amici.import_utils.SBMLexception

[PHvanLent]

Hi AMICI developers,

I am trying to compile a model using amici.assignmentRules2observables with a spline interpolation on some observable.

import amici
import pandas as pd
import libsbml
import numpy as np

domain=np.array([0.0, 5.0, 10.0, 15.0, 20.0, 30.0, 60.0, 90.0, 150.0, 180.0, 220.0, 250.0, 300.0, 350.0, 400.0])
drange=np.array([0.09436668 0.20660086 0.32938346 0.39271404 0.46033645 0.43051466
 0.38017434 0.31141232 0.22630089 0.18609768 0.14751637 0.12343035
 0.10829366 0.09658453 0.09436668])

spline = amici.splines.CubicHermiteSpline(
    sbml_id="ECglucose",
    evaluate_at=amici.sbml_utils.amici_time_symbol,  # the spline function is evaluated at the current time point
    nodes=domain,
    values_at_nodes=drange,)

spline.add_to_sbml_model(sbml_model)

libsbml.writeSBMLToFile(sbml_model.getSBMLDocument(),
                        f"models/manual_implementations/sbml_export/{model_name_spline}.xml")`

When I try to load this and run

sbml_file = f"{sbml_file_dir}/{model_name_spline}.xml"
# Create an SbmlImporter instance for our SBML model
sbml_importer = amici.SbmlImporter(sbml_file)

# Retrieve model output names and formulae from AssignmentRules and remove the respective rules
observables = amici.assignmentRules2observables(
    sbml_importer.sbml,  # the libsbml model object
    filter_function=lambda variable: variable.getId() == "ECglucose")

I receive the error

amici.import_utils.SBMLException: AMICI can not parse piecewise/event trigger functions with argument lt(time, 5).

Do you have an idea what I can do to solve this?

Best,

Paul

[dweindl]

Hi @PHvanLent, after modifying the example a bit, I was able to reproduce the issue. It is fixed in #2652. Thanks for reporting.

Reproducer

import libsbml
import numpy as np
import amici.sbml_utils
import amici.splines

sbml_doc = libsbml.SBMLDocument()
sbml_model = sbml_doc.createModel()
p = sbml_model.createParameter()
p.setId("ECglucose")
p.setConstant(False)


domain=np.array([0.0, 5.0, 10.0, 15.0, 20.0, 30.0, 60.0, 90.0, 150.0, 180.0, 220.0, 250.0, 300.0, 350.0, 400.0])
drange=np.array([0.09436668, 0.20660086, 0.32938346, 0.39271404, 0.46033645, 0.43051466,
 0.38017434, 0.31141232, 0.22630089, 0.18609768, 0.14751637, 0.12343035,
 0.10829366, 0.09658453, 0.09436668])

spline = amici.splines.CubicHermiteSpline(
    sbml_id="ECglucose",
    evaluate_at=amici.sbml_utils.amici_time_symbol,
    nodes=domain,
    values_at_nodes=drange,)

spline.add_to_sbml_model(sbml_model)

sbml_importer = amici.SbmlImporter(sbml_model)

observables = amici.assignmentRules2observables(
    sbml_importer.sbml,  # the libsbml model object
    filter_function=lambda variable: variable.getId() == "ECglucose")

sbml_importer.sbml2amici("gh2651", observables=observables)

EDIT: After #2652 is merged, you can install the latest unreleased version with pip3 install -e git+https://github.com/AMICI-dev/amici.git@develop#egg=amici\&subdirectory=python/sdist.