conversion api process model in the same way as map upload

CHANGELOG

@@ -11,6 +11,7 @@ minerva (15.0.2) stable; urgency=medium
   * Bug fix: user data overlays were not removed when user was deleted (#1301)
   * Bug fix: kinetic parameters exported to SBML created invalid SBML file
     (#1305)
+  * Bug fix: text area were not converted to GPML using conversion API (#1306)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Jun 2020 11:00:00 +0200
 

rest-api/src/main/java/lcsb/mapviewer/api/convert/ConvertRestImpl.java

@@ -40,29 +40,26 @@ public class ConvertRestImpl extends BaseRestImpl {
       QueryException {
     ConverterParams params = createConvertParams(input);
     MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
-    Model model;
+    Model original;
     try {
-      model = getModelParserByNameOrClass(fromFormat).createModel(params);
-      StringBuilder notes = new StringBuilder(model.getNotes());
+      original = getModelParserByNameOrClass(fromFormat).createModel(params);
+      StringBuilder notes = new StringBuilder(original.getNotes());
       if (!appender.getWarnings().isEmpty()) {
         for (String entry : new LogFormatter().createFormattedWarnings(appender.getWarnings())) {
           notes.append("\n" + entry);
         }
       }
-      model.setNotes(notes.toString());
+      original.setNotes(notes.toString());
     } finally {
       MinervaLoggerAppender.unregisterLogEventStorage(appender);
     }
+    Model model = getModelWithPathwayAndCompartment(original);
+
     Converter exporter = getModelParserByNameOrClass(toFormat);
     return IOUtils.toString(exporter.model2InputStream(model), StandardCharsets.UTF_8);
   }
 
-  public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, byte[] input,
-      Double targetWidth, Double targetHeight)
-      throws InvalidInputDataExecption, SBMLException, IOException, ConverterException, DrawingException,
-      QueryException {
-    Model original = getModelParserByNameOrClass(fromFormat).createModel(createConvertParams(input));
-
+  private Model getModelWithPathwayAndCompartment(Model original) {
     Model model = new CopyCommand(original).execute();
     try {
       new CreateHierarchyCommand(model, 10, 1024).execute();
@@ -73,6 +70,16 @@ public class ConvertRestImpl extends BaseRestImpl {
       logger.error("Problem with creating pathways", e);
       model = original;
     }
+    return model;
+  }
+
+  public ByteArrayOutputStream converToImage(String fromFormat, String toFormat, byte[] input,
+      Double targetWidth, Double targetHeight)
+      throws InvalidInputDataExecption, SBMLException, IOException, ConverterException, DrawingException,
+      QueryException {
+    Model original = getModelParserByNameOrClass(fromFormat).createModel(createConvertParams(input));
+
+    Model model = getModelWithPathwayAndCompartment(original);
 
     AbstractImageGenerator generator = getImageGenerator(toFormat, createImageParams(model, targetWidth, targetHeight));
     ByteArrayOutputStream os = new ByteArrayOutputStream();