feat: improved XML namespace processing

Dockerfile

@@ -1,7 +1,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.0.7"
+ARG VERSION="0.0.8"
 ARG SIMULATOR_VERSION=3.0.0b
 
 # metadata

biosimulators_ginsim/_version.py

@@ -1 +1 @@
-__version__ = '0.0.7'
+__version__ = '0.0.8'

biosimulators_ginsim/utils.py

@@ -18,6 +18,7 @@
 from kisao.utils import get_preferred_substitute_algorithm_by_ids
 from ginsim.gateway import japi as ginsim_japi
 import biolqm  # noqa: F401
+import biosimulators_utils.model_lang.sbml.utils
 import biosimulators_utils.sedml.validation
 import biosimulators_utils.xml.utils
 import lxml.etree  # noqa: F401
@@ -111,14 +112,14 @@ def get_variable_target_xpath_ids(variables, model_etree):
             corresponding qualitative species
     """
     namespaces = biosimulators_utils.xml.utils.get_namespaces_for_xml_doc(model_etree)
-
+    sbml_qual_prefix, sbml_qual_uri = biosimulators_utils.model_lang.sbml.utils.get_package_namespace('qual', namespaces)
     return biosimulators_utils.sedml.validation.validate_target_xpaths(
         variables,
         model_etree,
         attr={
             'namespace': {
-                'prefix': 'qual',
-                'uri': namespaces['qual'],
+                'prefix': sbml_qual_prefix,
+                'uri': sbml_qual_uri,
             },
             'name': 'id',
         }

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging,sbml] >= 0.1.120
+biosimulators_utils[logging,sbml] >= 0.1.122
 ginsim >= 0.4.4
 kisao >= 2.28
 lxml

tests/test_utils.py

@@ -47,8 +47,9 @@ def test_validate_simulation(self):
     def test_get_variable_target_xpath_ids(self):
         with mock.patch('lxml.etree.parse', return_value=None):
             with mock.patch('biosimulators_utils.xml.utils.get_namespaces_for_xml_doc', return_value={'qual': None}):
-                with mock.patch('biosimulators_utils.sedml.validation.validate_target_xpaths', return_value={'x': 'X'}):
-                    self.assertEqual(get_variable_target_xpath_ids([Variable(target='x')], None), {'x': 'X'})
+                with mock.patch('biosimulators_utils.model_lang.sbml.utils.get_package_namespace', return_value=('qual', None)):
+                    with mock.patch('biosimulators_utils.sedml.validation.validate_target_xpaths', return_value={'x': 'X'}):
+                        self.assertEqual(get_variable_target_xpath_ids([Variable(target='x')], None), {'x': 'X'})
 
     def test_read_model(self):
         filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'SuppMat_Model_Master_Model.zginml')