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io.py
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""" Utilities for reading and writing SED documents to SED-ML files
:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2020-12-06
:Copyright: 2020, Center for Reproducible Biomedical Modeling
:License: MIT
"""
from . import data_model
from .utils import add_namespaces_to_xml_node, convert_xml_node_to_string, get_namespaces_for_sed_object
from .validation import validate_doc
from .warnings import SedmlFeatureNotSupportedWarning
from ..biosimulations.data_model import Metadata, ExternalReferences, Citation
from ..config import Config # noqa: F401
from ..data_model import Person, Identifier, OntologyTerm
from ..warnings import warn, BioSimulatorsWarning
from ..utils.core import flatten_nested_list_of_strings
from xml.sax import saxutils
import dateutil.parser
import enum
import kisao
import libsedml
import os
__all__ = [
'SedmlSimulationReader',
'SedmlSimulationWriter',
]
class SedmlSimulationWriter(object):
""" SED-ML writer
Attributes:
_num_meta_id (:obj:`int`): number of assigned meta ids
_doc_sed (:obj:`libsedml.SedDocument`): SED document
_obj_to_sed_obj_map (:obj:`object` => :obj:`object`): map from data model objects to their corresponding libSED-ML objects
"""
def __init__(self):
self._num_meta_id = None
self._doc_sed = None
self._obj_to_sed_obj_map = None
def run(self, doc, filename, validate_semantics=True, validate_models_with_languages=True, validate_targets_with_model_sources=True,
config=None):
""" Save a SED document to an SED-ML XML file
Args:
doc (:obj:`data_model.SedDocument`): SED document
filename (:obj:`str`): Path to save simulation experiment in SED-ML format
validate_semantics (:obj:`bool`, optional): if :obj:`True`, check that SED-ML is semantically valid
validate_models_with_languages (:obj:`bool`, optional): if :obj:`True`, validate models
validate_targets_with_model_sources (:obj:`bool`, optional): if :obj:`True`, validate targets against
their models
config (:obj:`Config`, optional): whether to fail on missing includes
Raises:
:obj:`NotImplementedError`: document uses an supported type of task or output
"""
errors, warnings = validate_doc(doc,
working_dir=os.path.dirname(filename),
validate_semantics=validate_semantics,
validate_models_with_languages=validate_models_with_languages,
validate_targets_with_model_sources=validate_targets_with_model_sources,
config=config)
if warnings:
msg = 'The SED document is potentially incorrect.\n {}'.format(flatten_nested_list_of_strings(warnings).replace('\n', '\n '))
warn(msg, BioSimulatorsWarning)
if errors:
msg = 'The SED document is invalid.\n {}'.format(flatten_nested_list_of_strings(errors).replace('\n', '\n '))
raise ValueError(msg)
self._num_meta_id = 0
self._obj_to_sed_obj_map = {}
self._create_doc(doc)
self._add_metadata_to_obj(doc)
for style in doc.styles:
self._add_style_to_doc(style)
for model in doc.models:
self._add_model_to_doc(model)
for sim in doc.simulations:
self._add_sim_to_doc(sim)
for task in doc.tasks:
if isinstance(task, data_model.Task):
self._add_task_to_doc(task)
elif isinstance(task, data_model.RepeatedTask):
self._add_repeated_task_to_doc(task)
else:
raise NotImplementedError('Task type {} is not supported.'.format(task.__class__.__name__))
for data_gen in doc.data_generators:
self._add_data_gen_to_doc(data_gen)
for output in doc.outputs:
if isinstance(output, data_model.Report):
self._add_report_to_doc(output)
elif isinstance(output, data_model.Plot2D):
self._add_plot2d_to_doc(output)
elif isinstance(output, data_model.Plot3D):
self._add_plot3d_to_doc(output)
else:
raise NotImplementedError('Output type {} is not supported.'.format(output.__class__.__name__))
self._export_doc(filename)
def _create_doc(self, doc):
""" Create a SED document
Args:
doc (:obj:`data_model.SedDocument`): SED document
"""
doc_sed = self._doc_sed = libsedml.SedDocument()
self._doc_sed = doc_sed
self._obj_to_sed_obj_map[doc] = doc_sed
if doc.level is not None:
self._call_libsedml_method(doc_sed, 'setLevel', doc.level)
if doc.version is not None:
self._call_libsedml_method(doc_sed, 'setVersion', doc.version)
def _add_style_to_doc(self, style):
""" Add a graphical style to a SED document
Args:
style (:obj:`data_model.Style`): style
"""
style_sed = self._doc_sed.createStyle()
self._obj_to_sed_obj_map[style] = style_sed
if style.id is not None:
self._call_libsedml_method(style_sed, 'setId', style.id)
if style.name is not None:
self._call_libsedml_method(style_sed, 'setName', style.name)
if style.base is not None:
if not style.base.id: # pragma: no cover: already validated
raise ValueError('Style must have an id to be referenced')
self._call_libsedml_method(style_sed, 'setBaseStyle', style.base.id)
if style.line is not None:
line_style_sed = style_sed.createLineStyle()
if style.line.type is not None:
self._call_libsedml_method(line_style_sed, 'setType', style.line.type.value)
if style.line.color is not None:
self._call_libsedml_method(line_style_sed, 'setColor', style.line.color)
if style.line.thickness is not None:
self._call_libsedml_method(line_style_sed, 'setThickness', style.line.thickness)
if style.marker is not None:
marker_style_sed = style_sed.createMarkerStyle()
if style.marker.type is not None:
self._call_libsedml_method(marker_style_sed, 'setType', style.marker.type.value)
if style.marker.size is not None:
self._call_libsedml_method(marker_style_sed, 'setSize', style.marker.size)
if style.marker.fill_color is not None:
self._call_libsedml_method(marker_style_sed, 'setFill', style.marker.fill_color)
if style.marker.line_color is not None:
self._call_libsedml_method(marker_style_sed, 'setLineColor', style.marker.line_color)
if style.marker.line_thickness is not None:
self._call_libsedml_method(marker_style_sed, 'setLineThickness', style.marker.line_thickness)
if style.fill is not None:
fill_style_sed = style_sed.createFillStyle()
if style.fill.color is not None:
self._call_libsedml_method(fill_style_sed, 'setColor', style.fill.color)
def _add_model_to_doc(self, model):
""" Add a model to a SED document
Args:
model (:obj:`data_model.Model`): model
"""
model_sed = self._doc_sed.createModel()
self._obj_to_sed_obj_map[model] = model_sed
if model.id is not None:
self._call_libsedml_method(model_sed, 'setId', model.id)
if model.name is not None:
self._call_libsedml_method(model_sed, 'setName', model.name)
if model.source is not None:
self._call_libsedml_method(model_sed, 'setSource', model.source)
if model.language is not None:
self._call_libsedml_method(model_sed, 'setLanguage', model.language)
for change in model.changes:
if isinstance(change, data_model.ModelAttributeChange):
self._add_attribute_change_to_model(model, change)
elif isinstance(change, data_model.AddElementModelChange):
self._add_add_model_element_to_model(model, change)
elif isinstance(change, data_model.ReplaceElementModelChange):
self._add_change_model_element_to_model(model, change)
elif isinstance(change, data_model.RemoveElementModelChange):
self._add_remove_model_element_to_model(model, change)
elif isinstance(change, data_model.ComputeModelChange):
self._add_compute_change_to_model(model, change)
else:
raise NotImplementedError('Model change type {} is not supported.'.format(change.__class__.__name__))
def _add_attribute_change_to_model(self, model, change):
""" Add an attribute change change to a SED model
Args:
model (:obj:`data_model.Model`): model
change (:obj:`data_model.ModelAttributeChange`): model attribute change
Returns:
:obj:`libsedml.SedChangeAttribute`
"""
model_sed = self._obj_to_sed_obj_map[model]
change_sed = model_sed.createChangeAttribute()
self._obj_to_sed_obj_map[change] = change_sed
# if change.name is not None:
# self._call_libsedml_method(change_sed, 'setName', change.name)
if change.target is not None:
self._call_libsedml_method(change_sed, 'setTarget', change.target)
self._add_namespaces_to_obj(change_sed, change.target_namespaces)
if change.new_value is not None:
self._call_libsedml_method(change_sed, 'setNewValue', change.new_value)
return change_sed
def _add_add_model_element_to_model(self, model, change):
""" Add an add element change change to a SED model
Args:
model (:obj:`data_model.Model`): model
change (:obj:`data_model.ModelAttributeChange`): add model element change
Returns:
:obj:`libsedml.SedAddXML`
"""
model_sed = self._obj_to_sed_obj_map[model]
change_sed = model_sed.createAddXML()
self._obj_to_sed_obj_map[change] = change_sed
# if change.name is not None:
# self._call_libsedml_method(change_sed, 'setName', change.name)
if change.target is not None:
self._call_libsedml_method(change_sed, 'setTarget', change.target)
self._add_namespaces_to_obj(change_sed, change.target_namespaces)
if change.new_elements is not None:
new_xml = libsedml.XMLNode_convertStringToXMLNode(change.new_elements)
if new_xml is None:
raise ValueError('`{}` is invalid XML.'.format(change.new_elements))
self._call_libsedml_method(change_sed, 'setNewXML', new_xml)
return change_sed
def _add_change_model_element_to_model(self, model, change):
""" Add a change element change to a SED model
Args:
model (:obj:`data_model.Model`): model
change (:obj:`data_model.ReplaceElementModelChange`): change model element change
Returns:
:obj:`libsedml.SedChangeXML`
"""
model_sed = self._obj_to_sed_obj_map[model]
change_sed = model_sed.createChangeXML()
self._obj_to_sed_obj_map[change] = change_sed
# if change.name is not None:
# self._call_libsedml_method(change_sed, 'setName', change.name)
if change.target is not None:
self._call_libsedml_method(change_sed, 'setTarget', change.target)
self._add_namespaces_to_obj(change_sed, change.target_namespaces)
if change.new_elements is not None:
new_xml = libsedml.XMLNode_convertStringToXMLNode(change.new_elements)
if new_xml is None:
raise ValueError('`{}` is invalid XML.'.format(change.new_elements))
self._call_libsedml_method(change_sed, 'setNewXML', new_xml)
return change_sed
def _add_remove_model_element_to_model(self, model, change):
""" Add a remove element change to a SED model
Args:
model (:obj:`data_model.Model`): model
change (:obj:`data_model.RemoveElementModelChange`): remove model element change
Returns:
:obj:`libsedml.SedRemoveXML`
"""
model_sed = self._obj_to_sed_obj_map[model]
change_sed = model_sed.createRemoveXML()
self._obj_to_sed_obj_map[change] = change_sed
# if change.name is not None:
# self._call_libsedml_method(change_sed, 'setName', change.name)
if change.target is not None:
self._call_libsedml_method(change_sed, 'setTarget', change.target)
self._add_namespaces_to_obj(change_sed, change.target_namespaces)
return change_sed
def _add_compute_change_to_model(self, model, change):
""" Add a compute change to a SED model
Args:
model (:obj:`data_model.Model`): model
change (:obj:`data_model.ComputeModelChange`): compute change
Returns:
:obj:`libsedml.SedComputeChange`
"""
model_sed = self._obj_to_sed_obj_map[model]
change_sed = model_sed.createComputeChange()
self._obj_to_sed_obj_map[change] = change_sed
# if change.name is not None:
# self._call_libsedml_method(change_sed, 'setName', change.name)
if change.target is not None:
self._call_libsedml_method(change_sed, 'setTarget', change.target)
self._add_namespaces_to_obj(change_sed, change.target_namespaces)
for param in change.parameters:
self._add_param_to_obj(change, param)
for var in change.variables:
self._add_var_to_obj(change, var)
if change.math is not None:
self._call_libsedml_method(change_sed, 'setMath', libsedml.parseFormula(change.math))
return change_sed
def _add_sim_to_doc(self, sim):
""" Add a simulation to a SED document
Args:
sim (:obj:`data_model.Simulation`): simulation experiment
"""
if isinstance(sim, data_model.SteadyStateSimulation):
sim_sed = self._doc_sed.createSteadyState()
elif isinstance(sim, data_model.OneStepSimulation):
sim_sed = self._doc_sed.createOneStep()
if sim.step is not None:
self._call_libsedml_method(sim_sed, 'setStep', sim.step)
elif isinstance(sim, data_model.UniformTimeCourseSimulation):
sim_sed = self._doc_sed.createUniformTimeCourse()
if sim.initial_time is not None:
self._call_libsedml_method(sim_sed, 'setInitialTime', sim.initial_time)
if sim.output_start_time is not None:
self._call_libsedml_method(sim_sed, 'setOutputStartTime', sim.output_start_time)
if sim.output_end_time is not None:
self._call_libsedml_method(sim_sed, 'setOutputEndTime', sim.output_end_time)
if sim.number_of_steps is not None:
self._call_libsedml_method(sim_sed, 'setNumberOfSteps', sim.number_of_steps)
else: # pragma: no cover # unreachable due to earlier validation
raise NotImplementedError('Simulation type {} is not supported.'.format(sim.__class__.__name__))
self._obj_to_sed_obj_map[sim] = sim_sed
if sim.id is not None:
self._call_libsedml_method(sim_sed, 'setId', sim.id)
if sim.name is not None:
self._call_libsedml_method(sim_sed, 'setName', sim.name)
if sim.algorithm is not None:
self._add_algorithm_to_sim(sim, sim.algorithm)
def _add_algorithm_to_sim(self, sim, alg):
""" Add a simulation algorithm to a SED document
Args:
sim (:obj:`data_model.Simulation`): simulation
alg (:obj:`data_model.Algorithm`): simulation algorithm
"""
sim_sed = self._obj_to_sed_obj_map[sim]
alg_sed = sim_sed.createAlgorithm()
self._obj_to_sed_obj_map[alg] = alg_sed
if alg.kisao_id is not None:
self._set_kisao_id(alg)
for change in alg.changes:
if change.new_value is not None:
self._add_param_change_to_alg(alg, change)
def _add_param_change_to_alg(self, alg, change):
""" Add simulation algorithm parameter change to a SED document
Args:
alg (:obj:`data_model.Algorithm`): SED simulation algorithm
change (:obj:`data_model.AlgorithmParameterChange`): simulation algorithm parameter change
"""
alg_sed = self._obj_to_sed_obj_map[alg]
change_sed = alg_sed.createAlgorithmParameter()
self._obj_to_sed_obj_map[change] = change_sed
if change.kisao_id is not None:
self._set_kisao_id(change)
if change.new_value is not None:
self._call_libsedml_method(change_sed, 'setValue', change.new_value)
def _set_kisao_id(self, obj):
""" Set the KiSAO id of a SED object
Args:
obj (:obj:`data_model.Algorithm` or :obj:`data_model.AlgorithmParameterChange`): SED object
"""
obj_sed = self._obj_to_sed_obj_map[obj]
self._call_libsedml_method(obj_sed, 'setKisaoID', obj.kisao_id.replace('_', ':'))
def _add_task_to_doc(self, task):
""" Add a task to a SED document
Args:
task (:obj:`data_model.Task`): task
Raises:
:obj:`ValueError`: if the referenced model or simulation doesn't have an id
"""
task_sed = self._doc_sed.createTask()
self._obj_to_sed_obj_map[task] = task_sed
if task.id is not None:
self._call_libsedml_method(task_sed, 'setId', task.id)
if task.name is not None:
self._call_libsedml_method(task_sed, 'setName', task.name)
if task.model is not None:
if not task.model.id: # pragma: no cover: already validated
raise ValueError('Model must have an id to be referenced')
self._call_libsedml_method(task_sed, 'setModelReference', task.model.id)
if task.simulation is not None:
if not task.simulation.id: # pragma: no cover: already validated
raise ValueError('Simulation must have an id to be referenced')
self._call_libsedml_method(task_sed, 'setSimulationReference', task.simulation.id)
def _add_repeated_task_to_doc(self, task):
""" Add a repeated task to a SED document
Args:
task (:obj:`data_model.RepeatedTask`): task
Raises:
:obj:`ValueError`: if the referenced range doesn't have an id
"""
task_sed = self._doc_sed.createRepeatedTask()
self._obj_to_sed_obj_map[task] = task_sed
if task.id is not None:
self._call_libsedml_method(task_sed, 'setId', task.id)
if task.name is not None:
self._call_libsedml_method(task_sed, 'setName', task.name)
if task.reset_model_for_each_iteration is not None:
self._call_libsedml_method(task_sed, 'setResetModel', task.reset_model_for_each_iteration)
if task.range is not None:
if not task.range.id: # pragma: no cover: already validated
raise ValueError('Range must have an id to be referenced')
self._call_libsedml_method(task_sed, 'setRangeId', task.range.id)
for change in task.changes:
self._add_set_value_model_change_to_repeated_task(task, change)
for sub_task in task.sub_tasks:
self._add_sub_task_to_repeated_task(task, sub_task)
for range_obj in task.ranges:
self._add_range_to_repeated_task(task, range_obj)
def _add_set_value_model_change_to_repeated_task(self, task, change):
""" Add a set value change to a repeated task
Args:
task (:obj:`data_model.RepeatedTask`): task
change (:obj:`data_model.SetValueComputeModelChange`): change
Raises:
:obj:`ValueError`: if the referenced model or range doesn't have an id
"""
task_sed = self._obj_to_sed_obj_map[task]
change_sed = task_sed.createTaskChange()
self._obj_to_sed_obj_map[change] = change_sed
# if change.name is not None:
# self._call_libsedml_method(change_sed, 'setName', change.name)
if change.target is not None:
self._call_libsedml_method(change_sed, 'setTarget', change.target)
self._add_namespaces_to_obj(change_sed, change.target_namespaces)
for param in change.parameters:
self._add_param_to_obj(change, param)
for var in change.variables:
self._add_var_to_obj(change, var)
if change.math is not None:
self._call_libsedml_method(change_sed, 'setMath', libsedml.parseFormula(change.math))
if change.model is not None:
if not change.model.id: # pragma: no cover: already validated
raise ValueError('Model must have an id to be referenced')
self._call_libsedml_method(change_sed, 'setModelReference', change.model.id)
if change.range is not None:
if not change.range.id: # pragma: no cover: already validated
raise ValueError('Range must have an id to be referenced')
self._call_libsedml_method(change_sed, 'setRange', change.range.id)
if change.symbol is not None:
self._call_libsedml_method(change_sed, 'setSymbol', change.symbol)
def _add_sub_task_to_repeated_task(self, task, sub_task):
""" Add a sub-task to a repeated task
Args:
task (:obj:`data_model.RepeatedTask`): task
sub_task (:obj:`data_model.SubTask`): sub-task
Raises:
:obj:`ValueError`: if the referenced task doesn't have an id
"""
task_sed = self._obj_to_sed_obj_map[task]
sub_task_sed = task_sed.createSubTask()
self._obj_to_sed_obj_map[sub_task] = sub_task_sed
if sub_task.task is not None:
if not sub_task.task.id: # pragma: no cover: already validated
raise ValueError('Task must have an id to be referenced')
self._call_libsedml_method(sub_task_sed, 'setTask', sub_task.task.id)
if sub_task.order is not None:
self._call_libsedml_method(sub_task_sed, 'setOrder', sub_task.order)
def _add_range_to_repeated_task(self, task, range_obj):
""" Add a range to a repeated task
Args:
task (:obj:`data_model.RepeatedTask`): task
sub_task (:obj:`data_model.Range`): range
Raises:
:obj:`ValueError`: if the referenced range doesn't have an id
"""
task_sed = self._obj_to_sed_obj_map[task]
if isinstance(range_obj, data_model.UniformRange):
range_sed = task_sed.createUniformRange()
self._obj_to_sed_obj_map[range_obj] = range_sed
if range_obj.start is not None:
self._call_libsedml_method(range_sed, 'setStart', range_obj.start)
if range_obj.end is not None:
self._call_libsedml_method(range_sed, 'setEnd', range_obj.end)
if range_obj.number_of_steps is not None:
self._call_libsedml_method(range_sed, 'setNumberOfSteps', range_obj.number_of_steps)
if range_obj.type is not None:
self._call_libsedml_method(range_sed, 'setType', range_obj.type.value)
elif isinstance(range_obj, data_model.VectorRange):
range_sed = task_sed.createVectorRange()
self._obj_to_sed_obj_map[range_obj] = range_sed
for value in range_obj.values:
self._call_libsedml_method(range_sed, 'setValues', tuple(range_obj.values))
elif isinstance(range_obj, data_model.FunctionalRange):
range_sed = task_sed.createFunctionalRange()
self._obj_to_sed_obj_map[range_obj] = range_sed
if range_obj.range is not None:
if not range_obj.range.id: # pragma: no cover: already validated
raise ValueError('Range must have an id to be referenced')
self._call_libsedml_method(range_sed, 'setRange', range_obj.range.id)
for param in range_obj.parameters:
self._add_param_to_obj(range_obj, param)
for var in range_obj.variables:
self._add_var_to_obj(range_obj, var)
if range_obj.math is not None:
self._call_libsedml_method(range_sed, 'setMath', libsedml.parseFormula(range_obj.math))
else:
raise NotImplementedError('Range type {} is not supported.'.format(range_obj.__class__.__name__))
if range_obj.id is not None:
self._call_libsedml_method(range_sed, 'setId', range_obj.id)
def _add_data_gen_to_doc(self, data_gen):
""" Add a data generator to a SED document
Args:
data_gen (:obj:`data_model.DataGenerator`): data generator
"""
data_gen_sed = self._doc_sed.createDataGenerator()
self._obj_to_sed_obj_map[data_gen] = data_gen_sed
if data_gen.id is not None:
self._call_libsedml_method(data_gen_sed, 'setId', data_gen.id)
if data_gen.name is not None:
self._call_libsedml_method(data_gen_sed, 'setName', data_gen.name)
for param in data_gen.parameters:
self._add_param_to_obj(data_gen, param)
for var in data_gen.variables:
self._add_var_to_obj(data_gen, var)
if data_gen.math is not None:
self._call_libsedml_method(data_gen_sed, 'setMath', libsedml.parseFormula(data_gen.math))
def _add_param_to_obj(self, obj, param):
""" Add a parameter to a SED object
Args:
obj (:obj:`data_model.ComputeModelChange`, :obj:`data_model.DataGenerator`):
compute change, data generator, functional range or set value
param (:obj:`data_model.Parameter`): parameter
"""
obj_sed = self._obj_to_sed_obj_map[obj]
param_sed = obj_sed.createParameter()
self._obj_to_sed_obj_map[param] = param_sed
if param.id is not None:
self._call_libsedml_method(param_sed, 'setId', param.id)
if param.name is not None:
self._call_libsedml_method(param_sed, 'setName', param.name)
if param.value is not None:
self._call_libsedml_method(param_sed, 'setValue', param.value)
def _add_var_to_obj(self, obj, var):
""" Add a variable to a SED object
Args:
obj (:obj:`data_model.ComputeModelChange`, :obj:`data_model.DataGenerator`):
compute change, data generator, functional range or set value
var (:obj:`data_model.Variable`): variable
"""
obj_sed = self._obj_to_sed_obj_map[obj]
var_sed = obj_sed.createVariable()
self._obj_to_sed_obj_map[var] = var_sed
if var.id is not None:
self._call_libsedml_method(var_sed, 'setId', var.id)
if var.name is not None:
self._call_libsedml_method(var_sed, 'setName', var.name)
if var.symbol is not None:
self._call_libsedml_method(var_sed, 'setSymbol', var.symbol)
if var.target is not None:
self._call_libsedml_method(var_sed, 'setTarget', var.target)
self._add_namespaces_to_obj(var_sed, var.target_namespaces)
if var.task is not None:
if not var.task.id: # pragma: no cover: already validated
raise ValueError('Task must have an id to be referenced')
self._call_libsedml_method(var_sed, 'setTaskReference', var.task.id)
if var.model is not None:
if not var.model.id: # pragma: no cover: already validated
raise ValueError('Model must have an id to be referenced')
self._call_libsedml_method(var_sed, 'setModelReference', var.model.id)
def _add_report_to_doc(self, report):
""" Add a report to a SED document
Args:
report (:obj:`data_model.Report`): report
"""
report_sed = self._doc_sed.createReport()
self._obj_to_sed_obj_map[report] = report_sed
if report.id is not None:
self._call_libsedml_method(report_sed, 'setId', report.id)
if report.name is not None:
self._call_libsedml_method(report_sed, 'setName', report.name)
for data_set in report.data_sets:
dataset_sed = report_sed.createDataSet()
self._obj_to_sed_obj_map[data_set] = dataset_sed
if data_set.id is not None:
self._call_libsedml_method(dataset_sed, 'setId', data_set.id)
if data_set.name is not None:
self._call_libsedml_method(dataset_sed, 'setName', data_set.name)
if data_set.label is not None:
self._call_libsedml_method(dataset_sed, 'setLabel', data_set.label)
if data_set.data_generator is not None:
if not data_set.data_generator.id: # pragma: no cover: already validated
raise ValueError('Data generator must have an id to be referenced')
self._call_libsedml_method(dataset_sed, 'setDataReference', data_set.data_generator.id)
def _add_plot2d_to_doc(self, plot):
""" Add a 2D plot to a SED document
Args:
plot (:obj:`data_model.Plot2D`): 2D plot
"""
plot_sed = self._doc_sed.createPlot2D()
self._obj_to_sed_obj_map[plot] = plot_sed
if plot.id is not None:
self._call_libsedml_method(plot_sed, 'setId', plot.id)
if plot.name is not None:
self._call_libsedml_method(plot_sed, 'setName', plot.name)
for curve in plot.curves:
curve_sed = plot_sed.createCurve()
self._obj_to_sed_obj_map[curve] = curve_sed
if curve.id is not None:
self._call_libsedml_method(curve_sed, 'setId', curve.id)
if curve.name is not None:
self._call_libsedml_method(curve_sed, 'setName', curve.name)
self._set_axis_scale(curve, 'x')
self._set_axis_scale(curve, 'y')
if curve.x_data_generator is not None:
if not curve.x_data_generator.id: # pragma: no cover: already validated
raise ValueError('Data generator must have an id to be referenced')
self._call_libsedml_method(curve_sed, 'setXDataReference', curve.x_data_generator.id)
if curve.y_data_generator is not None:
if not curve.y_data_generator.id: # pragma: no cover: already validated
raise ValueError('Data generator must have an id to be referenced')
self._call_libsedml_method(curve_sed, 'setYDataReference', curve.y_data_generator.id)
if curve.style is not None:
if not curve.style.id: # pragma: no cover: already validated
raise ValueError('Style must have an id to be referenced')
self._call_libsedml_method(curve_sed, 'setStyle', curve.style.id)
def _add_plot3d_to_doc(self, plot):
""" Add a 3D plot to a SED document
Args:
plot (:obj:`data_model.Plot3D`): 3D plot
"""
plot_sed = self._doc_sed.createPlot3D()
self._obj_to_sed_obj_map[plot] = plot_sed
if plot.id is not None:
self._call_libsedml_method(plot_sed, 'setId', plot.id)
if plot.name is not None:
self._call_libsedml_method(plot_sed, 'setName', plot.name)
for surface in plot.surfaces:
surface_sed = plot_sed.createSurface()
self._obj_to_sed_obj_map[surface] = surface_sed
if surface.id is not None:
self._call_libsedml_method(surface_sed, 'setId', surface.id)
if surface.name is not None:
self._call_libsedml_method(surface_sed, 'setName', surface.name)
self._set_axis_scale(surface, 'x')
self._set_axis_scale(surface, 'y')
self._set_axis_scale(surface, 'z')
if surface.x_data_generator is not None:
if not surface.x_data_generator.id: # pragma: no cover: already validated
raise ValueError('Data generator must have an id to be referenced')
self._call_libsedml_method(surface_sed, 'setXDataReference', surface.x_data_generator.id)
if surface.y_data_generator is not None:
if not surface.y_data_generator.id: # pragma: no cover: already validated
raise ValueError('Data generator must have an id to be referenced')
self._call_libsedml_method(surface_sed, 'setYDataReference', surface.y_data_generator.id)
if surface.z_data_generator is not None:
if not surface.z_data_generator.id: # pragma: no cover: already validated
raise ValueError('Data generator must have an id to be referenced')
self._call_libsedml_method(surface_sed, 'setZDataReference', surface.z_data_generator.id)
if surface.style is not None:
if not surface.style.id: # pragma: no cover: already validated
raise ValueError('Style must have an id to be referenced')
self._call_libsedml_method(surface_sed, 'setStyle', surface.style.id)
def _set_axis_scale(self, obj, axis):
""" Set the scale of an axis of a curve of surface
Args:
obj (:obj:`data_model.Curve` or :obj:`data_model.Surface`): plot
axis (:obj:`str`): axis (`x`, `y`, or `z`)
"""
obj_sed = self._obj_to_sed_obj_map[obj]
axis_scale = getattr(obj, axis.lower() + '_scale')
if axis_scale == data_model.AxisScale.linear:
self._call_libsedml_method(obj_sed, 'setLog' + axis.upper(), False)
elif axis_scale == data_model.AxisScale.log:
self._call_libsedml_method(obj_sed, 'setLog' + axis.upper(), True)
else:
# this is an error rather than a warning because SED doesn't define any other types of scales
raise NotImplementedError('Axis scale type {} is not supported.'.format(axis_scale))
def _export_doc(self, filename):
""" Export a SED document to an XML file
Args:
filename (:obj:`str`): path to save document in XML format
"""
# save the SED document to a file
libsedml.writeSedML(self._doc_sed, filename)
def _add_metadata_to_obj(self, obj):
""" Add the metadata about a resource to the annotation of a SED object
* Name
* Authors
* Description
* Tags
* References
* License
Args:
obj (:obj:`object`): object
"""
if not obj.metadata:
return
obj_sed = self._obj_to_sed_obj_map[obj]
metadata = []
namespaces = set()
if obj.metadata.description:
metadata.append(XmlNode(
prefix='dc',
name='description',
type='description',
children=obj.metadata.description,
))
namespaces.add('dc')
if obj.metadata.tags:
metadata.append(
XmlNode(prefix='dc', name='description', type='tags', children=[
XmlNode(prefix='rdf', name='Bag', children=[
XmlNode(prefix='rdf', name='li', children=[
XmlNode(prefix='rdf', name='value', children=tag)
]) for tag in obj.metadata.tags
])
]))
namespaces.add('dc')
namespaces.add('rdf')
if obj.metadata.authors:
authors_xml = []
for author in obj.metadata.authors:
names_xml = []
if author.given_name:
names_xml.append(XmlNode(prefix='vcard', name='Given', children=author.given_name))
if author.other_name:
names_xml.append(XmlNode(prefix='vcard', name='Other', children=author.other_name))
if author.family_name:
names_xml.append(XmlNode(prefix='vcard', name='Family', children=author.family_name))
authors_xml.append(XmlNode(prefix='rdf', name='li', children=[
XmlNode(prefix='vcard', name='N', children=names_xml)
]))
metadata.append(
XmlNode(prefix='dc', name='creator', children=[
XmlNode(prefix='rdf', name='Bag', children=authors_xml)
])
)
namespaces.add('dc')
namespaces.add('rdf')
namespaces.add('vcard')
if obj.metadata.references and obj.metadata.references.citations:
refs_xml = []
for citation in obj.metadata.references.citations:
props_xml = []
if citation.authors:
props_xml.append(XmlNode(prefix='bibo', name='authorList', children=citation.authors))
if citation.title:
props_xml.append(XmlNode(prefix='dc', name='title', children=citation.title))
if citation.journal:
props_xml.append(XmlNode(prefix='bibo', name='journal', children=citation.journal))
if citation.volume:
props_xml.append(XmlNode(prefix='bibo', name='volume', children=citation.volume))
if citation.issue:
props_xml.append(XmlNode(prefix='bibo', name='issue', children=citation.issue))
if citation.pages:
props_xml.append(XmlNode(prefix='bibo', name='pages', children=citation.pages))
if citation.year:
props_xml.append(XmlNode(prefix='dc', name='date', children=citation.year))
doi = next((identifier.id for identifier in citation.identifiers if identifier.namespace.lower() == 'doi'), None)
if doi:
props_xml.append(XmlNode(prefix='bibo', name='doi', children=doi))
refs_xml.append(XmlNode(prefix='rdf', name='li', children=[
XmlNode(prefix='bibo', name='Article', children=props_xml)
]))
metadata.append(
XmlNode(prefix='dcterms', name='references', children=[
XmlNode(prefix='rdf', name='Bag', children=refs_xml)
])
)
namespaces.add('dcterms')
namespaces.add('rdf')
namespaces.add('bibo')
if obj.metadata.license:
if obj.metadata.license.namespace:
children = '{}:{}'.format(obj.metadata.license.namespace, obj.metadata.license.id)
else:
children = obj.metadata.license.id
metadata.append(XmlNode(
prefix='dcterms',
name='license',
children=children,
))
namespaces.add('dcterms')
metadata.append(XmlNode(prefix='dcterms', name='mediator', children='BioSimulators utils'))
if obj.metadata.created is not None:
metadata.append(XmlNode(prefix='dcterms', name='created',
children=obj.metadata.created.strftime('%Y-%m-%dT%H:%M:%SZ')))
if obj.metadata.updated is not None:
metadata.append(XmlNode(prefix='dcterms', name='date', type='update',
children=obj.metadata.updated.strftime('%Y-%m-%dT%H:%M:%SZ')))
namespaces.add('dcterms')
self._add_annotation_to_obj(metadata, obj_sed, namespaces)
def _add_annotation_to_obj(self, nodes, obj_sed, namespaces):
""" Add annotation to a SED object
Args:
nodes (:obj:`list` of :obj:`XmlNode`): annotation
obj_sed (:obj:`libsedml.SedBase`): SED object
namespaces (:obj:`set` of :obj:`str`): list of namespaces
"""
if nodes:
meta_id = self._set_meta_id(obj_sed)
about_xml = ' rdf:about="#{}"'.format(meta_id)
namespaces.add('rdf')
namespaces_xml = []
if 'rdf' in namespaces:
namespaces_xml.append(' xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"')
if 'dc' in namespaces:
namespaces_xml.append(' xmlns:dc="http://purl.org/dc/elements/1.1/"')
if 'dcterms' in namespaces:
namespaces_xml.append(' xmlns:dcterms="http://purl.org/dc/terms/"')
if 'vcard' in namespaces:
namespaces_xml.append(' xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"')
if 'bibo' in namespaces:
namespaces_xml.append(' xmlns:bibo="http://purl.org/ontology/bibo/"')
self._call_libsedml_method(obj_sed, 'setAnnotation',
('<annotation>'
' <rdf:RDF{}>'
' <rdf:Description{}>'
' {}'
' </rdf:Description>'
' </rdf:RDF>'
' </annotation>').format(
''.join(namespaces_xml),
about_xml,
''.join(node.encode() for node in nodes)))
def _set_meta_id(self, obj_sed):
""" Generate and set a unique meta id for a SED object