remove rdf upon omex read, inject rdf upon omex write

vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java

@@ -44,7 +44,7 @@ public OmexHandler(String omexPath, String outDir) throws IOException {
         this.omexName = omexPath.substring(indexOfLastSlash + 1);
         this.tempPath = RunUtils.getTempDir();
         try {
-            replaceXmlSchemaNamespaceInArchive(Paths.get(omexPath));
+            replaceMetadataRdfFile(Paths.get(omexPath));
             this.archive = new CombineArchive(new File(omexPath));
             if (this.archive.hasErrors()){
                 String message = "Unable to initialise OMEX archive "+this.omexName+": "+this.archive.getErrors();
@@ -58,20 +58,24 @@ public OmexHandler(String omexPath, String outDir) throws IOException {
         }
     }
 
-    private void replaceXmlSchemaNamespaceInArchive(Path zipFilePath) throws IOException {
+    private void replaceMetadataRdfFile(Path zipFilePath) throws IOException {
         String pathInZip = "/metadata.rdf";
         try( FileSystem fs = FileSystems.newFileSystem(zipFilePath) ) {
-            Path fileInsideZipPath = fs.getPath(pathInZip);
-//            if (!fileInsideZipPath.toFile().exists()) {
-//                return;
-//            }
-            // copy fileInsideZipPath to temp file
+            final Path fileInsideZipPath;
+            try {
+                fileInsideZipPath = fs.getPath(pathInZip);
+            } catch (InvalidPathException e) {
+                // there was no /metadata.rdf file in this archive
+                return;
+            }
+            // write empty RDF file to temp file and replace the file inside the zip
             Path tempFile = Files.createTempFile("temp", ".rdf");
-            Files.copy(fileInsideZipPath, tempFile, StandardCopyOption.REPLACE_EXISTING);
-            // replace namespace in temp file
-            String content = new String(Files.readAllBytes(tempFile));
-            content = content.replace("xmlns:xmls=", "xmlns:schemaxml=");
-            Files.write(tempFile, content.getBytes());
+            String new_rdf_content = """
+                    <?xml version='1.0' encoding='UTF-8'?>
+                    <rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'>
+                    </rdf:RDF>
+                    """;
+            Files.write(tempFile, new_rdf_content.getBytes());
             // replace fileInsideZipPath with temp file
             Files.delete(fileInsideZipPath);
             Files.copy(tempFile, fileInsideZipPath);

vcell-core/src/main/java/org/vcell/sedml/SEDMLExporter.java

@@ -22,7 +22,6 @@
 import cbit.vcell.solver.MathOverridesResolver.SymbolReplacement;
 import cbit.vcell.xml.*;
 import de.unirostock.sems.cbarchive.CombineArchive;
-import de.unirostock.sems.cbarchive.meta.MetaDataObject;
 import de.unirostock.sems.cbarchive.meta.OmexMetaDataObject;
 import de.unirostock.sems.cbarchive.meta.omex.OmexDescription;
 import org.apache.commons.io.FilenameUtils;
@@ -1307,12 +1306,15 @@ public boolean createOmexArchive(String srcFolder, String sFileName) {
 				Path filePath = Paths.get(srcFolder, sd);
 				if (sd.endsWith(".rdf")) {
 					rdfFilePath = filePath;
-//					archive.addEntry(
-//							filePath.toFile(),
-//							"./" + sd,
-//							new URI("http://identifiers.org/combine.specifications/omex-metadata"),
-//							false
-//					);
+					// the CombineArchive library does not allow to directly write to the /metadata.rdf file
+					// instead, we copy the file to /metadata.rdf later after the archive is closed
+					//
+					// archive.addEntry(
+					//		filePath.toFile(),
+					//		"./metadata.rdf",
+					//		new URI("http://identifiers.org/combine.specifications/omex-metadata"),
+					//		false
+					//	);
 				}
 				if (sd.endsWith(".png")) {
 					archive.addEntry(
@@ -1323,23 +1325,22 @@ public boolean createOmexArchive(String srcFolder, String sFileName) {
 					);
 				}
 			}
-			OmexDescription omexDescription = new OmexDescription();
-			omexDescription.setDescription("VCell Simulation Archive");
-			omexDescription.modified.add(new Date());
-			archive.addDescription(new OmexMetaDataObject(omexDescription));
+			if (rdfFilePath != null) {
+				// create temporary /metadata.rdf file so that an entry for /metadata.rdf is included in the Manifest
+				OmexDescription omexDescription = new OmexDescription();
+				omexDescription.setDescription("VCell Simulation Archive");
+				omexDescription.modified.add(new Date());
+				archive.addDescription(new OmexMetaDataObject(omexDescription));
+			}
 
 			archive.pack();
 			archive.close();
 
-			//
-			// wait until omex file is closed, and then replace the metadata.rdf file
-			// this is a workaround for the issue that CombineArchive library refuses to overwrite the /metadata.rdf file
-			//
-			// an alternative is the use the MetaDataObject classes from CombineArchive library - another day.
-			//
-//			if (rdfFilePath != null) {
-//				replaceFileInZip(omexFile.toPath(), rdfFilePath, "/metadata.rdf");
-//			}
+			if (rdfFilePath != null) {
+				// now that the OMEX archive is closed and written to disk, open it as a regular zip file
+				// and replace the generated metadata.rdf file with the one we created.
+				replaceMetadataRdfFileInArchive(omexFile.toPath(), rdfFilePath);
+			}
 
 			removeOtherFiles(srcFolder, files);
 
@@ -1349,7 +1350,8 @@ public boolean createOmexArchive(String srcFolder, String sFileName) {
 		return true;
 	}
 
-	private static void replaceFileInZip(Path zipFilePath, Path newFilePath, String pathInZip) throws IOException {
+	private static void replaceMetadataRdfFileInArchive(Path zipFilePath, Path newFilePath) throws IOException {
+		String pathInZip = "./metadata.rdf";
 		try( FileSystem fs = FileSystems.newFileSystem(zipFilePath) ) {
 			Path fileInsideZipPath = fs.getPath(pathInZip);
 			Files.delete(fileInsideZipPath);