def main (args):
"""Usage: print_sedml input-filename
"""
if len(args) != 2:
print(main.__doc__)
sys.exit(1)
doc = libsedml.readSedML(args[1]);
if ( doc.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR) > 0):
print doc.getErrorLog().toString();
sys.exit(2);
print 'The document has {0}" simulation(s).'.format(doc.getNumSimulations());
for i in range(0, doc.getNumSimulations()):
current = doc.getSimulation(i);
if (current.getTypeCode() == libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE):
tc = current;
kisaoid="none"
if tc.isSetAlgorithm():
kisaoid=tc.getAlgorithm().getKisaoID()
print "\tTimecourse id=", tc.getId()," start=",tc.getOutputStartTime()," end=",tc.getOutputEndTime()," numPoints=",tc.getNumberOfPoints()," kisao=",kisaoid,"\n";
else:
print "\tUncountered unknown simulation. ",current.getId(),"\n";
print "\n"
print "The document has ",doc.getNumModels() , " model(s)." , "\n";
for i in range(0,doc.getNumModels()):
current = doc.getModel(i);
print "\tModel id=" , current.getId() , " language=" , current.getLanguage() , " source=" , current.getSource() , " numChanges=" , current.getNumChanges() , "\n";
print "\n";
print "The document has " , doc.getNumTasks() , " task(s)." , "\n";
for i in range(0,doc.getNumTasks()):
current = doc.getTask(i);
print "\tTask id=" , current.getId() , " model=" , current.getModelReference() , " sim=" , current.getSimulationReference() , "\n";
print "\n";
print "The document has " , doc.getNumDataGenerators() , " datagenerators(s)." , "\n";
for i in range( 0, doc.getNumDataGenerators()):
current = doc.getDataGenerator(i);
print "\tDG id=" , current.getId() , " math=" , libsedml.formulaToString(current.getMath()) , "\n";
print "\n";
print "The document has " , doc.getNumOutputs() , " output(s)." , "\n";
for i in range (0, doc.getNumOutputs()):
current = doc.getOutput(i);
tc = current.getTypeCode();
if tc == libsedml.SEDML_OUTPUT_REPORT:
r = (current);
print "\tReport id=" , current.getId() , " numDataSets=" , r.getNumDataSets() , "\n";
elif tc == libsedml.SEDML_OUTPUT_PLOT2D:
p = (current);
print "\tPlot2d id=" , current.getId() , " numCurves=" , p.getNumCurves() , "\n";
elif tc == libsedml.SEDML_OUTPUT_PLOT3D:
p = (current);
print "\tPlot3d id=" , current.getId() , " numSurfaces=" , p.getNumSurfaces() , "\n";
else:
print "\tEncountered unknown output " , current.getId() , "\n";
def read(file_name):
""" Imports simulation configuration from SED-ML file
Args:
file_name (:obj:`str`): path to SED-ML file from which to import simulation configuration
Returns:
:obj:`WCSimulationConfig`: simulation configuration
"""
# initialize optional configuration
opt_config = {}
""" read SED-ML """
# read XML file
cfg_ml = libsedml.readSedML(file_name)
""" validate SED-ML """
# one model with
# - zero or more attribute changes
if cfg_ml.getNumModels() != 1:
raise SedMlError('SED-ML configuration must have one model')
mdl = cfg_ml.getModel(0)
if mdl.getId() or mdl.getName() or mdl.getLanguage() or mdl.getSource(
):
warnings.warn(
'SED-ML import ignoring all model metadata (id, name, language, source)',
SedMlWarning)
for change_ml in mdl.getListOfChanges():
if not isinstance(change_ml, libsedml.SedChangeAttribute):
raise SedMlError(
'Cannot import model changes except attribute changes')
# 1 simulation with
#- Initial time = 0
#- Output start time = 0
#- Algorithm = KISAO_0000352 (hybrid)
#- 1 algorithm parameters
# - random_seed (KISAO_0000488): int
if cfg_ml.getNumSimulations() != 1:
raise SedMlError('SED-ML configuration must have 1 simulation')
sim_ml = cfg_ml.getSimulation(0)
if sim_ml.getInitialTime() != sim_ml.getOutputStartTime():
raise SedMlError(
'Simulation initial time and output start time must be equal')
alg_ml = sim_ml.getAlgorithm()
if alg_ml.getKisaoID() != 'KISAO_0000352':
raise SedMlError(
'Unsupported algorithm. The only supported algorithm is KISAO_0000352 (hybrid)'
)
param_kisao_ids = set(
param_ml.getKisaoID()
for param_ml in alg_ml.getListOfAlgorithmParameters())
if len(param_kisao_ids) < alg_ml.getNumAlgorithmParameters():
raise SedMlError('Algorithm parameter KISAO ids must be unique')
unsupported_param_kisao_ids = param_kisao_ids - set(['KISAO_0000488'])
if unsupported_param_kisao_ids:
raise SedMlError(
'Algorithm parameters ({}) are not supported'.format(
', '.join(unsupported_param_kisao_ids)))
# zero or more repeated tasks each with
# - 1 set value task change
# - math equal to constant floating point value
# - 1 uniform or vector range of 1 value
# - no subtasks
for task_ml in cfg_ml.getListOfTasks():
if isinstance(task_ml, libsedml.SedRepeatedTask):
if task_ml.getNumTaskChanges() != 1:
raise SedMlError(
'Each repeated task must have one task change')
change_ml = task_ml.getTaskChange(0)
try:
float(libsedml.formulaToString(change_ml.getMath()))
except ValueError:
raise SedMlError(
'Set value maths must be floating point values')
if task_ml.getNumRanges() != 1:
raise SedMlError('Each repeated task must have one range')
range_ml = task_ml.getRange(0)
if not isinstance(
range_ml,
(libsedml.SedUniformRange, libsedml.SedVectorRange)):
raise SedMlError(
'Task ranges must be uniform or vector ranges')
if isinstance(range_ml, libsedml.SedUniformRange
) and range_ml.getNumberOfPoints() != 2**31 - 1:
raise SedMlError('Cannot import number of points')
if isinstance(range_ml, libsedml.SedUniformRange
) and range_ml.getType() != 'linear':
raise SedMlError('Only linear ranges are supported')
if isinstance(range_ml, libsedml.SedVectorRange) and len(
list(range_ml.getValues())) != 1:
raise SedMlError('Task vector ranges must have length 1')
if task_ml.getNumSubTasks() > 0:
raise SedMlError('Cannot import subtasks')
else:
raise SedMlError('Cannot import tasks except repeated tasks')
# no data generators
if cfg_ml.getNumDataGenerators() > 0:
raise SedMlError('Cannot import data generator information')
# no data descriptions
if cfg_ml.getNumDataDescriptions() > 0:
raise SedMlError('Cannot import data description information')
# no outputs
if cfg_ml.getNumOutputs() > 0:
raise SedMlError('Cannot import output information')
""" Read simulation configuration information from SED-ML document """
# changes
changes = []
mdl = cfg_ml.getModel(0)
for change_ml in mdl.getListOfChanges():
target = change_ml.getTarget()
change = Change()
change.attr_path = Change.attr_path_from_str(change_ml.getTarget())
change.value = float(change_ml.getNewValue())
changes.append(change)
# perturbations
perturbations = []
for task_ml in cfg_ml.getListOfTasks():
change_ml = task_ml.getTaskChange(0)
change = Change()
change.attr_path = Change.attr_path_from_str(change_ml.getTarget())
change.value = float(libsedml.formulaToString(change_ml.getMath()))
range_ml = task_ml.getRange(0)
if isinstance(range_ml, libsedml.SedUniformRange):
start_time = range_ml.getStart()
end_time = range_ml.getEnd()
else:
start_time = range_ml.getValues()[0]
end_time = float('nan')
perturbations.append(Perturbation(change, start_time, end_time))
# time
sim = cfg_ml.getSimulation(0)
time_init = sim.getOutputStartTime()
time_max = sim.getOutputEndTime()
ode_time_step = (time_max - time_init) / sim.getNumberOfPoints()
# algorithm parameters
alg = sim.getAlgorithm()
for param in alg.getListOfAlgorithmParameters():
if param.getKisaoID() == 'KISAO_0000488':
try:
opt_config['random_seed'] = float(param.getValue())
except ValueError:
raise SedMlError('random_seed must be an integer')
if opt_config['random_seed'] != math.ceil(
opt_config['random_seed']):
raise SedMlError('random_seed must be an integer')
opt_config['random_seed'] = int(opt_config['random_seed'])
""" build simulation configuration object """
de_simulation_config = SimulationConfig(time_max=time_max,
time_init=time_init)
cfg = WCSimulationConfig(de_simulation_config=de_simulation_config,
ode_time_step=ode_time_step,
changes=changes,
perturbations=perturbations,
**opt_config)
return cfg
def getAllObservables(iSEDML, core_iSbml):
# list of all directories + SBML files
#list_directory_sedml = sorted(os.listdir(base_path_sedml))
# create new sbml file with observables
#for iSEDML in list_directory_sedml:
# iSEDML = 'kouril2017_fig1a'
# list_files = sorted(os.listdir(base_path_sedml + '/' + iSEDML + '/sbml_models'))
# for iSBML in list_files:
# split iSBML
#core_iSbml, XML = iSBML.split('.')
#iSEDML = 'bachmann2011'
#core_iSbml = 'bachmann'
# important paths
base_path_sedml = './sedml_models'
sedml_path = './sedml_models/' + iSEDML + '/' + iSEDML + '.sedml'
sbml_path = './sedml_models/' + iSEDML + '/sbml_models/' + core_iSbml + '.sbml'
new_sbml_path = base_path_sedml + '/' + iSEDML + '/sbml_models_with_observables/' + core_iSbml + '_with_observabels.xml'
if not os.path.exists(sedml_path):
print('No Observables!')
else:
# new folder for all sbml models with observables
if not os.path.exists(base_path_sedml + '/' + iSEDML +
'/sbml_models_with_observables'):
os.makedirs(base_path_sedml + '/' + iSEDML +
'/sbml_models_with_observables')
# read in sedml file
sedml_file = libsedml.readSedML(sedml_path)
# get number of tasks and observables
num_task = sedml_file.getNumTasks()
num_obs = sedml_file.getNumDataGenerators()
# read in sbml model
reader = libsbml.SBMLReader()
sbml_file = reader.readSBML(sbml_path)
sbml_model = sbml_file.getModel()
for iTask in range(0, num_task):
task_id = sedml_file.getTask(iTask).getId()
# create list with all parameter-ids to check for uniqueness
# all_par_id = []
almost_all_par_id = []
'''
# get all species-Ids
num_spec = len(model.getListOfSpecies())
list_spec = []
for iSpec in range(0, num_spec):
spec_Id = model.getSpecies(iSpec).getId()
list_spec.append(spec_Id)
# get all parameter-Ids
num_par_old = len(model.getListOfParameters())
list_par_old = []
for iPar in range(0, num_par_old):
par_Id = model.getParameter(iPar).getId()
list_par_old.append(par_Id)
'''
for iObservable in range(0, num_obs):
# get important formula
obs_Formula = libsedml.formulaToString(
sedml_file.getDataGenerator(iObservable).getMath())
obs_Id = sedml_file.getDataGenerator(iObservable).getId()
# SBML_model_Id,Observable_Id = obs_Id.split('_',1)
new_obs_Id = 'observable_' + obs_Id
# get variables
num_var = sedml_file.getDataGenerator(
iObservable).getNumVariables()
list_var_id = []
for iVar in range(0, num_var):
var_Id = sedml_file.getDataGenerator(
iObservable).getVariable(iVar).getId()
target_Id = sedml_file.getDataGenerator(
iObservable).getVariable(iVar).getTarget()
if not target_Id == '':
try:
_, new_var_Id, _ = target_Id.split("'")
if var_Id in obs_Formula:
obs_Formula = obs_Formula.replace(
var_Id, new_var_Id)
except:
print(
'target_Id can not be splitted / does not need to be splitted!'
)
else:
print('target_Id does not exists!')
# only if it was not defined earlier
#if not var_Id in list_spec:
# if not var_Id in list_par_old:
# if not var_Id in list_var_id:
# list_var_id.append(var_Id)
# get right compartment
#compartment = model.getCompartment(0).getId()
# get list of parameters
list_par_id = []
list_par_value = []
num_par = sedml_file.getDataGenerator(
iObservable).getNumParameters()
if num_par == 0:
print(obs_Id + ' has no parameters as observables!')
else:
for iCount in range(0, num_par):
list_par_id.append(
sedml_file.getDataGenerator(
iObservable).getParameter(iCount).getId())
# list_par_value.append(sedml_file.getDataGenerator(iObservable).getParameter(iCount).getValue())
# all_par_id.append(sedml_file.getDataGenerator(iObservable).getParameter(iCount).getId())
list_par_value.append(
sedml_file.getDataGenerator(
iObservable).getParameter(iCount).getValue())
almost_all_par_id.append(
sedml_file.getDataGenerator(
iObservable).getParameter(iCount).getId())
# check for uniqueness of parameter-ids
# for iNum in range(0, len(all_par_id)):
# almost_all_par_id = all_par_id.remove(all_par_id[len(all_par_id) - 1])
for iNum in range(0, len(almost_all_par_id)):
all_par_id = almost_all_par_id[iNum]
almost_all_par_id.remove(
almost_all_par_id[len(almost_all_par_id) - 1])
last_element = list(all_par_id[len(all_par_id) -
1])
intersection = [
i for i in last_element
if i in almost_all_par_id
]
if len(intersection) != 0:
print(
'Two or more parameters have the same Id!')
# sys.exit(1)
# look for correct observables: with target and with task_id == task_ref
if sedml_file.getDataGenerator(iObservable).getVariable(
0).getTarget() != '':
# get task reference
task_target = sedml_file.getDataGenerator(
iObservable).getVariable(0).getTarget()
task_ref = sedml_file.getDataGenerator(
iObservable).getVariable(0).getTaskReference()
if task_id == task_ref:
# create formula
assignmentRule = sbml_model.createAssignmentRule()
assignmentRule.setId(new_obs_Id)
assignmentRule.setVariable(new_obs_Id)
assignmentRule.setFormula(obs_Formula)
# create parameter to formula for observables
obs_parameter = sbml_model.createParameter()
obs_parameter.setId(new_obs_Id)
obs_parameter.setConstant(False)
# create parameter to formula for parameters
for iCount in range(0, num_par):
iPar_id = list_par_id[iCount]
iPar_value = list_par_value[iCount]
parameter = sbml_model.createParameter()
parameter.setId(iPar_id)
parameter.setConstant(False)
parameter.setValue(iPar_value)
# create species to formula
#for iCount in range(0, len(list_var_id)):
# iVar_id = list_var_id[iCount]
# variable = model.createSpecies()
# variable.setId(iVar_id)
# variable.setCompartment(compartment)
# variable.setHasOnlySubstanceUnits(False)
# variable.setBoundaryCondition(False)
# variable.setConstant(False)
libsbml.writeSBMLToFile(sbml_file, new_sbml_path)
def build(self, sedml, base_location):
"""
Build this experiment manifest from the provided SED-ML document. We assume that the SED-ML document
has been checked for errors prior to its use here.
:param sedml: The SED-ML document as parsed by libsedml.
:param base_location: The base location to use in resolving relative model locations.
"""
for i in range(0, sedml.getNumSimulations()):
current = sedml.getSimulation(i)
if current.getTypeCode(
) == libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE:
tc = current
kisaoid = "none"
if tc.isSetAlgorithm():
kisaoid = tc.getAlgorithm().getKisaoID()
sId = tc.getId()
self._simulations[sId] = {
'type': libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE,
'initial': tc.getInitialTime(),
'start': tc.getOutputStartTime(),
'end': tc.getOutputEndTime(),
'numPoints': tc.getNumberOfPoints(),
'kisao': kisaoid
}
print_simulation(sId, self._simulations[sId])
else:
print("\tEncountered unknown simulation type. ",
current.getId(), "\n")
for i in range(0, sedml.getNumModels()):
current = sedml.getModel(i)
if current.getLanguage() != 'urn:sedml:language:cellml.2_0':
print("\tEncountered unknown model format (" +
current.getLanguage() + ") for model: " +
current.getId())
continue # assume there are other useful models so continue?
# resolve the model file name
model_file = os.path.join(base_location, current.getSource())
model_tree = etree.parse(model_file)
# handle changes
for c in range(0, current.getNumChanges()):
change = current.getChange(c)
target = change.getTarget()
xmlns = get_xpath_namespaces(change)
if change.getTypeCode() == libsedml.SEDML_CHANGE_ATTRIBUTE:
new_value = change.getNewValue()
result = model_tree.xpath(target, namespaces=xmlns)
attribute = result[0]
attribute.getparent().attrib[
attribute.attrname] = new_value
else:
print("\tEncountered unknown model change for model: " +
current.getId())
continue # ignore for now...
# the final string representation of the model
model_string = str(etree.tostring(model_tree, pretty_print=True),
'utf-8')
# quick test to make sure we can use this model - should be removed.
parser = libcellml.Parser()
parser.parseModel(model_string)
if parser.errorCount():
for e in range(0, parser.errorCount()):
print(parser.error(e).description())
print(parser.error(e).referenceHeading())
else:
mId = current.getId()
self._models[mId] = {
'location': model_file,
'tree': model_tree,
'cellml': model_string
}
print_model(mId, self._models[mId])
for i in range(0, sedml.getNumTasks()):
current = sedml.getTask(i)
if current.getTypeCode() != libsedml.SEDML_TASK:
print("\tEncountered unknown task type: " +
libsedml.SedTypeCode_toString(current.getTypeCode()) +
"; for task: " + current.getId())
continue
tId = current.getId()
m = current.getModelReference()
s = current.getSimulationReference()
if not m in self._models:
print("\tEncountered a non-existing model reference: " + m +
"; for task: " + tId)
continue
if not s in self._simulations:
print("\tEncountered a non-existing simulation reference: " +
s + "; for task: " + tId)
continue
self._tasks[tId] = {'model': m, 'simulation': s}
print_task(tId, self._tasks[tId])
for i in range(0, sedml.getNumDataGenerators()):
current = sedml.getDataGenerator(i)
variables = {}
for v in range(0, current.getNumVariables()):
cv = current.getVariable(v)
t = cv.getTaskReference()
if not t in self._tasks:
print("\tEncountered a non-existing task reference: " + t +
"; for data generator: " + current.getId())
continue
xmlns = get_xpath_namespaces(cv)
model_tree = self._models[self._tasks[t]['model']]['tree']
variable_element = model_tree.xpath(cv.getTarget(),
namespaces=xmlns)[0]
variables[cv.getId()] = {
'name': variable_element.attrib['name'],
'component': variable_element.getparent().attrib['name'],
'task': t,
'array': -1,
'index': 0
}
dgId = current.getId()
self._data_generators[dgId] = {
'variables': variables,
'math': libsedml.formulaToString(current.getMath())
}
print_datagenerator(dgId, self._data_generators[dgId])
for i in range(0, sedml.getNumOutputs()):
current = sedml.getOutput(i)
tc = current.getTypeCode()
if tc == libsedml.SEDML_OUTPUT_REPORT:
r = current
dss = []
for d in range(0, r.getNumDataSets()):
ds = r.getDataSet(d)
label = ds.getLabel()
if label == '':
label = ds.getId()
dg = r.getDataReference()
if not dg in self._data_generators:
print(
"\tEncountered a non-existing dataGenerator reference: "
+ dg + "; for data set: " + ds.getId())
continue
dss.append({'label': label, 'dg': dg})
self._outputs[r.getId()] = {
'type': libsedml.SEDML_OUTPUT_REPORT,
'data-sets': dss
}
elif tc == libsedml.SEDML_OUTPUT_PLOT2D:
p = current
curves = []
for c in range(0, p.getNumCurves()):
curve = p.getCurve(c)
label = curve.getName()
if label == '':
label = curve.getId()
dgX = curve.getXDataReference()
if not dgX in self._data_generators:
print(
"\tEncountered a non-existing X dataGenerator reference: "
+ dgX + "; for curve: " + curve.getId())
continue
dgY = curve.getYDataReference()
if not dgY in self._data_generators:
print(
"\tEncountered a non-existing Y dataGenerator reference: "
+ dgY + "; for curve: " + curve.getId())
continue
curves.append({'label': label, 'dgX': dgX, 'dgY': dgY})
self._outputs[p.getId()] = {
'type': libsedml.SEDML_OUTPUT_PLOT2D,
'curves': curves
}
else:
print("\tEncountered unknown output ", current.getId(), "\n")
def generateDataLoop(sedmlDoc,
currentModel,
task1,
variablesList,
variablesDictionary,
repeatedTaskIndex,
repeatedTask=None,
dataGeneratorsList=None):
# Each dataGenerator is calculated from the resulting output
for s in range(0, sedmlDoc.getNumSimulations()):
currentSimulation = sedmlDoc.getSimulation(s)
if task1.getSimulationReference() == currentSimulation.getId():
break
# we found the simulation referred to by this task (can't be more than one)
dataGeneratorOutputList = []
dataGeneratorTemp = str()
for j in range(0, len(variablesDictionary)):
m = variablesDictionary[j]
current = sedmlDoc.getDataGenerator(m.datagenID)
dataGeneratorResult = libsedml.formulaToString(current.getMath())
if current.getId() == m.datagenID:
stringToReplace = m.sedmlID
position = m.sbmlID
for k in range(0, len(variablesList)):
if position == variablesList[k]:
position = k
break
if repeatedTaskIndex == -1:
taskId = task1.getId()
else:
taskId = repeatedTask.getId() + "_" + str(repeatedTaskIndex)
if currentSimulation.getTypeCode(
) == libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE:
tc = currentSimulation
totNumPoints = tc.getOutputEndTime() * tc.getNumberOfPoints(
) / (tc.getOutputEndTime() - tc.getOutputStartTime())
replacementString = taskId + "[" + str(
totNumPoints - currentSimulation.getNumberOfPoints()
) + ":," + str(position) + "]"
elif currentSimulation.getTypeCode(
) == libsedml.SEDML_SIMULATION_STEADYSTATE:
replacementString = taskId + "[0:," + str(position) + "]"
elif currentSimulation.getTypeCode(
) == libsedml.SEDML_SIMULATION_ONESTEP:
replacementString = taskId + "[0:," + str(position) + "]"
else:
print "# Unsupported type " + str(
currentSimulation.getTypeCode(
)) + " for simulation " + currentSimulation.getName()
if dataGeneratorResult != dataGeneratorTemp:
if stringToReplace in dataGeneratorResult:
dataGeneratorReplaced = dataGeneratorResult.replace(
stringToReplace, replacementString)
else:
dataGeneratorReplaced = stringToReplace.replace(
stringToReplace, replacementString)
dataGeneratorId = current.getId(
) # we expand the datagen id because they need to be flattened for repeated tasks
if repeatedTaskIndex != -1:
dataGeneratorId += "_" + str(repeatedTaskIndex)
dataGeneratorElement = dataGeneratorId + " = " + dataGeneratorReplaced
dataGeneratorOutputList.append(dataGeneratorElement)
dataGeneratorTemp = dataGeneratorResult
else:
dataGeneratorOutputList[-1] = dataGeneratorOutputList[
-1].replace(stringToReplace, replacementString)
if repeatedTaskIndex != -1: # list of data generators flattening (when part of a range)
position = -1
for i in range(0, len(dataGeneratorsList)):
rtdg = dataGeneratorsList[i]
if rtdg.datagenID == current.getId(): # already present
position = i
break
if position == -1: # create it
rtdg = MatchingSetsOfRepeatedTasksDataGenerators(
current.getId(), repeatedTaskIndex + 1)
dataGeneratorsList.append(rtdg)
else:
rtdg = MatchingSetsOfRepeatedTasksDataGenerators(
current.getId(), repeatedTaskIndex + 1)
dataGeneratorsList[position] = rtdg
dataGeneratorOutput = '\n'.join(dataGeneratorOutputList)
for k, v in mapping:
dataGeneratorOutput = dataGeneratorOutput.replace(k, v)
print dataGeneratorOutput
def generateDataLoop(sedmlDoc, currentModel, task1, variablesList, variablesDictionary, repeatedTaskIndex, repeatedTask = None, dataGeneratorsList = None):
# Each dataGenerator is calculated from the resulting output
for s in range(0, sedmlDoc.getNumSimulations()):
currentSimulation = sedmlDoc.getSimulation(s)
if task1.getSimulationReference() == currentSimulation.getId():
break; # we found the simulation referred to by this task (can't be more than one)
dataGeneratorOutputList = []
dataGeneratorTemp = str()
for j in range(0, len(variablesDictionary)):
m = variablesDictionary[j]
current = sedmlDoc.getDataGenerator(m.datagenID)
dataGeneratorResult = libsedml.formulaToString(current.getMath())
if current.getId() == m.datagenID:
stringToReplace = m.sedmlID
position = m.sbmlID
for k in range(0, len(variablesList)):
if position == variablesList[k]:
position = k
break
if repeatedTaskIndex == -1:
taskId = task1.getId()
else:
taskId = repeatedTask.getId() + "_" + str(repeatedTaskIndex)
if currentSimulation.getTypeCode() == libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE:
tc = currentSimulation
totNumPoints = tc.getOutputEndTime() * tc.getNumberOfPoints() / (tc.getOutputEndTime() - tc.getOutputStartTime())
replacementString = taskId + "[" + str(totNumPoints - currentSimulation.getNumberOfPoints()) + ":," + str(position) + "]"
elif currentSimulation.getTypeCode() == libsedml.SEDML_SIMULATION_STEADYSTATE:
replacementString = taskId + "[0:," + str(position) + "]"
elif currentSimulation.getTypeCode() == libsedml.SEDML_SIMULATION_ONESTEP:
replacementString = taskId + "[0:," + str(position) + "]"
else:
print "# Unsupported type " + str(currentSimulation.getTypeCode()) + " for simulation " + currentSimulation.getName()
if dataGeneratorResult != dataGeneratorTemp:
if stringToReplace in dataGeneratorResult:
dataGeneratorReplaced = dataGeneratorResult.replace(stringToReplace, replacementString)
else:
dataGeneratorReplaced = stringToReplace.replace(stringToReplace, replacementString)
dataGeneratorId = current.getId() # we expand the datagen id because they need to be flattened for repeated tasks
if repeatedTaskIndex != -1:
dataGeneratorId += "_" + str(repeatedTaskIndex)
dataGeneratorElement = dataGeneratorId + " = " + dataGeneratorReplaced
dataGeneratorOutputList.append(dataGeneratorElement)
dataGeneratorTemp = dataGeneratorResult
else:
dataGeneratorOutputList[-1] = dataGeneratorOutputList[-1].replace(stringToReplace, replacementString)
if repeatedTaskIndex != -1: # list of data generators flattening (when part of a range)
position = -1
for i in range(0, len(dataGeneratorsList)):
rtdg = dataGeneratorsList[i]
if rtdg.datagenID == current.getId(): # already present
position = i
break
if position == -1: # create it
rtdg = MatchingSetsOfRepeatedTasksDataGenerators(current.getId(), repeatedTaskIndex+1 )
dataGeneratorsList.append(rtdg)
else:
rtdg = MatchingSetsOfRepeatedTasksDataGenerators(current.getId(), repeatedTaskIndex+1 )
dataGeneratorsList[position] = rtdg
dataGeneratorOutput = '\n'.join(dataGeneratorOutputList)
for k, v in mapping:
dataGeneratorOutput = dataGeneratorOutput.replace(k, v)
print dataGeneratorOutput
almost_all_par_id = []
# check if parameter in data generators even exist + if not, write pd.Series(NaN)
all_observables = []
for iObservable in range(0, num_obs):
num_par_all = sedml_file.getDataGenerator(iObservable).getNumParameters()
all_observables.append(num_par_all)
if sum(all_observables) == 0:
for iNan in range(0, len(new_species)):
new_observables.append('NaN')
else:
for iObservable in range(0, num_obs): # each observable from data generator
# get important formula
obs_Formula = libsedml.formulaToString(sedml_file.getDataGenerator(iObservable).getMath())
obs_Id = sedml_file.getDataGenerator(iObservable).getId()
# SBML_model_Id,Observable_Id = obs_Id.split('_',1)
new_obs_Id = 'observable_' + obs_Id
# get list of parameters
list_par_id = []
list_par_value = []
num_par = sedml_file.getDataGenerator(iObservable).getNumParameters()
# get observable name
data_generator_name = sedml_file.getDataGenerator(iObservable).getName()
if num_par == 0: # parameter from each observable
print(iModel + '_' + iData + '_' + obs_Id + ' has no parameters as observables!')
new_observables.append(pd.Series('NaN'))
def main(args):
"""Usage: print_sedml input-filename
"""
if len(args) != 2:
print(main.__doc__)
sys.exit(1)
doc = libsedml.readSedML(args[1])
if (doc.getErrorLog().getNumFailsWithSeverity(libsedml.LIBSEDML_SEV_ERROR)
> 0):
print doc.getErrorLog().toString()
sys.exit(2)
print 'The document has {0}" simulation(s).'.format(
doc.getNumSimulations())
for i in range(0, doc.getNumSimulations()):
current = doc.getSimulation(i)
if (current.getTypeCode() ==
libsedml.SEDML_SIMULATION_UNIFORMTIMECOURSE):
tc = current
kisaoid = "none"
if tc.isSetAlgorithm():
kisaoid = tc.getAlgorithm().getKisaoID()
print "\tTimecourse id=", tc.getId(
), " start=", tc.getOutputStartTime(
), " end=", tc.getOutputEndTime(
), " numPoints=", tc.getNumberOfPoints(), " kisao=", kisaoid, "\n"
else:
print "\tUncountered unknown simulation. ", current.getId(), "\n"
print "\n"
print "The document has ", doc.getNumModels(), " model(s).", "\n"
for i in range(0, doc.getNumModels()):
current = doc.getModel(i)
print "\tModel id=", current.getId(
), " language=", current.getLanguage(), " source=", current.getSource(
), " numChanges=", current.getNumChanges(), "\n"
print "\n"
print "The document has ", doc.getNumTasks(), " task(s).", "\n"
for i in range(0, doc.getNumTasks()):
current = doc.getTask(i)
print "\tTask id=", current.getId(
), " model=", current.getModelReference(
), " sim=", current.getSimulationReference(), "\n"
print "\n"
print "The document has ", doc.getNumDataGenerators(
), " datagenerators(s).", "\n"
for i in range(0, doc.getNumDataGenerators()):
current = doc.getDataGenerator(i)
print "\tDG id=", current.getId(), " math=", libsedml.formulaToString(
current.getMath()), "\n"
print "\n"
print "The document has ", doc.getNumOutputs(), " output(s).", "\n"
for i in range(0, doc.getNumOutputs()):
current = doc.getOutput(i)
tc = current.getTypeCode()
if tc == libsedml.SEDML_OUTPUT_REPORT:
r = (current)
print "\tReport id=", current.getId(
), " numDataSets=", r.getNumDataSets(), "\n"
elif tc == libsedml.SEDML_OUTPUT_PLOT2D:
p = (current)
print "\tPlot2d id=", current.getId(
), " numCurves=", p.getNumCurves(), "\n"
elif tc == libsedml.SEDML_OUTPUT_PLOT3D:
p = (current)
print "\tPlot3d id=", current.getId(
), " numSurfaces=", p.getNumSurfaces(), "\n"
else:
print "\tEncountered unknown output ", current.getId(), "\n"