fixing handling attributes in XML namespaces

biosimulators_utils/_version.py

@@ -1 +1 @@
-__version__ = '0.1.42'
+__version__ = '0.1.43'

biosimulators_utils/sedml/utils.py

@@ -505,6 +505,10 @@ def get_value_of_variable_model_xml_targets(variable, model_etrees):
     if len(obj) != 1:
         raise ValueError('xpath {} must match a single object in model {}'.format(obj_xpath, variable.model.id))
 
+    ns, _, attr = attr.rpartition(':')
+    if ns:
+        attr = '{{{}}}{}'.format(variable.target_namespaces[ns], attr)
+
     value = obj[0].get(attr)
     if value is None:
         raise ValueError('Target `{}` is not defined in model `{}`.'.format(variable.target, variable.model.id))
@@ -1070,7 +1074,6 @@ def get_xml_node_namespace_tag_target(etree, target_namespaces=None):
             * :obj:`str`: tag
             * :obj:`str`: target for use with SED target XPATHs
             * :obj:`dict`: dictionary that maps the prefixes of namespaces to their URIs
-            * :obj:`str`, optional: default namespace prefix
     """
     target_namespaces = dict(target_namespaces or {})
     uri, _, tag = etree.tag.rpartition('}')

tests/sedml/test_sedml_utils.py

@@ -727,7 +727,7 @@ def test_apply_compute_model_change_new_value(self):
         model_filename = os.path.join(self.tmp_dir, 'model_1.xml')
         with open(model_filename, 'w') as file:
             file.write('<model>')
-            file.write('<parameter id="x" value="2.0" strValue="a value" />')
+            file.write('<parameter id="x" value="2.0" strValue="a value" qual:attrA="2.3" xmlns:qual="https://qual.sbml.org" />')
             file.write('<parameter id="y" value="3.0" />')
             file.write('</model>')
         models = {
@@ -761,6 +761,11 @@ def test_apply_compute_model_change_new_value(self):
         self.assertEqual(utils.get_value_of_variable_model_xml_targets(change.variables[0], models), 2.0)
         self.assertEqual(utils.get_value_of_variable_model_xml_targets(change.variables[1], models), 3.0)
 
+        var = data_model.Variable(id='var', model=data_model.Model(id='model_1'), 
+            target="/model/parameter[@id='x']/@qual:attrA", 
+            target_namespaces={'qual': 'https://qual.sbml.org'})
+        self.assertEqual(utils.get_value_of_variable_model_xml_targets(var, models), 2.3)
+
         doc = data_model.SedDocument(models=[change.variables[0].model, change.variables[1].model])
 
         change.variables[0].model.source = 'https://models.com/model_1.xml'