# Path: tellurium/utils/omex.py
# MANIFEST_PATTERN = "manifest.xml"
# METADAT_PATTERN = "metadata.*"
# class Entry(object):
# class Creator(object):
#     def __init__(self, location, format=None, formatKey=None, master=False, description=None, creators=None):
#     def __str__(self):
#     def __init__(self, givenName, familyName, organization, email):
# def combineArchiveFromDirectory(directory, omexPath, creators=None, creators_for_all=False):
# def combineArchiveFromEntries(omexPath, entries, workingDir):
# def addEntriesToCombineArchive(omexPath, entries, workingDir):
# def _addEntriesToArchive(omexPath, entries, workingDir, add_entries):
# def extractCombineArchive(omexPath, directory, method="zip"):
# def getLocationsByFormat(omexPath, formatKey=None, method="omex"):
# def listContents(omexPath, method="omex"):
# def printContents(omexPath):
# 
# Path: tellurium/sedml/mathml.py
# def evaluableMathML(astnode, variables={}, array=False):
#     """ Create evaluable python string.
# 
#     """
#     # replace variables with provided values
#     for key, value in variables.items():
#         astnode.replaceArgument(key, libsbml.parseFormula(str(value)))
# 
#     # get formula
#     formula = libsbml.formulaToL3String(astnode)
# 
#     # <replacements>
#     # FIXME: these are not exhaustive, but are improved with examples
#     if array is False:
#         # scalar
#         formula = formula.replace("&&", 'and')
#         formula = formula.replace("||", 'or')
#     else:
#         # np.array
#         formula = formula.replace("max", 'np.nanmax')
#         formula = formula.replace("min", 'np.nanmin')
#         formula = formula.replace("sum", 'np.nansum')
#         formula = formula.replace("product", 'np.prod')
# 
#     return formula


import sys
import platform
import tempfile
import shutil
import traceback
import os.path
import warnings
import datetime
import zipfile
import re
import numpy as np
import jinja2
    import libsedml
    import tesedml as libsedml
import tellurium as te
    import pandas
    import matplotlib.pyplot as plt
    import mpl_toolkits.mplot3d
                    import os
    import os
    import matplotlib
from collections import namedtuple
from tellurium.utils import omex
from .mathml import evaluableMathML
        from tellurium.sedml.data import DataDescriptionParser
                from xml.etree import ElementTree
    from tellurium.tests.testdata import SEDML_TEST_DIR, OMEX_TEST_DIR
    :return: generated python code
    """
    factory = SEDMLCodeFactory(inputStr, workingDir=workingDir)
    return factory.toPython()


def executeSEDML(inputStr, workingDir=None):
    """ Run a SED-ML file or combine archive with results.

    If a workingDir is provided the files and results are written in the workingDir.

    :param inputStr:
    :type inputStr:
    :return:
    :rtype:
    """
    # execute the sedml
    factory = SEDMLCodeFactory(inputStr, workingDir=workingDir)
    factory.executePython()


def combineArchiveToPython(omexPath):
    """ All python code generated from given combine archive.

    :param omexPath:
    :return: dictionary of { sedml_location: pycode }
    """
    tmp_dir = tempfile.mkdtemp()
    pycode = {}
    try:

# Path: tellurium/utils/omex.py
# MANIFEST_PATTERN = "manifest.xml"
# METADAT_PATTERN = "metadata.*"
# class Entry(object):
# class Creator(object):
#     def __init__(self, location, format=None, formatKey=None, master=False, description=None, creators=None):
#     def __str__(self):
#     def __init__(self, givenName, familyName, organization, email):
# def combineArchiveFromDirectory(directory, omexPath, creators=None, creators_for_all=False):
# def combineArchiveFromEntries(omexPath, entries, workingDir):
# def addEntriesToCombineArchive(omexPath, entries, workingDir):
# def _addEntriesToArchive(omexPath, entries, workingDir, add_entries):
# def extractCombineArchive(omexPath, directory, method="zip"):
# def getLocationsByFormat(omexPath, formatKey=None, method="omex"):
# def listContents(omexPath, method="omex"):
# def printContents(omexPath):
# 
# Path: tellurium/sedml/mathml.py
# def evaluableMathML(astnode, variables={}, array=False):
#     """ Create evaluable python string.
# 
#     """
#     # replace variables with provided values
#     for key, value in variables.items():
#         astnode.replaceArgument(key, libsbml.parseFormula(str(value)))
# 
#     # get formula
#     formula = libsbml.formulaToL3String(astnode)
# 
#     # <replacements>
#     # FIXME: these are not exhaustive, but are improved with examples
#     if array is False:
#         # scalar
#         formula = formula.replace("&&", 'and')
#         formula = formula.replace("||", 'or')
#     else:
#         # np.array
#         formula = formula.replace("max", 'np.nanmax')
#         formula = formula.replace("min", 'np.nanmin')
#         formula = formula.replace("sum", 'np.nansum')
#         formula = formula.replace("product", 'np.prod')
# 
#     return formula


# Path: tellurium/sedml/tesedml.py
import sys
import platform
import tempfile
import shutil
import traceback
import os.path
import warnings
import datetime
import zipfile
import re
import numpy as np
import jinja2
    import libsedml
    import tesedml as libsedml
import tellurium as te
    import pandas
    import matplotlib.pyplot as plt
    import mpl_toolkits.mplot3d
                    import os
    import os
    import matplotlib
from collections import namedtuple
from tellurium.utils import omex
from .mathml import evaluableMathML
        from tellurium.sedml.data import DataDescriptionParser
                from xml.etree import ElementTree
    from tellurium.tests.testdata import SEDML_TEST_DIR, OMEX_TEST_DIR

    :return: generated python code
    """
    factory = SEDMLCodeFactory(inputStr, workingDir=workingDir)
    return factory.toPython()


def executeSEDML(inputStr, workingDir=None):
    """ Run a SED-ML file or combine archive with results.

    If a workingDir is provided the files and results are written in the workingDir.

    :param inputStr:
    :type inputStr:
    :return:
    :rtype:
    """
    # execute the sedml
    factory = SEDMLCodeFactory(inputStr, workingDir=workingDir)
    factory.executePython()


def combineArchiveToPython(omexPath):
    """ All python code generated from given combine archive.

    :param omexPath:
    :return: dictionary of { sedml_location: pycode }
    """
    tmp_dir = tempfile.mkdtemp()
    pycode = {}
    try:

        omex.extractCombineArchive(omexPath, directory=tmp_dir, method="zip")