incorporating validation for CellML 2.0

README.md

@@ -28,6 +28,11 @@ pip install git+https://github.com/biosimulators/Biosimulators_utils.git#biosimu
 
 ### Installation optional features
 
+To use BioSimulators utils to validate CellML models, install BioSimulators utils with the `cellml` option:
+```
+pip install biosimulators-utils[cellml]
+```
+
 To use BioSimulators utils to validate NeuroML models, install BioSimulators utils with the `neuroml` option:
 ```
 pip install biosimulators-utils[neuroml]

biosimulators_utils/cellml/validation.py

@@ -0,0 +1,61 @@
+""" Utilities for validating CellML models
+
+:Author: Jonathan Karr <[email protected]>
+:Date: 2021-05-10
+:Copyright: 2021, Center for Reproducible Biomedical Modeling
+:License: MIT
+"""
+
+import libcellml
+import os
+
+
+def validate_model(filename, name=None):
+    """ Check that a model is valid
+
+    Args:
+        filename (:obj:`str`): path to model
+        name (:obj:`str`, optional): name of model for use in error messages
+
+    Returns:
+        :obj:`tuple`:
+
+            * nested :obj:`list` of :obj:`str`: nested list of errors (e.g., required ids missing or ids not unique)
+            * nested :obj:`list` of :obj:`str`: nested list of errors (e.g., required ids missing or ids not unique)
+    """
+    errors = []
+    warnings = []
+
+    if not os.path.isfile(filename):
+        errors.append(['`{}` is not a file.'.format(filename)])
+        return (errors, warnings)
+
+    # read model
+    parser = libcellml.Parser()
+    with open(filename, 'r') as file:
+        model = parser.parseModel(file.read())
+
+    for i_error in range(parser.errorCount()):
+        error = parser.error(i_error)
+        errors.append([error.description()])
+
+    for i_warning in range(parser.warningCount()):
+        warning = parser.warning(i_warning)
+        warnings.append([warning.description()])
+
+    if errors:
+        return (errors, warnings)
+
+    # validate model
+    validator = libcellml.Validator()
+    validator.validateModel(model)
+
+    for i_error in range(validator.errorCount()):
+        error = validator.error(i_error)
+        errors.append([error.description()])
+
+    for i_warning in range(validator.warningCount()):
+        warning = validator.warning(i_warning)
+        warnings.append([warning.description()])
+
+    return (errors, warnings)

biosimulators_utils/sedml/validation.py

@@ -723,7 +723,10 @@ def validate_model_with_language(source, language, name=None):
     errors = []
     warnings = []
 
-    if language and re.match(ModelLanguagePattern.NeuroML, language):
+    if language and re.match(ModelLanguagePattern.CellML, language):
+        from ..cellml.validation import validate_model
+
+    elif language and re.match(ModelLanguagePattern.NeuroML, language):
         from ..neuroml.validation import validate_model
 
     elif language and re.match(ModelLanguagePattern.SBML, language):

docs-src/installation.rst

@@ -37,6 +37,12 @@ After installing `Python <https://www.python.org/downloads/>`_ (>= 3.7) and `pip
 Installing the optional features
 --------------------------------
 
+To use BioSimulators utils to validate models encoded in CellML, install BioSimulators utils with the ``cellml`` option:
+
+.. code-block:: text
+
+    pip install biosimulators-utils[cellml]
+
 To use BioSimulators utils to validate models encoded in NeuroML, install BioSimulators utils with the ``neuroml`` option:
 
 .. code-block:: text

requirements.optional.txt

@@ -1,5 +1,5 @@
-# [cellml]
-# libcellml
+[cellml]
+libcellml
 
 [neuroml]
 libneuroml

tests/cellml/test_cellml_validation.py

@@ -0,0 +1,25 @@
+from biosimulators_utils.cellml.validation import validate_model
+from biosimulators_utils.utils.core import flatten_nested_list_of_strings
+import os
+import unittest
+
+
+class CellMlValidationTestCase(unittest.TestCase):
+    FIXTURE_DIR = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'cellml')
+
+    def test(self):
+        errors, warnings = validate_model(os.path.join(self.FIXTURE_DIR, 'level2.xml'))
+        self.assertEqual(errors, [])
+        self.assertEqual(warnings, [])
+
+        errors, warnings = validate_model(os.path.join(self.FIXTURE_DIR, 'not_a_path.xml'))
+        self.assertIn("is not a file", flatten_nested_list_of_strings(errors))
+        self.assertEqual(warnings, [])
+
+        errors, warnings = validate_model(os.path.join(self.FIXTURE_DIR, 'invalid_cellml_2.0.xml'))
+        self.assertIn("Start tag expected", flatten_nested_list_of_strings(errors))
+        self.assertEqual(warnings, [])
+
+        errors, warnings = validate_model(os.path.join(self.FIXTURE_DIR, 'missing-attribute.xml'))
+        self.assertIn("does not have a valid name attribute", flatten_nested_list_of_strings(errors))
+        self.assertEqual(warnings, [])

tests/fixtures/cellml/invalid_cellml_2.0.xml

@@ -0,0 +1 @@
+This is not a CellML file.

tests/fixtures/cellml/level2.xml

@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<model xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#" xmlns:xlink="http://www.w3.org/1999/xlink" name="level2_model">
+    <component name="level2_component">
+        <variable name="time" units="dimensionless" interface="public"/>
+        <variable name="parameter" units="dimensionless" interface="public"/>
+        <variable name="cosine" units="dimensionless" interface="public" initial_value="0"/>
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply><eq/>
+                <apply><diff/>
+                    <bvar><ci>time</ci></bvar>
+                    <ci>cosine</ci>
+                </apply>
+                <apply><sin/>
+                    <apply><times/>
+                        <ci>parameter</ci>
+                        <ci>time</ci>
+                    </apply>
+                </apply>
+            </apply>
+        </math>
+    </component>
+    <component name="isnt_imported"/>
+    <import xlink:href="this_file_should_not_exist..._ever!.xml">
+        <component name="also_never_imported" component_ref="not_sure_what_to_look_for"/>
+    </import>
+</model>

tests/fixtures/cellml/missing-attribute.xml

@@ -0,0 +1,26 @@
+<?xml version="1.0"?>
+<model xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#" xmlns:xlink="http://www.w3.org/1999/xlink" name="level2_model">
+    <component>
+        <variable name="time" units="dimensionless" interface="public"/>
+        <variable name="parameter" units="dimensionless" interface="public"/>
+        <variable name="cosine" units="dimensionless" interface="public" initial_value="0"/>
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply><eq/>
+                <apply><diff/>
+                    <bvar><ci>time</ci></bvar>
+                    <ci>cosine</ci>
+                </apply>
+                <apply><sin/>
+                    <apply><times/>
+                        <ci>parameter</ci>
+                        <ci>time</ci>
+                    </apply>
+                </apply>
+            </apply>
+        </math>
+    </component>
+    <component name="isnt_imported"/>
+    <import xlink:href="this_file_should_not_exist..._ever!.xml">
+        <component name="also_never_imported" component_ref="not_sure_what_to_look_for"/>
+    </import>
+</model>

tests/neuroml/test_neuroml_validation.py

@@ -5,7 +5,7 @@
 
 
 class NeuroMlValidationTestCase(unittest.TestCase):
-    FIXTURE_DIR = os.path.join(os.path.dirname(__file__), '..', 'fixtures')
+    FIXTURE_DIR = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'neuroml')
 
     def test(self):
         errors, warnings = validate_model(os.path.join(self.FIXTURE_DIR, 'IM.channel.nml'))

tests/sedml/test_sedml_exec.py

@@ -46,7 +46,7 @@ def test_successful(self):
         doc.models.append(data_model.Model(
             id='model2',
             source='https://models.edu/model1.xml',
-            language=data_model.ModelLanguage.CellML.value,
+            language=data_model.ModelLanguage.VCML.value,
         ))
 
         doc.simulations.append(data_model.SteadyStateSimulation(

tests/sedml/test_sedml_validation.py

@@ -719,12 +719,24 @@ def test_validate_model_with_language(self):
         self.assertEqual(errors, [])
         self.assertIn('No validation is available for', flatten_nested_list_of_strings(warnings))
 
-        filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'IM.channel.nml')
+        # CellML
+        filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'cellml', 'level2.xml')
+        errors, warnings = validation.validate_model_with_language(filename, data_model.ModelLanguage.CellML)
+        self.assertEqual(errors, [])
+        self.assertEqual(warnings, [])
+
+        filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'cellml', 'missing-attribute.xml')
+        errors, warnings = validation.validate_model_with_language(filename, data_model.ModelLanguage.CellML)
+        self.assertNotEqual(errors, [])
+        self.assertEqual(warnings, [])
+
+        # NeuroML
+        filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'neuroml', 'IM.channel.nml')
         errors, warnings = validation.validate_model_with_language(filename, data_model.ModelLanguage.NeuroML)
         self.assertEqual(errors, [])
         self.assertEqual(warnings, [])
 
-        filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'invalid-model.nml')
+        filename = os.path.join(os.path.dirname(__file__), '..', 'fixtures', 'neuroml', 'invalid-model.nml')
         errors, warnings = validation.validate_model_with_language(filename, data_model.ModelLanguage.NeuroML)
         self.assertIn("Not a valid NeuroML 2 doc", flatten_nested_list_of_strings(errors))
         self.assertEqual(warnings, [])