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Linting fixes
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@CodeByDrescher
CodeByDrescher committed Oct 2, 2024
1 parent 179012b commit 7c06ffb
Showing 1 changed file with 35 additions and 24 deletions.
59 changes: 35 additions & 24 deletions biosimulators_utils/sedml/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +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,
Expand Down Expand Up @@ -320,7 +321,8 @@ def resolve_model_and_apply_xml_changes(orig_model, sed_doc, working_dir,
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.
Expand All @@ -335,7 +337,8 @@ def resolve_model_and_apply_xml_changes(orig_model, sed_doc, working_dir,
# 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

Expand Down Expand Up @@ -452,7 +455,7 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
# First pass: Must-be-XML changes:
non_xml_changes = []
possible_changes = (AddElementModelChange, ReplaceElementModelChange,
RemoveElementModelChange, ModelAttributeChange, ComputeModelChange)
RemoveElementModelChange, ModelAttributeChange, ComputeModelChange)
for change in model.changes:
if not isinstance(change, possible_changes):
error_msg = (f"Change {' ' + change.name if change.name else ''} "
Expand Down Expand Up @@ -481,7 +484,8 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
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)))

Expand All @@ -504,7 +508,7 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
parent.remove(element)

elif isinstance(change, ModelAttributeChange):
xpath_captures = regex.split("[\[|\]]", change.target)
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
obj_xpath, sep, attr = change.target.rpartition('/@')
Expand All @@ -526,23 +530,23 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
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))
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("[\@|=]", xpath_captures[1])
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_attribute = eval_xpath(model_etree, change.target, change.target_namespaces)
if validate_unique_xml_targets and len(xml_model_attribute) != 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(f'No namespace is defined')
raise ValueError('No namespace is defined')
existing_namespace = regex.split(":", xpath_tiers[0])[0]
if change.target_namespaces.get(existing_namespace) is None:
raise ValueError(f'No namespace is defined with prefix `{existing_namespace}`')
Expand All @@ -557,12 +561,15 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
# 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:
Expand Down Expand Up @@ -591,7 +598,6 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
for obj in objs:
obj.set(attr, new_value)


# Interlude: set up the preprocessed task, if there's a set_value_executor
preprocessed_task = None
if preprocessed_task_sub_executer:
Expand All @@ -607,16 +613,18 @@ def apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=Non
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')
raise NotImplementedError(
'target ' + change.target + ' cannot be changed by XML manipulation, as the target '
'is not an attribute of a model element')
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
Expand Down Expand Up @@ -771,7 +779,8 @@ def calc_data_generator_results(data_generator, variable_results):
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 = []
Expand Down Expand Up @@ -859,7 +868,8 @@ def calc_data_generators_results(data_generators, variable_results, output, task

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

Expand Down Expand Up @@ -1164,7 +1174,8 @@ def resolve_range(range, model_etrees=None):
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
Expand Down Expand Up @@ -1276,11 +1287,11 @@ def does_model_language_use_xpath_variable_targets(language):
: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)
)


Expand Down

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