- fix an issue with importing SBML

basico/model_io.py

@@ -233,10 +233,10 @@ def load_model_from_string(content):
     if type(content) is bytes:
         content = content.decode("utf8")
 
-    if '<COPASI ' in content and model.loadModelFromString(content, os.getcwd()):
+    if '<sbml ' in content and model.importSBMLFromString(content):
         return set_current_model(model)
 
-    if '<sbml ' in content and model.importSBMLFromString(content):
+    if '<COPASI ' in content and model.loadModelFromString(content, os.getcwd()):
         return set_current_model(model)
 
     if '<sedML '  in content and model.importSEDMLFromString(content):
@@ -332,7 +332,7 @@ def remove_annotations(content, annotations):
         for annotation in root.iter('{%s}%s' % (namespace, element)):
             annotation.getparent().remove(annotation)
 
-    return etree.tostring(root, pretty_print=True).decode('utf-8')
+    return etree.tostring(root, pretty_print=True, xml_declaration=True, encoding="UTF-8").decode('utf-8')
 
 
 def load_model(location, remove_user_defined_functions=False):

tests/test_basico_io.py

@@ -163,7 +163,26 @@ def test_import_sbml_with_pre_processing(self):
 
         basico.remove_datamodel(dm)
 
+    @unittest.skipUnless(_have_lxml, "lxml not available")
+    def test_import_sbml_with_pre_processing(self):
+        filename = os.path.join(os.path.dirname(__file__), 'test_data', 'import_sbml_issue.xml')
+        self.assertTrue(os.path.exists(filename))
 
+        # this file contains special processing instructions 
+        # since an initial value is used in an expression. 
+
+        dm = basico.import_sbml(filename, annotations_to_remove=[
+            ('initialValue', 'http://copasi.org/initialValue')],
+            ensure_unique_names=True
+        )
+
+        self.assertTrue(dm is not None)
+        species = basico.as_dict(basico.get_species())
+        self.assertEqual(len(species), 13)
+        params = basico.as_dict(basico.get_parameters())
+        self.assertEqual(len(params), 7)
+
+        basico.remove_datamodel(dm)
 
 
 if __name__ == "__main__":