Merge pull request #151 from biosimulators/update-lxml

lxml doesn't have xpath.execute() any more.
biosimulators · Feb 16, 2024 · 87d4732 · 87d4732
2 parents ea6fd5f + 795e370
commit 87d4732
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Showing 3 changed files with 5 additions and 12 deletions.
diff --git a/biosimulators_utils/_version.py b/biosimulators_utils/_version.py
@@ -1 +1 @@
-__version__ = '0.1.186'
+__version__ = '0.1.187'
diff --git a/biosimulators_utils/sedml/validation.py b/biosimulators_utils/sedml/validation.py
@@ -1666,7 +1666,7 @@ def validate_target(target, namespaces, context, language, model_id, model_etree
             xpath = lxml.etree.XPath(target, namespaces=namespaces)
             root = lxml.etree.Element("root")
             try:
-                xpath.evaluate(root)
+                root.xpath(target, namespaces=namespaces)
 
                 if model_etree and check_in_model_source:
                     if context == DataGenerator and '/@' in target:

diff --git a/tests/sedml/test_sedml_validation.py b/tests/sedml/test_sedml_validation.py
@@ -1318,19 +1318,18 @@ def test_validate_target_xpaths(self):
 
     def test_validate_target(self):
         self.assertEqual(validation.validate_target('/sbml:sbml/sbml:model',
-                                                    {None: 'sed-ml', 'sbml': 'sbml'},
+                                                    {'sbml': 'sbml'},
                                                     data_model.Calculation,
                                                     data_model.ModelLanguage.SBML.value,
                                                     ''), ([], [['XPath could not be validated.']]))
         self.assertEqual(validation.validate_target('/sbml:sbml/sbml:model/@sbml:value',
-                                                    {None: 'sed-ml', 'sbml': 'sbml'},
+                                                    {'sbml': 'sbml'},
                                                     data_model.Calculation,
                                                     data_model.ModelLanguage.SBML.value,
                                                     ''), ([], [['XPath could not be validated.']]))
         self.assertEqual(validation.validate_target(
             "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='A']/@qual:level",
             {
-                None: 'sed-ml',
                 'sbml': 'sbml',
                 'qual': 'qual',
             },
@@ -1341,7 +1340,6 @@ def test_validate_target(self):
         self.assertEqual(validation.validate_target(
             "/sbml/model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='A']/@qual:level",
             {
-                None: 'sed-ml',
                 'sbml': 'sbml',
                 'qual': 'qual',
             },
@@ -1355,7 +1353,6 @@ def test_validate_target(self):
         self.assertEqual(validation.validate_target(
             "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='erk']/@qual:compartment",
             {
-                None: 'sed-ml',
                 'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
                 'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
             },
@@ -1369,7 +1366,6 @@ def test_validate_target(self):
         self.assertEqual(validation.validate_target(
             "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='erk']/@qual:level",
             {
-                None: 'sed-ml',
                 'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
                 'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
             },
@@ -1382,7 +1378,7 @@ def test_validate_target(self):
 
         self.assertIn('not a valid XML XPath',
                       flatten_nested_list_of_strings(validation.validate_target('/sbml:sbml@sbml:model',
-                                                                                {None: 'sed-ml', 'sbml': 'sbml'},
+                                                                                {'sbml': 'sbml'},
                                                                                 data_model.Calculation,
                                                                                 data_model.ModelLanguage.SBML.value, '')[0]))
         self.assertIn('No namespaces are defined',
@@ -1400,7 +1396,6 @@ def test_validate_target(self):
                       flatten_nested_list_of_strings(validation.validate_target(
                           "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='erk']/@qual:level",
                           {
-                              None: 'sed-ml',
                               'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
                               'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
                           },
@@ -1415,7 +1410,6 @@ def test_validate_target(self):
                       flatten_nested_list_of_strings(validation.validate_target(
                           "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='ERK']/@qual:compartment",
                           {
-                              None: 'sed-ml',
                               'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
                               'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
                           },
@@ -1430,7 +1424,6 @@ def test_validate_target(self):
                       flatten_nested_list_of_strings(validation.validate_target(
                           "/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies",
                           {
-                              None: 'sed-ml',
                               'sbml': 'http://www.sbml.org/sbml/level3/version1/core',
                               'qual': 'http://www.sbml.org/sbml/level3/version1/qual/version1',
                           },