From c62956616c196740b0bac52c281e436b570a8ba0 Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 14:51:03 +0100
Subject: [PATCH 01/12] Add base functionality and tests

---
 .../neverblink/jelly/cli/JellyCommand.scala   |   6 ++-
 .../jelly/cli/command/rdf/RdfFromJelly.scala  |  38 ++++++++++++++----
 .../command/rdf/RdfFromJelly.scala.semanticdb | Bin 0 -> 46792 bytes
 .../jelly/cli/command/RdfFromJellySpec.scala  |  19 ++++++++-
 ...AfterTest.scala => CleanUpAfterTest.scala} |   3 +-
 .../cli/command/helpers/DataGenHelper.scala   |  35 ++++++++++++++--
 6 files changed, 87 insertions(+), 14 deletions(-)
 create mode 100644 src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb
 rename src/test/scala/eu/neverblink/jelly/cli/command/helpers/{CleanUpFilesAfterTest.scala => CleanUpAfterTest.scala} (72%)

diff --git a/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala b/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
index 9bb527e..de0e072 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
@@ -3,7 +3,7 @@ package eu.neverblink.jelly.cli
 import caseapp.*
 import eu.neverblink.jelly.cli.JellyCommand.emptyRemainingArgs
 
-import java.io.{ByteArrayOutputStream, PrintStream}
+import java.io.{ByteArrayOutputStream, OutputStream, PrintStream}
 import scala.compiletime.uninitialized
 
 object JellyCommand:
@@ -39,6 +39,10 @@ abstract class JellyCommand[T: {Parser, Help}] extends Command[T]:
       s
     else throw new IllegalStateException("Not in test mode")
 
+  def getOutputStream: OutputStream =
+    if isTest then osOut
+    else System.out
+
   def getErr: String =
     if isTest then
       err.flush()
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
index 31af120..db54991 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
@@ -1,16 +1,40 @@
 package eu.neverblink.jelly.cli.command.rdf
 import caseapp.*
 import eu.neverblink.jelly.cli.JellyCommand
+import eu.ostrzyciel.jelly.convert.jena.riot.JellyLanguage
+import org.apache.jena.riot.system.StreamRDFWriter
+import org.apache.jena.riot.{RDFLanguages, RDFParser}
 
-case class FromJellyRdfOptions()
+import java.io.{ByteArrayInputStream, ByteArrayOutputStream, File, FileInputStream, InputStream}
+
+case class RdfFromJellyOptions(
+    @ExtraName("input-file") inputFile: Option[String],
+)
+
+object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
+  override def group = "rdf"
 
-object RdfFromJelly extends JellyCommand[FromJellyRdfOptions]:
   override def names: List[List[String]] = List(
     List("rdf", "from-jelly"),
   )
 
-  override def run(options: FromJellyRdfOptions, remainingArgs: RemainingArgs): Unit =
-    // This is a placeholder for the actual implementation
-    println("rdf from-jelly")
-    println(options)
-    println(remainingArgs)
+  override def run(options: RdfFromJellyOptions, remainingArgs: RemainingArgs): Unit =
+    val inputStream = options.inputFile match {
+      case Some(fileName: String) =>
+        FileInputStream(File(fileName))
+      case None => System.in
+    }
+    rewriteFormats(inputStream)
+
+  /*
+    This method reads the Jelly file, rewrite it to NQuads and writes it to the output stream
+   * @param inputStream InputStream
+   */
+  private def rewriteFormats(inputStream: InputStream): Unit =
+    // TODO: Add error handling; return success/failure in the future
+    val interStream = new ByteArrayOutputStream()
+    val interWriter = StreamRDFWriter.getWriterStream(interStream, RDFLanguages.NQUADS)
+    RDFParser.source(inputStream).lang(JellyLanguage.JELLY).parse(interWriter)
+    val readerStream = new ByteArrayInputStream(interStream.toByteArray)
+    val nQuadWriter = StreamRDFWriter.getWriterStream(getOutputStream, RDFLanguages.NQUADS)
+    RDFParser.source(readerStream).lang(RDFLanguages.NQUADS).parse(nQuadWriter)
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb
new file mode 100644
index 0000000000000000000000000000000000000000..388b3124811028edaf51a99f835e441083e6ad3c
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HcmV?d00001

diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
index 1b5f9ed..d1b6a1b 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
@@ -1,12 +1,29 @@
 package eu.neverblink.jelly.cli.command
 
 import eu.neverblink.jelly.cli.command.helpers.*
+import eu.neverblink.jelly.cli.command.rdf.*
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpec
 
-class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpFilesAfterTest:
+class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
   "rdf from-jelly command" should {
     "be able to convert a Jelly file to NTriples" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
+      val nQuadString = DataGenHelper.generateNQuadString(3)
+      val options = RdfFromJellyOptions(inputFile = Some(jellyFile))
+      val (out, err) = RdfFromJelly.runTest(options)
+      val sortedOut = out.split("\n").map(_.trim).sorted
+      val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
+      sortedOut should contain theSameElementsAs sortedQuads
+    }
+    "be able to convert a Jelly stream to NTriples" in {
+      val jellyStream = DataGenHelper.generateJellyInputStream(3)
+      System.setIn(jellyStream)
+      val nQuadString = DataGenHelper.generateNQuadString(3)
+      val options = RdfFromJellyOptions(inputFile = None)
+      val (out, err) = RdfFromJelly.runTest(options)
+      val sortedOut = out.split("\n").map(_.trim).sorted
+      val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
+      sortedOut should contain theSameElementsAs sortedQuads
     }
   }
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpFilesAfterTest.scala b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpAfterTest.scala
similarity index 72%
rename from src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpFilesAfterTest.scala
rename to src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpAfterTest.scala
index 6a3c705..d162389 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpFilesAfterTest.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpAfterTest.scala
@@ -3,9 +3,10 @@ package eu.neverblink.jelly.cli.command.helpers
 import org.scalatest.BeforeAndAfterEach
 import org.scalatest.wordspec.AnyWordSpec
 
-trait CleanUpFilesAfterTest extends BeforeAndAfterEach {
+trait CleanUpAfterTest extends BeforeAndAfterEach {
   this: AnyWordSpec =>
   override def afterEach(): Unit = {
     DataGenHelper.cleanUpFile()
+    DataGenHelper.resetInputStream()
   }
 }
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
index d81cf91..9509bed 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
@@ -2,9 +2,9 @@ package eu.neverblink.jelly.cli.command.helpers
 
 import eu.ostrzyciel.jelly.convert.jena.riot.JellyLanguage
 import org.apache.jena.rdf.model.{Model, ModelFactory, ResourceFactory}
-import org.apache.jena.riot.RDFDataMgr
+import org.apache.jena.riot.{RDFDataMgr, RDFLanguages}
 
-import java.io.FileOutputStream
+import java.io.{ByteArrayInputStream, ByteArrayOutputStream, FileOutputStream}
 import java.nio.file.{Files, Paths}
 import scala.util.Using
 
@@ -14,6 +14,7 @@ import scala.util.Using
 object DataGenHelper:
 
   private val testFile = "testInput.jelly"
+  private val inputStream = System.in
 
   /*
    * This method generates a triple model with nTriples
@@ -37,14 +38,40 @@ object DataGenHelper:
   /* This method generates a Jelly file with nTriples
    * @param nTriples number of triples to generate
    * @param fileName name of the file to generate
+   * @return String
    */
-  def generateJellyFile(nTriples: Int): Unit =
+  def generateJellyFile(nTriples: Int): String =
     val model = generateTripleModel(nTriples)
     // TODO: Add configurable generation for different variants of Jelly (small strict etc)
     Using.resource(FileOutputStream(testFile)) { file =>
       RDFDataMgr.write(file, model, JellyLanguage.JELLY)
     }
+    testFile
+
+  /*
+   * This method generates a Jelly byte input stream with nTriples
+   * @param nTriples number of triples to generate
+   * @return String
+   */
+  def generateJellyInputStream(nTriples: Int): ByteArrayInputStream =
+    val model = generateTripleModel(nTriples)
+    val outputStream = new ByteArrayOutputStream()
+    RDFDataMgr.write(outputStream, model, JellyLanguage.JELLY)
+    new ByteArrayInputStream(outputStream.toByteArray)
+
+  /*
+   * This method generates a NQuad string with nTriples
+   * @param nTriples number of triples to generate
+   * @return String
+   */
+  def generateNQuadString(nTriples: Int): String =
+    val model = generateTripleModel(nTriples)
+    val outputStream = new ByteArrayOutputStream()
+    RDFDataMgr.write(outputStream, model, RDFLanguages.NQUADS)
+    outputStream.toString
 
-  /* This method cleans up the file after the test*/
   def cleanUpFile(): Unit =
     Files.deleteIfExists(Paths.get(testFile))
+
+  def resetInputStream(): Unit =
+    System.setIn(inputStream)

From dd60627c3a89ddcf2add3a84a72172388480ee7d Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 16:11:37 +0100
Subject: [PATCH 02/12] Simplify cod

---
 .../neverblink/jelly/cli/JellyCommand.scala   |   2 +-
 .../jelly/cli/command/rdf/RdfFromJelly.scala  |  25 +++++++-----
 .../command/rdf/RdfFromJelly.scala.semanticdb | Bin 46792 -> 49539 bytes
 .../jelly/cli/command/RdfFromJellySpec.scala  |  38 ++++++++++++++++--
 .../command/helpers/CleanUpAfterTest.scala    |   2 +-
 .../cli/command/helpers/DataGenHelper.scala   |  16 +++++++-
 .../helpers/DataGenHelper.scala.semanticdb    | Bin 0 -> 46703 bytes
 7 files changed, 64 insertions(+), 19 deletions(-)
 create mode 100644 src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb

diff --git a/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala b/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
index de0e072..69d3e32 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/JellyCommand.scala
@@ -39,7 +39,7 @@ abstract class JellyCommand[T: {Parser, Help}] extends Command[T]:
       s
     else throw new IllegalStateException("Not in test mode")
 
-  def getOutputStream: OutputStream =
+  protected def getStdOut: OutputStream =
     if isTest then osOut
     else System.out
 
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
index db54991..810549e 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
@@ -5,10 +5,11 @@ import eu.ostrzyciel.jelly.convert.jena.riot.JellyLanguage
 import org.apache.jena.riot.system.StreamRDFWriter
 import org.apache.jena.riot.{RDFLanguages, RDFParser}
 
-import java.io.{ByteArrayInputStream, ByteArrayOutputStream, File, FileInputStream, InputStream}
+import java.io.{File, FileInputStream, FileOutputStream, InputStream, OutputStream}
 
 case class RdfFromJellyOptions(
-    @ExtraName("input-file") inputFile: Option[String],
+    @ExtraName("") inputFile: Option[String],
+    @ExtraName("to") outputFile: Option[String],
 )
 
 object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
@@ -24,17 +25,19 @@ object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
         FileInputStream(File(fileName))
       case None => System.in
     }
-    rewriteFormats(inputStream)
+    val outputStream = options.outputFile match {
+      case Some(fileName: String) =>
+        FileOutputStream(fileName)
+      case None => getStdOut
+    }
+    doConversion(inputStream, outputStream)
 
   /*
-    This method reads the Jelly file, rewrite it to NQuads and writes it to the output stream
+    This method reads the Jelly file, rewrite it to NQuads and writes it to some output stream
    * @param inputStream InputStream
+   * @param outputStream OutputStream
    */
-  private def rewriteFormats(inputStream: InputStream): Unit =
+  private def doConversion(inputStream: InputStream, outputStream: OutputStream): Unit =
     // TODO: Add error handling; return success/failure in the future
-    val interStream = new ByteArrayOutputStream()
-    val interWriter = StreamRDFWriter.getWriterStream(interStream, RDFLanguages.NQUADS)
-    RDFParser.source(inputStream).lang(JellyLanguage.JELLY).parse(interWriter)
-    val readerStream = new ByteArrayInputStream(interStream.toByteArray)
-    val nQuadWriter = StreamRDFWriter.getWriterStream(getOutputStream, RDFLanguages.NQUADS)
-    RDFParser.source(readerStream).lang(RDFLanguages.NQUADS).parse(nQuadWriter)
+    val nQuadWriter = StreamRDFWriter.getWriterStream(outputStream, RDFLanguages.NQUADS)
+    RDFParser.source(inputStream).lang(JellyLanguage.JELLY).parse(nQuadWriter)
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb
index 388b3124811028edaf51a99f835e441083e6ad3c..4afec816ef8c8041469a8ed8da1f5807f6c353d7 100644
GIT binary patch
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diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
index d1b6a1b..4ca357a 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
@@ -2,28 +2,58 @@ package eu.neverblink.jelly.cli.command
 
 import eu.neverblink.jelly.cli.command.helpers.*
 import eu.neverblink.jelly.cli.command.rdf.*
+import org.apache.jena.riot.RDFLanguages
 import org.scalatest.matchers.should.Matchers
 import org.scalatest.wordspec.AnyWordSpec
 
+import scala.io.Source
+import scala.util.Using
+
 class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
   "rdf from-jelly command" should {
-    "be able to convert a Jelly file to NTriples" in {
+    "be able to convert a Jelly file to NTriples output stream" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(inputFile = Some(jellyFile))
+      val options = RdfFromJellyOptions(inputFile = Some(jellyFile), outputFile = None)
       val (out, err) = RdfFromJelly.runTest(options)
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
       sortedOut should contain theSameElementsAs sortedQuads
     }
-    "be able to convert a Jelly stream to NTriples" in {
+    "be able to convert a Jelly stream to NTriples output stream" in {
       val jellyStream = DataGenHelper.generateJellyInputStream(3)
       System.setIn(jellyStream)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(inputFile = None)
+      val options = RdfFromJellyOptions(inputFile = None, outputFile = None)
       val (out, err) = RdfFromJelly.runTest(options)
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
       sortedOut should contain theSameElementsAs sortedQuads
     }
+    "be able to convert a Jelly file to NTriples file" in {
+      val jellyFile = DataGenHelper.generateJellyFile(3)
+      val nQuadString = DataGenHelper.generateNQuadString(3)
+      val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
+      val options = RdfFromJellyOptions(inputFile = Some(jellyFile), outputFile = Some(outputFile))
+      val (out, err) = RdfFromJelly.runTest(options)
+      val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
+        content.getLines().toList.map(_.trim).sorted
+      }
+      val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
+      sortedOut should contain theSameElementsAs sortedQuads
+      out.length should be(0)
+    }
+    "be able to convert a Jelly stream to NTriples file" in {
+      val jellyStream = DataGenHelper.generateJellyInputStream(3)
+      val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
+      val nQuadString = DataGenHelper.generateNQuadString(3)
+      val options = RdfFromJellyOptions(inputFile = None, outputFile = Some(outputFile))
+      val (out, err) = RdfFromJelly.runTest(options)
+      val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
+        content.getLines().toList.map(_.trim).sorted
+      }
+      val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
+      sortedOut should contain theSameElementsAs sortedQuads
+      out.length should be(0)
+    }
   }
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpAfterTest.scala b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpAfterTest.scala
index d162389..4d73c62 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpAfterTest.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/CleanUpAfterTest.scala
@@ -6,7 +6,7 @@ import org.scalatest.wordspec.AnyWordSpec
 trait CleanUpAfterTest extends BeforeAndAfterEach {
   this: AnyWordSpec =>
   override def afterEach(): Unit = {
-    DataGenHelper.cleanUpFile()
+    DataGenHelper.cleanUpFiles()
     DataGenHelper.resetInputStream()
   }
 }
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
index 9509bed..766c0cd 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
@@ -2,10 +2,11 @@ package eu.neverblink.jelly.cli.command.helpers
 
 import eu.ostrzyciel.jelly.convert.jena.riot.JellyLanguage
 import org.apache.jena.rdf.model.{Model, ModelFactory, ResourceFactory}
-import org.apache.jena.riot.{RDFDataMgr, RDFLanguages}
+import org.apache.jena.riot.{RDFDataMgr, RDFLanguages, Lang}
 
 import java.io.{ByteArrayInputStream, ByteArrayOutputStream, FileOutputStream}
 import java.nio.file.{Files, Paths}
+import scala.collection.mutable.ListBuffer
 import scala.util.Using
 
 /*
@@ -15,6 +16,7 @@ object DataGenHelper:
 
   private val testFile = "testInput.jelly"
   private val inputStream = System.in
+  protected val outputFiles = ListBuffer[String]()
 
   /*
    * This method generates a triple model with nTriples
@@ -70,8 +72,18 @@ object DataGenHelper:
     RDFDataMgr.write(outputStream, model, RDFLanguages.NQUADS)
     outputStream.toString
 
-  def cleanUpFile(): Unit =
+  /*
+   * Generates and then cleans the file for test purposes
+   */
+  def generateOutputFile(format: Lang = RDFLanguages.NQUADS): String =
+    val extension = format.getFileExtensions.get(0)
+    val fileName = s"testOutput${outputFiles.size}.${extension}"
+    outputFiles += fileName
+    fileName
+
+  def cleanUpFiles(): Unit =
     Files.deleteIfExists(Paths.get(testFile))
+    for file <- outputFiles do Files.deleteIfExists(Paths.get(file))
 
   def resetInputStream(): Unit =
     System.setIn(inputStream)
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb
new file mode 100644
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literal 0
HcmV?d00001


From 130ee75bc51b8dcfbd22fcd4a23ef66c9448624a Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 16:25:10 +0100
Subject: [PATCH 03/12] Correct test error

---
 .../jelly/cli/command/RdfFromJellySpec.scala  |   5 ++---
 .../cli/command/helpers/DataGenHelper.scala   |   6 +++---
 .../helpers/DataGenHelper.scala.semanticdb    | Bin 46703 -> 49577 bytes
 3 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
index 4ca357a..3cb2bb1 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
@@ -21,8 +21,7 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
       sortedOut should contain theSameElementsAs sortedQuads
     }
     "be able to convert a Jelly stream to NTriples output stream" in {
-      val jellyStream = DataGenHelper.generateJellyInputStream(3)
-      System.setIn(jellyStream)
+      DataGenHelper.generateJellyInputStream(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
       val options = RdfFromJellyOptions(inputFile = None, outputFile = None)
       val (out, err) = RdfFromJelly.runTest(options)
@@ -44,7 +43,7 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
       out.length should be(0)
     }
     "be able to convert a Jelly stream to NTriples file" in {
-      val jellyStream = DataGenHelper.generateJellyInputStream(3)
+      DataGenHelper.generateJellyInputStream(3)
       val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
       val nQuadString = DataGenHelper.generateNQuadString(3)
       val options = RdfFromJellyOptions(inputFile = None, outputFile = Some(outputFile))
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
index 766c0cd..d6e5f89 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala
@@ -53,13 +53,13 @@ object DataGenHelper:
   /*
    * This method generates a Jelly byte input stream with nTriples
    * @param nTriples number of triples to generate
-   * @return String
    */
-  def generateJellyInputStream(nTriples: Int): ByteArrayInputStream =
+  def generateJellyInputStream(nTriples: Int): Unit =
     val model = generateTripleModel(nTriples)
     val outputStream = new ByteArrayOutputStream()
     RDFDataMgr.write(outputStream, model, JellyLanguage.JELLY)
-    new ByteArrayInputStream(outputStream.toByteArray)
+    val jellyStream = new ByteArrayInputStream(outputStream.toByteArray)
+    System.setIn(jellyStream)
 
   /*
    * This method generates a NQuad string with nTriples
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb
index 5efa4a2526abdfc179dcdf84ba75bed124f16621..babc834012d5222a91e0dad966b46e9a00b67365 100644
GIT binary patch
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Cl)JG2


From 61f385b78415597cb243d6180794fdcef6a6bbe1 Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 16:32:44 +0100
Subject: [PATCH 04/12] Uncommit semanticdb files

---
 .gitignore                                      |   2 +-
 .../command/rdf/RdfFromJelly.scala.semanticdb   | Bin 49539 -> 0 bytes
 .../helpers/DataGenHelper.scala.semanticdb      | Bin 49577 -> 0 bytes
 3 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 100644 src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb
 delete mode 100644 src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb

diff --git a/.gitignore b/.gitignore
index a6fcde6..03ba4de 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,7 +26,7 @@ out/
 bin/
 !**/src/main/**/bin/
 !**/src/test/**/bin/
-
+*.semanticdb
 ### NetBeans ###
 /nbproject/private/
 /nbbuild/
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala.semanticdb
deleted file mode 100644
index 4afec816ef8c8041469a8ed8da1f5807f6c353d7..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 49539
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diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb b/src/test/scala/eu/neverblink/jelly/cli/command/helpers/DataGenHelper.scala.semanticdb
deleted file mode 100644
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From 12fe5edd554324739ea99b9f7f4ab147f1474f93 Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 16:34:36 +0100
Subject: [PATCH 05/12] Move to more meaningful part of gitignore

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 03ba4de..18269d2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,7 +26,7 @@ out/
 bin/
 !**/src/main/**/bin/
 !**/src/test/**/bin/
-*.semanticdb
+
 ### NetBeans ###
 /nbproject/private/
 /nbbuild/
@@ -45,6 +45,7 @@ build/
 
 ### Scala ###
 .bsp/
+*.semanticdb
 
 ### IDEA ###
 /.idea/

From 2819d7078743616b26e71ba3d98485d55110d36c Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 18:59:19 +0100
Subject: [PATCH 06/12] Move input file to remaining parameters to make it
 positional

---
 .gitignore                                    |  1 +
 .../jelly/cli/command/rdf/RdfFromJelly.scala  |  8 +++-----
 .../jelly/cli/command/RdfFromJellySpec.scala  | 19 +++++++++++++------
 3 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/.gitignore b/.gitignore
index 18269d2..a463476 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@ target/
 !.mvn/wrapper/maven-wrapper.jar
 !**/src/main/**/target/
 !**/src/test/**/target/
+testData/**
 
 ### IntelliJ IDEA ###
 .idea/modules.xml
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
index 810549e..7b90697 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
@@ -8,8 +8,7 @@ import org.apache.jena.riot.{RDFLanguages, RDFParser}
 import java.io.{File, FileInputStream, FileOutputStream, InputStream, OutputStream}
 
 case class RdfFromJellyOptions(
-    @ExtraName("") inputFile: Option[String],
-    @ExtraName("to") outputFile: Option[String],
+    @ExtraName("to") outputFile: Option[String] = None,
 )
 
 object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
@@ -20,10 +19,10 @@ object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
   )
 
   override def run(options: RdfFromJellyOptions, remainingArgs: RemainingArgs): Unit =
-    val inputStream = options.inputFile match {
+    val inputStream = remainingArgs.remaining.headOption match {
       case Some(fileName: String) =>
         FileInputStream(File(fileName))
-      case None => System.in
+      case _ => System.in
     }
     val outputStream = options.outputFile match {
       case Some(fileName: String) =>
@@ -38,6 +37,5 @@ object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
    * @param outputStream OutputStream
    */
   private def doConversion(inputStream: InputStream, outputStream: OutputStream): Unit =
-    // TODO: Add error handling; return success/failure in the future
     val nQuadWriter = StreamRDFWriter.getWriterStream(outputStream, RDFLanguages.NQUADS)
     RDFParser.source(inputStream).lang(JellyLanguage.JELLY).parse(nQuadWriter)
diff --git a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
index 3cb2bb1..e7721bd 100644
--- a/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
+++ b/src/test/scala/eu/neverblink/jelly/cli/command/RdfFromJellySpec.scala
@@ -1,5 +1,6 @@
 package eu.neverblink.jelly.cli.command
 
+import caseapp.core.{Indexed, RemainingArgs}
 import eu.neverblink.jelly.cli.command.helpers.*
 import eu.neverblink.jelly.cli.command.rdf.*
 import org.apache.jena.riot.RDFLanguages
@@ -14,8 +15,13 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
     "be able to convert a Jelly file to NTriples output stream" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(inputFile = Some(jellyFile), outputFile = None)
-      val (out, err) = RdfFromJelly.runTest(options)
+      val options = RdfFromJellyOptions(outputFile = None)
+      val args = RemainingArgs(indexedRemaining = List(Indexed(jellyFile)), Seq.empty)
+      val (out, err) =
+        RdfFromJelly.runTest(
+          options,
+          args,
+        )
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
       sortedOut should contain theSameElementsAs sortedQuads
@@ -23,7 +29,7 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
     "be able to convert a Jelly stream to NTriples output stream" in {
       DataGenHelper.generateJellyInputStream(3)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(inputFile = None, outputFile = None)
+      val options = RdfFromJellyOptions(outputFile = None)
       val (out, err) = RdfFromJelly.runTest(options)
       val sortedOut = out.split("\n").map(_.trim).sorted
       val sortedQuads = nQuadString.split("\n").map(_.trim).sorted
@@ -31,10 +37,11 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
     }
     "be able to convert a Jelly file to NTriples file" in {
       val jellyFile = DataGenHelper.generateJellyFile(3)
+      val args = RemainingArgs(indexedRemaining = List(Indexed(jellyFile)), Seq.empty)
       val nQuadString = DataGenHelper.generateNQuadString(3)
       val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
-      val options = RdfFromJellyOptions(inputFile = Some(jellyFile), outputFile = Some(outputFile))
-      val (out, err) = RdfFromJelly.runTest(options)
+      val options = RdfFromJellyOptions(outputFile = Some(outputFile))
+      val (out, err) = RdfFromJelly.runTest(options, args)
       val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
         content.getLines().toList.map(_.trim).sorted
       }
@@ -46,7 +53,7 @@ class RdfFromJellySpec extends AnyWordSpec with Matchers with CleanUpAfterTest:
       DataGenHelper.generateJellyInputStream(3)
       val outputFile = DataGenHelper.generateOutputFile(RDFLanguages.NQUADS)
       val nQuadString = DataGenHelper.generateNQuadString(3)
-      val options = RdfFromJellyOptions(inputFile = None, outputFile = Some(outputFile))
+      val options = RdfFromJellyOptions(outputFile = Some(outputFile))
       val (out, err) = RdfFromJelly.runTest(options)
       val sortedOut = Using.resource(Source.fromFile(outputFile)) { content =>
         content.getLines().toList.map(_.trim).sorted

From d5554f6462e02fe5bbe796c31fbc30f7be1963a1 Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 19:21:41 +0100
Subject: [PATCH 07/12] Move to a stable version of jelly

---
 build.sbt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.sbt b/build.sbt
index 09be481..23e207d 100644
--- a/build.sbt
+++ b/build.sbt
@@ -5,7 +5,7 @@ resolvers +=
   "Sonatype OSS Snapshots" at "https://s01.oss.sonatype.org/content/repositories/snapshots"
 
 lazy val jenaV = "5.3.0"
-lazy val jellyV = "2.8.0+14-4181e89a-SNAPSHOT"
+lazy val jellyV = "2.8.0"
 
 addCommandAlias("fixAll", "scalafixAll; scalafmtAll")
 

From 5fb4631e5e4634229cfef100752624791510980e Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 19:44:07 +0100
Subject: [PATCH 08/12] Check if lifecycle changes help

---
 .../eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala    | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
index 7b90697..f6185ff 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
@@ -1,7 +1,7 @@
 package eu.neverblink.jelly.cli.command.rdf
 import caseapp.*
 import eu.neverblink.jelly.cli.JellyCommand
-import eu.ostrzyciel.jelly.convert.jena.riot.JellyLanguage
+import eu.ostrzyciel.jelly.convert.jena.riot.{JellyLanguage, JellySubsystemLifecycle}
 import org.apache.jena.riot.system.StreamRDFWriter
 import org.apache.jena.riot.{RDFLanguages, RDFParser}
 
@@ -37,5 +37,7 @@ object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
    * @param outputStream OutputStream
    */
   private def doConversion(inputStream: InputStream, outputStream: OutputStream): Unit =
+    val mod = JellySubsystemLifecycle()
+    mod.start()
     val nQuadWriter = StreamRDFWriter.getWriterStream(outputStream, RDFLanguages.NQUADS)
     RDFParser.source(inputStream).lang(JellyLanguage.JELLY).parse(nQuadWriter)

From 66a7f520135c5df210b843c80955241b82c1bc61 Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 19:56:55 +0100
Subject: [PATCH 09/12] Change jena versions

---
 build.sbt                                                     | 2 +-
 .../eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala    | 4 +---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/build.sbt b/build.sbt
index 23e207d..dd3dd9b 100644
--- a/build.sbt
+++ b/build.sbt
@@ -4,7 +4,7 @@ ThisBuild / scalaVersion := "3.6.4"
 resolvers +=
   "Sonatype OSS Snapshots" at "https://s01.oss.sonatype.org/content/repositories/snapshots"
 
-lazy val jenaV = "5.3.0"
+lazy val jenaV = "5.2.0"
 lazy val jellyV = "2.8.0"
 
 addCommandAlias("fixAll", "scalafixAll; scalafmtAll")
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
index f6185ff..7b90697 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
@@ -1,7 +1,7 @@
 package eu.neverblink.jelly.cli.command.rdf
 import caseapp.*
 import eu.neverblink.jelly.cli.JellyCommand
-import eu.ostrzyciel.jelly.convert.jena.riot.{JellyLanguage, JellySubsystemLifecycle}
+import eu.ostrzyciel.jelly.convert.jena.riot.JellyLanguage
 import org.apache.jena.riot.system.StreamRDFWriter
 import org.apache.jena.riot.{RDFLanguages, RDFParser}
 
@@ -37,7 +37,5 @@ object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
    * @param outputStream OutputStream
    */
   private def doConversion(inputStream: InputStream, outputStream: OutputStream): Unit =
-    val mod = JellySubsystemLifecycle()
-    mod.start()
     val nQuadWriter = StreamRDFWriter.getWriterStream(outputStream, RDFLanguages.NQUADS)
     RDFParser.source(inputStream).lang(JellyLanguage.JELLY).parse(nQuadWriter)

From ae9a4cf0391b055379a6db99efd400b67d0a20fe Mon Sep 17 00:00:00 2001
From: Karolina Bogacka <karolina@neverblink.eu>
Date: Thu, 20 Mar 2025 20:04:09 +0100
Subject: [PATCH 10/12] Revert "Change jena versions"

This reverts commit 66a7f520135c5df210b843c80955241b82c1bc61.
---
 build.sbt                                                     | 2 +-
 .../eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala    | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/build.sbt b/build.sbt
index dd3dd9b..23e207d 100644
--- a/build.sbt
+++ b/build.sbt
@@ -4,7 +4,7 @@ ThisBuild / scalaVersion := "3.6.4"
 resolvers +=
   "Sonatype OSS Snapshots" at "https://s01.oss.sonatype.org/content/repositories/snapshots"
 
-lazy val jenaV = "5.2.0"
+lazy val jenaV = "5.3.0"
 lazy val jellyV = "2.8.0"
 
 addCommandAlias("fixAll", "scalafixAll; scalafmtAll")
diff --git a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
index 7b90697..f6185ff 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/command/rdf/RdfFromJelly.scala
@@ -1,7 +1,7 @@
 package eu.neverblink.jelly.cli.command.rdf
 import caseapp.*
 import eu.neverblink.jelly.cli.JellyCommand
-import eu.ostrzyciel.jelly.convert.jena.riot.JellyLanguage
+import eu.ostrzyciel.jelly.convert.jena.riot.{JellyLanguage, JellySubsystemLifecycle}
 import org.apache.jena.riot.system.StreamRDFWriter
 import org.apache.jena.riot.{RDFLanguages, RDFParser}
 
@@ -37,5 +37,7 @@ object RdfFromJelly extends JellyCommand[RdfFromJellyOptions]:
    * @param outputStream OutputStream
    */
   private def doConversion(inputStream: InputStream, outputStream: OutputStream): Unit =
+    val mod = JellySubsystemLifecycle()
+    mod.start()
     val nQuadWriter = StreamRDFWriter.getWriterStream(outputStream, RDFLanguages.NQUADS)
     RDFParser.source(inputStream).lang(JellyLanguage.JELLY).parse(nQuadWriter)

From 0e27d8ce4fe908dfb3fc3e5e118be44a2c82a263 Mon Sep 17 00:00:00 2001
From: Ostrzyciel <ostrzycielnozyczek@gmail.com>
Date: Thu, 20 Mar 2025 20:29:32 +0100
Subject: [PATCH 11/12] Fix AOT

- Set up a static initializer of the Jena system to avoid issues with race conditions.
- Added a thingy for Graal to know which classes from Caffeine to compile into the binary. See: https://github.com/ben-manes/caffeine/issues/1840
---
 build.sbt                                     |   1 +
 .../caffeine/reflect-config.json              | 605 ++++++++++++++++++
 .../scala/eu/neverblink/jelly/cli/App.scala   |   4 +
 3 files changed, 610 insertions(+)
 create mode 100644 src/main/resources/META-INF/native-image/com.github.ben-manes.caffeine/caffeine/reflect-config.json

diff --git a/build.sbt b/build.sbt
index 23e207d..998137d 100644
--- a/build.sbt
+++ b/build.sbt
@@ -45,4 +45,5 @@ lazy val root = (project in file("."))
     Compile / mainClass := Some("eu.neverblink.jelly.cli.App"),
     // Do a fast build if it's a dev build
     graalVMNativeImageOptions := (if (isDevBuild) Seq("-Ob") else Seq("--emit build-report")),
+    graalVMNativeImageCommand := "/opt/graalvm_2025_02/bin/native-image",
   )
diff --git a/src/main/resources/META-INF/native-image/com.github.ben-manes.caffeine/caffeine/reflect-config.json b/src/main/resources/META-INF/native-image/com.github.ben-manes.caffeine/caffeine/reflect-config.json
new file mode 100644
index 0000000..feb2266
--- /dev/null
+++ b/src/main/resources/META-INF/native-image/com.github.ben-manes.caffeine/caffeine/reflect-config.json
@@ -0,0 +1,605 @@
+[
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BBHeader$ReadAndWriteCounterRef"
+    },
+    "name": "com.github.benmanes.caffeine.cache.BBHeader$ReadAndWriteCounterRef",
+    "fields": [
+      {
+        "name": "writeCounter"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BBHeader$ReadAndWriteCounterRef"
+    },
+    "name": "com.github.benmanes.caffeine.cache.BBHeader$ReadCounterRef",
+    "fields": [
+      {
+        "name": "readCounter"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BLCHeader$DrainStatusRef"
+    },
+    "name": "com.github.benmanes.caffeine.cache.BLCHeader$DrainStatusRef",
+    "fields": [
+      {
+        "name": "drainStatus"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BaseMpscLinkedArrayQueue"
+    },
+    "name": "com.github.benmanes.caffeine.cache.BaseMpscLinkedArrayQueueColdProducerFields",
+    "fields": [
+      {
+        "name": "producerLimit"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BaseMpscLinkedArrayQueue"
+    },
+    "name": "com.github.benmanes.caffeine.cache.BaseMpscLinkedArrayQueueConsumerFields",
+    "fields": [
+      {
+        "name": "consumerIndex"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BaseMpscLinkedArrayQueue"
+    },
+    "name": "com.github.benmanes.caffeine.cache.BaseMpscLinkedArrayQueueProducerFields",
+    "fields": [
+      {
+        "name": "producerIndex"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.BoundedLocalCache",
+    "fields": [
+      {
+        "name": "refreshes"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.Caffeine"
+    },
+    "name": "com.github.benmanes.caffeine.cache.CacheLoader",
+    "methods": [
+      {
+        "name": "asyncLoadAll",
+        "parameterTypes": [
+          "java.util.Set",
+          "java.util.concurrent.Executor"
+        ]
+      },
+      {
+        "name": "loadAll",
+        "parameterTypes": [
+          "java.util.Set"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.LocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.CacheLoader",
+    "methods": [
+      {
+        "name": "loadAll",
+        "parameterTypes": [
+          "java.util.Set"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.FS"
+    },
+    "name": "com.github.benmanes.caffeine.cache.FS",
+    "fields": [
+      {
+        "name": "key"
+      },
+      {
+        "name": "value"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.WS"
+    },
+    "name": "com.github.benmanes.caffeine.cache.FS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.FW"
+    },
+    "name": "com.github.benmanes.caffeine.cache.FW",
+    "fields": [
+      {
+        "name": "value"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.WI"
+    },
+    "name": "com.github.benmanes.caffeine.cache.FW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.PD"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PD",
+    "fields": [
+      {
+        "name": "value"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.PS"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PS",
+    "fields": [
+      {
+        "name": "key"
+      },
+      {
+        "name": "value"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.PSA"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSA",
+    "fields": [
+      {
+        "name": "accessTime"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.SSA"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSA",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.SSSMS"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSMS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.SSMW"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSMW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.PSR"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSR",
+    "fields": [
+      {
+        "name": "writeTime"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.SSMSR"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSRMS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.PSW"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSW",
+    "fields": [
+      {
+        "name": "writeTime"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.SSA"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.SSW"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.SSSMW"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSWMW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.PW"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PW",
+    "fields": [
+      {
+        "name": "value"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalManualCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SI",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSA",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "name": "com.github.benmanes.caffeine.cache.SSMS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSMSR",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalAsyncCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSMSW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalAsyncLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSMSW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalManualCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSMSW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSMW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalManualCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSSMS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSSMWW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.SSW",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.StripedBuffer"
+    },
+    "name": "com.github.benmanes.caffeine.cache.StripedBuffer",
+    "fields": [
+      {
+        "name": "tableBusy"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.UnboundedLocalCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.UnboundedLocalCache",
+    "fields": [
+      {
+        "name": "refreshes"
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.WI",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache"
+    },
+    "name": "com.github.benmanes.caffeine.cache.WS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.Caffeine"
+    },
+    "name": "com.github.benmanes.caffeine.cache.WS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": [
+          "com.github.benmanes.caffeine.cache.Caffeine",
+          "com.github.benmanes.caffeine.cache.AsyncCacheLoader",
+          "boolean"
+        ]
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.NodeFactory"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PSWMS",
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.NodeFactory"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PD",
+    "fields": [
+      {
+        "name": "value"
+      }
+    ],
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  },
+  {
+    "condition": {
+      "typeReachable": "com.github.benmanes.caffeine.cache.NodeFactory"
+    },
+    "name": "com.github.benmanes.caffeine.cache.PW",
+    "fields": [
+      {
+        "name": "value"
+      }
+    ],
+    "methods": [
+      {
+        "name": "<init>",
+        "parameterTypes": []
+      }
+    ]
+  }
+]
diff --git a/src/main/scala/eu/neverblink/jelly/cli/App.scala b/src/main/scala/eu/neverblink/jelly/cli/App.scala
index 6741882..bb1c8de 100644
--- a/src/main/scala/eu/neverblink/jelly/cli/App.scala
+++ b/src/main/scala/eu/neverblink/jelly/cli/App.scala
@@ -3,10 +3,14 @@ package eu.neverblink.jelly.cli
 import caseapp.*
 import eu.neverblink.jelly.cli.command.*
 import eu.neverblink.jelly.cli.command.rdf.*
+import org.apache.jena.sys.JenaSystem
 
 /** Main entrypoint.
   */
 object App extends CommandsEntryPoint:
+  // Initialize Jena now to avoid race conditions later
+  JenaSystem.init()
+
   override def progName: String = "jelly-cli"
 
   override def commands: Seq[Command[?]] = Seq(

From c6d3d51152d81ac3fa101901fc9424454aa7495c Mon Sep 17 00:00:00 2001
From: Ostrzyciel <ostrzycielnozyczek@gmail.com>
Date: Thu, 20 Mar 2025 20:31:15 +0100
Subject: [PATCH 12/12] revert build.sbt change

---
 build.sbt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/build.sbt b/build.sbt
index 998137d..23e207d 100644
--- a/build.sbt
+++ b/build.sbt
@@ -45,5 +45,4 @@ lazy val root = (project in file("."))
     Compile / mainClass := Some("eu.neverblink.jelly.cli.App"),
     // Do a fast build if it's a dev build
     graalVMNativeImageOptions := (if (isDevBuild) Seq("-Ob") else Seq("--emit build-report")),
-    graalVMNativeImageCommand := "/opt/graalvm_2025_02/bin/native-image",
   )