Resolve "newt catalysis protein-phenotype is not drawn in MINERVA"

Closes #1116 (closed)

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java

@@ -3,7 +3,11 @@ package lcsb.mapviewer.converter.model.sbgnml;
 import java.io.*;
 
 import javax.xml.bind.JAXBException;
+import javax.xml.transform.*;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
 
+import org.apache.commons.io.output.ByteArrayOutputStream;
 import org.apache.commons.text.StringEscapeUtils;
 import org.apache.logging.log4j.core.LogEvent;
 import org.sbgn.SbgnUtil;
@@ -23,7 +27,7 @@ public class SbgnmlXmlConverter extends Converter {
     SbgnmlXmlParser parser = new SbgnmlXmlParser();
     File inputFile = null;
     try {
-      inputFile = inputStream2File(params.getInputStream());
+      inputFile = createFileWithModifiedStyleIdList(params.getInputStream());
       return parser.createModel(params.getFilename(), inputFile);
     } catch (IOException e) {
       throw new ConverterException("Failed to convert input stream to file.", e);
@@ -32,6 +36,33 @@ public class SbgnmlXmlConverter extends Converter {
     }
   }
 
+  private File createFileWithModifiedStyleIdList(InputStream inputStream) throws ConverterException, IOException {
+
+    try {
+      TransformerFactory factory = TransformerFactory.newInstance();
+
+      ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+
+      // Use the factory to create a template containing the xsl file that deals with these issues:
+      // https://github.com/iVis-at-Bilkent/newt/issues/536
+      // https://git-r3lab.uni.lu/minerva/core/issues/1127
+      Templates template = factory
+          .newTemplates(new StreamSource(classLoader.getResourceAsStream("rename_id_list_attribute.xsl")));
+
+      Transformer xformer = template.newTransformer();
+
+      ByteArrayOutputStream output = new ByteArrayOutputStream();
+      Source source = new StreamSource(inputStream);
+      Result result = new StreamResult(output);
+
+      xformer.transform(source, result);
+      return inputStream2File(output.toInputStream());
+
+    } catch (Exception e) {
+      throw new ConverterException(e);
+    }
+  }
+
   @Override
   public String model2String(Model model) throws ConverterException {
     MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();