

In [1]:

    
from __future__ import print_function
import os
import importlib
import tellurium
import matplotlib

tellurium.setDefaultPlottingEngine("matplotlib")
# tellurium.setDefaultPlottingEngine("plotly")

outputDir = "./__tellurium__"
if not os.path.exists(outputDir):
    os.makedirs(outputDir)

omex_dir = "./omex"
archives = [f for f in os.listdir(omex_dir) if os.path.isfile(os.path.join(omex_dir, f))]
f_archives = [os.path.join(omex_dir, archive) for archive in archives]

if False:
    for f in f_archives:
        print("*" * 80)
        print(f)
        print("*" * 80)
        dgs = tellurium.executeCombineArchive(f, printPython=False, outputDir=outputDir, saveOutputs=True)
    
dgs = tellurium.executeCombineArchive("./omex/L1V3_parameter-scan-2d.omex", printPython=True, outputDir=outputDir, saveOutputs=True)









    











    



"""
####################################################################################################
                            tellurium 2.0.2
-+++++++++++++++++-         Python Environment for Modeling and Simulating Biological Systems
 .+++++++++++++++.
  .+++++++++++++.           Homepage:      http://tellurium.analogmachine.org/
-//++++++++++++/.   -:/-`   Documentation: https://tellurium.readthedocs.io/en/latest/index.html
.----:+++++++/.++  .++++/   Forum:         https://groups.google.com/forum/#!forum/tellurium-discuss
      :+++++:  .+:` .--++   Bug reports:   https://github.com/sys-bio/tellurium/issues
       -+++-    ./+:-://.   Repository:    https://github.com/sys-bio/tellurium
        .+.       `...`

SED-ML simulation experiments: http://www.sed-ml.org/
    sedmlDoc: L1V3  
    inputType:      'SEDML_FILE'
    workingDir:     '/tmp/tmp28bgsq9i'
    saveOutputs:    'True'
    outputDir:      './__tellurium__'
    plottingEngine: '<MatplotlibEngine>'

Linux-4.10.0-35-generic-x86_64-with-Ubuntu-16.04-xenial
python 3.6.2 (default, Jul 20 2017, 08:43:29) 
[GCC 5.4.1 20170519]
####################################################################################################
"""
import tellurium as te
from roadrunner import Config
from tellurium.sedml.mathml import *
# from tellurium.sedml.tesedml import process_trace, terminate_trace, fix_endpoints

import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d
try:
    import tesedml as libsedml
except ImportError:
    import libsedml
import pandas
import os.path
Config.LOADSBMLOPTIONS_RECOMPILE = True

workingDir = r'/tmp/tmp28bgsq9i'

# --------------------------------------------------------
# Models
# --------------------------------------------------------
# Model <model1>
model1 = te.loadSBMLModel(os.path.join(workingDir, 'BorisEJB.xml'))




# --------------------------------------------------------
# Tasks
# --------------------------------------------------------
# Task <task0>
# not part of any DataGenerator: task0
# Task <task1>

task1 = []
__range__current = [1.0, 5.0, 10.0, 50.0, 60.0, 70.0, 80.0, 90.0, 100.0]
for __k__current, __value__current in enumerate(__range__current):
    if __k__current == 0:
        model1.reset()
    
    task2 = []
    __range__current1 = np.linspace(start=1.0, stop=40.0, num=101)
    for __k__current1, __value__current1 in enumerate(__range__current1):
        if __k__current1 == 0:
            model1.reset()
        # Task: <task0>
        task0 = [None]
        model1.setSteadyStateSolver('nleq')
        if model1.conservedMoietyAnalysis == False: model1.conservedMoietyAnalysis = True
        model1['J1_KK2'] = __value__current
        model1['J4_KK5'] = __value__current1
        model1.steadyStateSelections = ['J1_KK2', 'J4_KK5', '[MKK]', '[MKK_PP]', '[MKK_P]']
        model1.simulate()
        task0[0] = model1.steadyStateNamedArray()

        task2.extend(task0)

    task1.extend(task2)
# Task <task2>
# not part of any DataGenerator: task2

####################################################################################################






    



---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-1-a11f3de60387> in <module>()
     23         dgs = tellurium.executeCombineArchive(f, printPython=False, outputDir=outputDir, saveOutputs=True)
     24 
---> 25 dgs = tellurium.executeCombineArchive("./omex/L1V3_parameter-scan-2d.omex", printPython=True, outputDir=outputDir, saveOutputs=True)

~/git/tellurium/tellurium/sedml/tesedml.py in executeCombineArchive(omexPath, workingDir, printPython, createOutputs, saveOutputs, outputDir, plottingEngine)
    353                     print(code)
    354 
--> 355                 results[sedmlFile] = factory.executePython()
    356 
    357             return results

~/git/tellurium/tellurium/sedml/tesedml.py in executePython(self)
    509             for dg in self.doc.getListOfDataGenerators():
    510                 dg_id = dg.getId()
--> 511                 dg_data[dg_id] = symbols[dg_id]
    512             result['dataGenerators'] = dg_data
    513             return result

KeyError: 'J4_KK5_1'

Combine Archives