Bug in exporting boundary species to graphical formats

When converting, e.g., neurcon_cd.xml to PDF, the boundary species have wrong z-index:

changed milestone to %v12.2.0~beta.0

created branch 571-bug-in-exporting-boundary-species-to-graphical-formats

mentioned in merge request !501 (closed)

Dear @david.hoksza

Can you provide me with the code that produce the error. In my case result looks like (elements are inside complex and the x index is correct):

assigned to @david.hoksza

Attached is the file causing troubles (it has indeed shifted nodes in complexes) and the following code can be used to reproduce the wrong order of elements in the resulting imaged.

neuron_cd.xml

@Test
  public void testCelDesigner2SPdf() throws Exception {
    try {
    	File file = new File("testFiles/convert/neuron_cd.xml");
    	String content = FileUtils.readFileToString(file);
    	
    	FileOutputStream outputStream = new FileOutputStream("testFiles/convert/neuron-cd.pdf");
    	outputStream.write(convertRestImpl.converToImage(token, "CellDesigner_SBML", "pdf", content).toByteArray());
    	outputStream.close();
        
    	//assertTrue(result.contains("<rect"));    	
    } catch (Exception e) {
      e.printStackTrace();
      throw e;
    }

assigned to @piotr.gawron and unassigned @david.hoksza

mentioned in merge request !504 (merged)

mentioned in commit 92749ad3

closed via merge request !504 (merged)