKNOW-2545): Fix issues with GZipStream

buildSrc/src/main/groovy/gor.java-common.gradle

@@ -178,7 +178,7 @@ tasks.withType(Test) {
     props.load(new FileInputStream("${project.rootDir}/tests/config/unittest.sysproperties"))
     systemProperties = props
 
-    jvmArgs = Arrays.asList("--add-opens java.base/java.nio=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED".split(" "))
+    jvmArgs = Arrays.asList("--enable-native-access=ALL-UNNAMED --add-opens java.base/java.nio=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED".split(" "))
 
     // Set logback config file.
     systemProperty 'logback.configurationFile', new File("${project.rootDir}/tests/config/logback-test.xml").absolutePath

drivers/src/main/java/org/gorpipe/s3/driver/S3SourceProvider.java

@@ -136,6 +136,7 @@ private S3Client createSyncCrtClient(Credentials cred) {
         AwsCrtHttpClient.Builder httpClientBuilder = AwsCrtHttpClient.builder()
                 .connectionTimeout(s3Config.connectionTimeout())  // Default was 2s
                 .maxConcurrency(s3Config.connectionPoolSize())
+                //.readBufferSizeInBytes(16*1024*1024L)
                 .tcpKeepAliveConfiguration(b -> b
                         .keepAliveInterval(Duration.ofMillis(s3Config.socketTimeout().toMillis()/2))
                         .keepAliveTimeout(s3Config.connectionTimeout()))

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

model/src/main/java/org/gorpipe/gor/model/DriverBackedFileReader.java

@@ -31,6 +31,7 @@
 import org.gorpipe.gor.driver.GorDriverFactory;
 import org.gorpipe.gor.driver.PluggableGorDriver;
 import org.gorpipe.gor.driver.SourceProvider;
+import org.gorpipe.gor.driver.adapters.PositionAwareInputStream;
 import org.gorpipe.gor.driver.adapters.StreamSourceRacFile;
 import org.gorpipe.gor.driver.meta.DataType;
 import org.gorpipe.gor.driver.meta.SourceReference;
@@ -43,6 +44,7 @@
 import org.gorpipe.gor.table.dictionary.gor.GorDictionaryTable;
 import org.gorpipe.gor.table.util.PathUtils;
 import org.gorpipe.gor.util.DataUtil;
+import org.gorpipe.gor.util.NCGZIPInputStream;
 import org.gorpipe.gor.util.StringUtil;
 import org.gorpipe.util.standalone.GorStandalone;
 import org.slf4j.Logger;
@@ -65,6 +67,8 @@ public class DriverBackedFileReader extends FileReader {
 
     private static final String DEFAULT_COMMON_ROOT = "./";
 
+    final static int GZIP_BUFFER_SIZE = Integer.parseInt(System.getProperty("gor.gzip.buffer.size", "2046"));
+
     private final boolean DEPENDENTS = System.getProperty("gor.filereader.dependents", "true").equalsIgnoreCase("true");
 
     private final String securityContext;
@@ -378,7 +382,7 @@ private static class SourceReader extends BufferedReader {
 
         SourceReader(DataSource source) throws IOException {
             super(DataUtil.isGZip(source.getName()) ?
-                    new BufferedReader(new InputStreamReader(new GZIPInputStream(((StreamSource) source).open()/*, 32*1024*/))) :
+                    new BufferedReader(new InputStreamReader(new GZIPInputStream(new NCGZIPInputStream(((StreamSource) source).open()), GZIP_BUFFER_SIZE))) :
                     new InputStreamReader(((StreamSource) source).open()));
             this.source = source;
         }

model/src/main/java/org/gorpipe/gor/model/VcfGzGenomicIterator.java

@@ -46,6 +46,8 @@ public class VcfGzGenomicIterator extends GenomicIteratorBase {
     final static int VCF_COLUMN_RENAME_COUNT = 10;
     final static String VCF_COLUMN_RENAME_NAME = "VALUES";
 
+    final static int GZIP_BUFFER_SIZE = Integer.parseInt(System.getProperty("gor.gzip.buffer.size", "2046"));
+
     public BufferedReader reader;
     private StreamSource streamSource;
     final ChromoLookup lookup; // chromosome name lookup service
@@ -62,7 +64,7 @@ public enum ChrNameSystem {
 
 
     public VcfGzGenomicIterator(ChromoLookup lookup, String file, StreamSource streamsource, boolean compressed) throws IOException {
-        this(lookup, file, new BufferedReader(new InputStreamReader(compressed ? new GZIPInputStream(new NCGZIPInputStream(new PositionAwareInputStream(streamsource.open()))) : streamsource.open())));
+        this(lookup, file, new BufferedReader(new InputStreamReader(compressed ? new GZIPInputStream(new NCGZIPInputStream(new PositionAwareInputStream(streamsource.open())), GZIP_BUFFER_SIZE) : streamsource.open())));
         this.streamSource = streamsource;
     }
 

model/src/main/java/org/gorpipe/gor/util/NCGZIPInputStream.java

@@ -52,6 +52,8 @@ public NCGZIPInputStream(InputStream in) {
      * http://bugs.java.com/bugdatabase/view_bug.do?bug_id=7036144
      * <p>
      * Reference TT: 0034867351
+     *
+     * 2025-06-20:  This is fixed in Java 23 b15
      */
     @Override
     public int available() throws IOException {