Sys bio model fixes

biosimulators_utils/sedml/exec.py

@@ -165,7 +165,10 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
             ' ' * 2 * (indent + 2),
             ('\n' + ' ' * 2 * (indent + 2)).join(sorted('`' + output.id + '`' for output in doc.outputs)),
         ))
-        for i_task, task in enumerate(expected_tasks):
+        for i_task in range(0, len(expected_tasks)):
+            task = expected_tasks[i_task]
+            task_status = Status.QUEUED
+            task_exception = None
             print('{}Executing task {}: `{}`'.format(' ' * 2 * indent, i_task + 1, task.id))
 
             if config.LOG:

biosimulators_utils/sedml/utils.py

@@ -5,6 +5,7 @@
 :Copyright: 2020, Center for Reproducible Biomedical Modeling
 :License: MIT
 """
+import regex
 
 from ..log.data_model import Status
 from ..report.data_model import VariableResults, DataGeneratorResults  # noqa: F401
@@ -13,7 +14,8 @@
 from ..xml.utils import eval_xpath
 from .data_model import (SedBase, SedIdGroupMixin, SedDocument,  # noqa: F401
                          Model, ModelLanguagePattern, ModelChange, ModelAttributeChange, AddElementModelChange,
-                         ReplaceElementModelChange, RemoveElementModelChange, ComputeModelChange, SetValueComputeModelChange,
+                         ReplaceElementModelChange, RemoveElementModelChange, ComputeModelChange,
+                         SetValueComputeModelChange,
                          OneStepSimulation, SteadyStateSimulation, UniformTimeCourseSimulation,
                          Task, RepeatedTask, Output, Report, Plot, Plot2D, Plot3D,
                          DataGenerator, Variable,
@@ -319,7 +321,8 @@
         try:
             model_etree = etree.parse(model.source)
         except Exception as exception:
-            raise ValueError('The model could not be parsed because the model is not a valid XML document: {}'.format(str(exception)))
+            raise ValueError('The model could not be parsed because the model is not a valid XML document: {}'.format(
+                str(exception)))
 
         if model.changes:
             # Change source here so that tasks point to actual source they can find.
@@ -334,7 +337,8 @@
             # write model to file
             if save_to_file:
                 if temp_model_source is None:
-                    modified_model_file, temp_model_source = tempfile.mkstemp(suffix='.xml', dir=os.path.dirname(model.source))
+                    modified_model_file, temp_model_source = tempfile.mkstemp(suffix='.xml',
+                                                                              dir=os.path.dirname(model.source))
                     os.close(modified_model_file)
                     model.source = temp_model_source
 
@@ -450,7 +454,14 @@
 
     # First pass:  Must-be-XML changes:
     non_xml_changes = []
+    possible_changes = (AddElementModelChange, ReplaceElementModelChange,
+                        RemoveElementModelChange, ModelAttributeChange, ComputeModelChange)
     for change in model.changes:
+        if not isinstance(change, possible_changes):
+            error_msg = (f"Change {' ' + change.name if change.name else ''} "
+                         f"of type {change.__class__.__name__} is not supported.")
+            raise NotImplementedError(error_msg)
+
         if isinstance(change, AddElementModelChange):
             parents = eval_xpath(model_etree, change.target, change.target_namespaces)
 
@@ -473,7 +484,8 @@
                 raise ValueError('xpath {} must match a single object'.format(change.target))
 
             try:
-                new_elements = etree.parse(io.StringIO('<root>' + change.new_elements + '</root>')).getroot().getchildren()
+                new_elements = etree.parse(
+                    io.StringIO('<root>' + change.new_elements + '</root>')).getroot().getchildren()
             except etree.XMLSyntaxError as exception:
                 raise ValueError('`{}` is invalid XML. {}'.format(change.new_elements, str(exception)))
 
@@ -496,41 +508,71 @@
                 parent.remove(element)
 
         elif isinstance(change, ModelAttributeChange):
-            obj_xpath, sep, attr = change.target.rpartition('/@')
-            if sep != '/@':
-                change.model = model
-                non_xml_changes.append(change)
-                continue
-            # get object to change
-            obj_xpath, sep, attr = change.target.rpartition('/@')
-            if sep != '/@':
-                raise NotImplementedError('target ' + change.target + ' cannot be changed by XML manipulation, as the target '
-                                          'is not an attribute of a model element')
-            objs = eval_xpath(model_etree, obj_xpath, change.target_namespaces)
-            if validate_unique_xml_targets and len(objs) != 1:
-                raise ValueError('xpath {} must match a single object'.format(obj_xpath))
-
-            ns_prefix, _, attr = attr.rpartition(':')
-            if ns_prefix:
-                ns = change.target_namespaces.get(ns_prefix, None)
-                if ns is None:
-                    raise ValueError('No namespace is defined with prefix `{}`'.format(ns_prefix))
-                attr = '{{{}}}{}'.format(ns, attr)
-
-            # change value
-            for obj in objs:
-                obj.set(attr, change.new_value)
+            xpath_captures = regex.split(r"[\[|\]]", change.target)
+            if len(xpath_captures) != 3 or "@" not in xpath_captures[1] or xpath_captures[2] != "":
+                # Old method for ModelAttributeChange
+                # get object to change
+                obj_xpath, sep, attr = change.target.rpartition('/@')
+                if sep != '/@':
+                    change.model = model
+                    non_xml_changes.append(change)
+                    continue
+
+                objs = eval_xpath(model_etree, obj_xpath, change.target_namespaces)
+                if validate_unique_xml_targets and len(objs) != 1:
+                    raise ValueError('xpath {} must match a single object'.format(obj_xpath))
+
+                ns_prefix, _, attr = attr.rpartition(':')
+                if ns_prefix:
+                    ns = change.target_namespaces.get(ns_prefix, None)
+                    if ns is None:
+                        raise ValueError(f'No namespace is defined with prefix `{ns_prefix}`')
+                    attr = '{{{}}}{}'.format(ns, attr)
+
+                # change value
+                for obj in objs:
+                    obj.set(attr, change.new_value)
+            else:
+                # New Method for ModelAttributeChange
+                xml_target_captures = regex.split(r"[\@|=]", xpath_captures[1])
+                xml_target_captures[2] = xml_target_captures[2][1:-1]
+                _, target_type, target_value = tuple(xml_target_captures)
+                xml_model_element = eval_xpath(model_etree, change.target, change.target_namespaces)
+                if validate_unique_xml_targets and len(xml_model_element) != 1:
+                    raise ValueError(f'xpath {change.target} must match a single object')
+                xpath_tiers = [elem for elem in regex.split("/", xpath_captures[0]) if ":" in elem]
+                if len(xpath_tiers) == 0:
+                    raise ValueError("Unexpected number of tokens in model element xpath")
+                element_type = regex.split(":", xpath_tiers[-1])
+
+                namespace_prefix, type_suffix = tuple(element_type)
+                if change.target_namespaces.get(namespace_prefix) is None:
+                    raise ValueError(f'No namespace is defined with prefix `{namespace_prefix}`')
+                # change value
+                for attribute in xml_model_element:
+                    if type_suffix == "species" and attribute.get("initialConcentration") is not None:
+                        attribute.set("initialConcentration", change.new_value)
+                    elif type_suffix == "compartment" and attribute.get("size") is not None:
+                        attribute.set("size", change.new_value)
+                    elif type_suffix == "parameter" and attribute.get("value") is not None:
+                        attribute.set("value", change.new_value)
+                    else:
+                        change.model = model
+                        non_xml_changes.append(change)
+                        continue
 
         elif isinstance(change, ComputeModelChange):
             # get the values of model variables referenced by compute model changes
             if variable_values is None:
                 model_etrees = {model.id: model_etree}
-                iter_variable_values = get_values_of_variable_model_xml_targets_of_model_change(change, sed_doc, model_etrees, working_dir)
+                iter_variable_values = \
+                    get_values_of_variable_model_xml_targets_of_model_change(change, sed_doc, model_etrees, working_dir)
             else:
                 iter_variable_values = variable_values
 
             # calculate new value
-            new_value = calc_compute_model_change_new_value(change, variable_values=iter_variable_values, range_values=range_values)
+            new_value = calc_compute_model_change_new_value(change, variable_values=iter_variable_values,
+                                                            range_values=range_values)
             if new_value == int(new_value):
                 new_value = str(int(new_value))
             else:
@@ -559,10 +601,6 @@
             for obj in objs:
                 obj.set(attr, new_value)
 
-        else:
-            raise NotImplementedError('Change{} of type {} is not supported.'.format(
-                ' ' + change.name if change.name else '', change.__class__.__name__))
-
     # Interlude:  set up the preprocessed task, if there's a set_value_executor
     preprocessed_task = None
     if preprocessed_task_sub_executer:
@@ -577,17 +615,24 @@
     # Second pass:  changes that need to be interpreter-based:
     for change in non_xml_changes:
         if isinstance(change, ModelAttributeChange):
+
             if not set_value_executer:
-                raise NotImplementedError('target ' + change.target + ' cannot be changed by XML manipulation, as the target '
-                                          'is not an attribute of a model element')
+                xpath_captures = regex.split(r"[\[|\]]", change.target)
+                if len(xpath_captures) != 3 or "@" not in xpath_captures[1] or xpath_captures[2] != "":
+                    raise NotImplementedError(
+                        'target ' + change.target + ' cannot be changed by XML manipulation, as the target '
+                                                    'is not an attribute of a model element')
+                else:
+                    raise ValueError(f"SBML attribute to apply `{change.new_value}` to can not be figured out.")
             else:
                 set_value_executer(change.model, change.target, None, change.new_value, preprocessed_task)
 
         elif isinstance(change, ComputeModelChange):
             obj_xpath, sep, attr = change.target.rpartition('/@')
             if not set_value_executer:
-                raise NotImplementedError('target ' + change.target + ' cannot be changed by XML manipulation, as the target '
-                                          'is not an attribute of a model element')
+                raise NotImplementedError(
+                    'target ' + change.target + ' cannot be changed by XML manipulation, as the target '
+                                                'is not an attribute of a model element')
             set_value_executer(change.model, change.target, change.symbol, change.new_value, preprocessed_task)
 
     return preprocessed_task
@@ -742,7 +787,8 @@
     else:
         for aggregate_func in AGGREGATE_MATH_FUNCTIONS:
             if re.search(aggregate_func + r' *\(', data_generator.math):
-                msg = 'Evaluation of aggregate mathematical functions such as `{}` is not supported.'.format(aggregate_func)
+                msg = 'Evaluation of aggregate mathematical functions such as `{}` is not supported.'.format(
+                    aggregate_func)
                 raise NotImplementedError(msg)
 
         padded_var_shapes = []
@@ -830,7 +876,8 @@
 
         if vars_failed:
             status = Status.FAILED
-            msg = 'Data generator {} cannot be calculated because its variables were not successfully produced.'.format(data_gen.id)
+            msg = 'Data generator {} cannot be calculated because its variables were not successfully produced.'.format(
+                data_gen.id)
             exceptions.append(ValueError(msg))
             result = None
 
@@ -1135,7 +1182,8 @@
             if var.symbol:
                 raise NotImplementedError('Symbols are not supported for variables of functional ranges')
             if model_etrees[var.model.id] is None:
-                raise NotImplementedError('Functional ranges that involve variables of non-XML-encoded models are not supported.')
+                raise NotImplementedError(
+                    'Functional ranges that involve variables of non-XML-encoded models are not supported.')
             workspace[var.id] = get_value_of_variable_model_xml_targets(var, model_etrees)
 
         # calculate the values of the range
@@ -1247,11 +1295,11 @@
         :obj:`bool`: :obj:`True`, if the model language is encoded in XML
     """
     return (
-        re.match(ModelLanguagePattern.CellML, language)
-        or re.match(ModelLanguagePattern.CopasiML, language)
-        or re.match(ModelLanguagePattern.MorpheusML, language)
-        or re.match(ModelLanguagePattern.SBML, language)
-        or re.match(ModelLanguagePattern.VCML, language)
+            re.match(ModelLanguagePattern.CellML, language)
+            or re.match(ModelLanguagePattern.CopasiML, language)
+            or re.match(ModelLanguagePattern.MorpheusML, language)
+            or re.match(ModelLanguagePattern.SBML, language)
+            or re.match(ModelLanguagePattern.VCML, language)
     )
 
 

biosimulators_utils/sedml/validation.py

@@ -1179,11 +1179,11 @@ def validate_simulation_type(simulation, types):
     errors = []
 
     if not isinstance(simulation, types):
+        valid_types = "\n  - ".join(type.__name__ for type in types)
         errors.append([
-            'Simulation {} of type `{}` is not supported. Simulation must be an instance of one of the following:\n  - {}'.format(
-                simulation.id, simulation.__class__.__name__, '\n  - '.join(type.__name__ for type in types))
+            f'Simulation {simulation.id} of type `{simulation.__class__.__name__}` is not supported. '
+            f'Simulation must be an instance of one of the following:\n  - {valid_types}'
         ])
-
     return errors
 
 

tests/fixtures/sbml-list-of-species.xml

@@ -14,5 +14,9 @@
       <species compartment="compartment" id="SpeciesToReplace" initialConcentration="0.0035491784" name="Sic1" sboTerm="SBO:0000245">
       </species>
     </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="false" id="parameter_1" name="Fe2GutQUant" value="1E-7" units="second">
+      </parameter>
+    </listOfParameters>
   </model>
 </sbml>