<reponame>cjarmstrong97/PyBioNetGen<filename>bionetgen/atomizer/writer/bnglWriter.py
#!/usr/bin/env python

# import sys
# from importlib import reload
# reload(sys)
# sys.setdefaultencoding("ISO-8859-1")

import re
from copy import deepcopy
from bionetgen.atomizer.utils.util import logMess
import string

try:
    # 3.0.0 and above
    from pyparsing import pyparsing_common

    csl = pyparsing_common.comma_separated_list
except ImportError:
    # below 3.0.0
    from pyparsing import commaSeparatedList as csl
import pyparsing
from itertools import dropwhile

# import StringIO
from io import StringIO
import pyparsing as pyp


def evaluatePiecewiseFunction(function):
    pass


def bnglReaction(
    reactant,
    product,
    rate,
    tags,
    translator=[],
    isCompartments=False,
    reversible=True,
    comment="",
    reactionName=None,
):
    finalString = ""
    # if translator != []:
    #    translator = balanceTranslator(reactant,product,translator)
    if len(reactant) == 0 or (len(reactant) == 1 and reactant[0][1] == 0):
        finalString += "0 "
    for index in range(0, len(reactant)):
        tag = ""
        if reactant[index][2] in tags and isCompartments:
            tag = tags[reactant[index][2]]
        translated = printTranslate(reactant[index], tag, translator)
        finalString += translated
        if index < len(reactant) - 1:
            finalString += " + "

    if reversible:
        finalString += " <-> "
    else:
        finalString += " -> "
    if len(product) == 0:
        finalString += "0 "

    for index in range(0, len(product)):
        tag = ""
        if isCompartments:
            if len(product[index]) > 2 and product[index][2] in tags:
                tag = tags[product[index][2]]
        translated = printTranslate(product[index], tag, translator)

        finalString += translated
        if index < len(product) - 1:
            finalString += " + "
    finalString += " " + rate + " " + comment
    finalString = re.sub(r"(\W|^)0\(\)", "0", finalString)
    if reactionName:
        finalString = "{0}: {1}".format(reactionName, finalString)
    return finalString


def printTranslate(chemical, tags, translator={}):
    tmp = []
    if chemical[0] not in translator:
        app = chemical[0] + "()" + tags
    else:
        translator[chemical[0]].addCompartment(tags)
        app = str(translator[chemical[0]])
    if float(int(chemical[1])) == chemical[1]:
        for item in range(0, int(chemical[1])):
            tmp.append(app)
    else:
        idx = logMess(
            "ERROR:SIM205",
            "Cannot deal with non integer stoicheometries: {0}* {1}".format(
                chemical[1], chemical[0]
            ),
        )
        tmp.append(app)
    return " + ".join(tmp)


def balanceTranslator(reactant, product, translator):
    rMolecules = []
    pMolecules = []
    newTranslator = {}
    for species in reactant:
        if species[0] in translator:
            newTranslator[species[0]] = deepcopy(translator[species[0]])
            rMolecules.extend(newTranslator[species[0]].molecules)
    for species in product:
        if species[0] in translator:
            newTranslator[species[0]] = deepcopy(translator[species[0]])
            pMolecules.extend(newTranslator[species[0]].molecules)

    for rMolecule in rMolecules:
        for pMolecule in pMolecules:
            if rMolecule.name == pMolecule.name:
                overFlowingComponents = [
                    x
                    for x in rMolecule.components
                    if x.name not in [y.name for y in pMolecule.components]
                ]
                overFlowingComponents.extend(
                    [
                        x
                        for x in pMolecule.components
                        if x.name not in [y.name for y in rMolecule.components]
                    ]
                )
                rMolecule.removeComponents(overFlowingComponents)
                pMolecule.removeComponents(overFlowingComponents)
    return newTranslator


def rindex(lst, item):
    """
    returns the last ocurrence of an element in alist
    """
    try:
        return next(dropwhile(lambda x: lst[x] != item, reversed(range(len(lst)))))
    except StopIteration:
        raise ValueError("rindex(lst, item): item not in list")


def bnglFunction(
    rule, functionTitle, reactants, compartments=[], parameterDict={}, reactionDict={}
):
    def powParse(match):
        if match.group(1) == "root":
            exponent = "(1/%s)" % match.group(3)
        else:
            exponent = match.group(3)
        if match.group(1) in ["root", "pow"]:
            operator = "^"
        return "({0}){1}({2})".format(match.group(2), operator, exponent)

    def compParse(match):
        translator = {
            "gt": ">",
            "lt": "<",
            "and": "&&",
            "or": "||",
            "geq": ">=",
            "leq": "<=",
            "eq": "==",
            "neq": "!=",
        }
        exponent = match.group(3)
        operator = translator[match.group(1)]
        return "{0} {1} {2}".format(match.group(2), operator, exponent)

    def ceilfloorParse(math):
        flag = False
        if math.group(1) == "ceil":
            flag = True
        if flag:
            return "min(rint({0}+0.5),rint({0} + 1))".format(math.group(2))
        else:
            return "min(rint({0}-0.5),rint({0}+0.5))".format(math.group(2))

    def parameterRewrite(match):
        return match.group(1) + "param_" + match.group(2) + match.group(3)

    def constructFromList(argList, optionList):
        parsedString = ""
        idx = 0
        translator = {
            "gt": ">",
            "lt": "<",
            "and": "&&",
            "or": "||",
            "geq": ">=",
            "leq": "<=",
            "eq": "==",
        }
        while idx < len(argList):
            if type(argList[idx]) is list:
                parsedString += "(" + constructFromList(argList[idx], optionList) + ")"
            elif argList[idx] in optionList:
                if argList[idx] == "ceil":
                    parsedString += "min(rint(({0}) + 0.5),rint(({0}) + 1))".format(
                        constructFromList(argList[idx + 1], optionList)
                    )
                    idx += 1
                elif argList[idx] == "floor":
                    parsedString += "min(rint(({0}) -0.5),rint(({0}) + 0.5))".format(
                        constructFromList(argList[idx + 1], optionList)
                    )
                    idx += 1
                elif argList[idx] in ["pow"]:
                    index = rindex(argList[idx + 1], ",")
                    parsedString += (
                        "(("
                        + constructFromList(argList[idx + 1][0:index], optionList)
                        + ")"
                    )
                    parsedString += (
                        " ^ "
                        + "("
                        + constructFromList(argList[idx + 1][index + 1 :], optionList)
                        + "))"
                    )
                    idx += 1
                elif argList[idx] in ["sqr", "sqrt"]:
                    tag = "1/" if argList[idx] == "sqrt" else ""
                    parsedString += (
                        "(("
                        + constructFromList(argList[idx + 1], optionList)
                        + ") ^ ({0}2))".format(tag)
                    )
                    idx += 1
                elif argList[idx] == "root":
                    index = rindex(argList[idx + 1], ",")
                    tmp = (
                        "1/("
                        + constructFromList(argList[idx + 1][0:index], optionList)
                        + "))"
                    )
                    parsedString += (
                        "(("
                        + constructFromList(argList[idx + 1][index + 1 :], optionList)
                        + ") ^ "
                        + tmp
                    )
                    idx += 1
                elif argList[idx] == "piecewise":
                    index1 = argList[idx + 1].index(",")
                    try:
                        index2 = argList[idx + 1][index1 + 1 :].index(",") + index1 + 1
                        try:
                            index3 = (
                                argList[idx + 1][index2 + 1 :].index(",") + index2 + 1
                            )
                        except ValueError:
                            index3 = -1
                    except ValueError:
                        parsedString += constructFromList(
                            [argList[idx + 1][index1 + 1 :]], optionList
                        )
                        index2 = -1
                    if index2 != -1:
                        condition = constructFromList(
                            [argList[idx + 1][index1 + 1 : index2]], optionList
                        )
                        result = constructFromList(
                            [argList[idx + 1][:index1]], optionList
                        )
                        if index3 == -1:
                            result2 = constructFromList(
                                [argList[idx + 1][index2 + 1 :]], optionList
                            )
                        else:
                            result2 = constructFromList(
                                ["piecewise", argList[idx + 1][index2 + 1 :]],
                                optionList,
                            )
                        parsedString += "if({0},{1},{2})".format(
                            condition, result, result2
                        )
                    idx += 1
                elif argList[idx] in ["and", "or"]:
                    symbolDict = {"and": " && ", "or": " || "}
                    indexArray = [-1]
                    elementArray = []
                    for idx2, element in enumerate(argList[idx + 1]):
                        if element == ",":
                            indexArray.append(idx2)
                    indexArray.append(len(argList[idx + 1]))
                    tmpStr = argList[idx + 1]
                    for idx2, _ in enumerate(indexArray[0:-1]):
                        elementArray.append(
                            constructFromList(
                                tmpStr[indexArray[idx2] + 1 : indexArray[idx2 + 1]],
                                optionList,
                            )
                        )
                    parsedString += symbolDict[argList[idx]].join(elementArray)
                    idx += 1
                elif argList[idx] == "lambda":

                    tmp = "("
                    # ASS2019 - I'm not sure if this is an actual solution or
                    # this should just never happen. argList[idx+1] sometimes
                    # returns _only_ ['0'] and thus the following call fails with
                    # ValueError. Not sure if the list is built wrong or this
                    # result is not handled correctly. Either way, this, for now,
                    # skirts the issue.
                    try:
                        upperLimit = rindex(argList[idx + 1], ",")
                    except ValueError:
                        idx += 1
                        continue
                    parsedParams = []
                    for x in argList[idx + 1][0:upperLimit]:
                        if x == ",":
                            tmp += ", "
                        else:
                            tmp += "param_" + x
                            parsedParams.append(x)

                    # tmp = ''.join([x for x in constructFromList(argList[idx+1][0:upperLimit])])
                    tmp2 = ") = " + constructFromList(
                        argList[idx + 1][rindex(argList[idx + 1], ",") + 1 :],
                        optionList,
                    )
                    for x in parsedParams:
                        while re.search(r"(\W|^)({0})(\W|$)".format(x), tmp2) != None:
                            tmp2 = re.sub(
                                r"(\W|^)({0})(\W|$)".format(x), r"\1param_\2 \3", tmp2
                            )
                    idx += 1
                    parsedString += tmp + tmp2
            else:
                parsedString += argList[idx]
            idx += 1
        return parsedString

    def changeToBNGL(functionList, rule, function):
        oldrule = ""
        # if the rule contains any mathematical function we need to reformat
        while any(
            [
                re.search(r"(\W|^)({0})(\W|$)".format(x), rule) != None
                for x in functionList
            ]
        ) and (oldrule != rule):
            oldrule = rule
            for x in functionList:
                rule = re.sub("({0})\(([^,]+),([^)]+)\)".format(x), function, rule)
            if rule == oldrule:
                logMess("ERROR:TRS001", "Malformed pow or root function %s" % rule)
                print("meep")
        return rule

    # rule = changeToBNGL(['pow','root'],rule,powParse)
    rule = changeToBNGL(["gt", "lt", "leq", "geq", "eq"], rule, compParse)
    # rule = changeToBNGL(['and','or'],rule,compParse)
    flag = True
    contentRule = (
        pyparsing.Word(pyparsing.alphanums + "_")
        | ","
        | "."
        | "+"
        | "-"
        | "*"
        | "/"
        | "^"
        | "&"
        | ">"
        | "<"
        | "="
        | "|"
    )
    parens = pyparsing.nestedExpr("(", ")", content=contentRule)
    finalString = ""
    # remove ceil,floor

    if any(
        [
            re.search(r"(\W|^)({0})(\W|$)".format(x), rule) != None
            for x in ["ceil", "floor", "pow", "sqrt", "sqr", "root", "and", "or"]
        ]
    ):
        argList = parens.parseString("(" + rule + ")").asList()
        rule = constructFromList(
            argList[0], ["floor", "ceil", "pow", "sqrt", "sqr", "root", "and", "or"]
        )

    while "piecewise" in rule:
        argList = parens.parseString("(" + rule + ")").asList()
        rule = constructFromList(argList[0], ["piecewise"])
    # remove references to lambda functions
    if "lambda(" in rule:
        lambdaList = parens.parseString("(" + rule + ")")
        functionBody = constructFromList(lambdaList[0].asList(), ["lambda"])
        flag = False
        rule = "{0}{1}".format(functionTitle, functionBody)

    tmp = rule
    # delete the compartment from the rate function since cBNGL already does it
    # this is not true as seen by the test
    for compartment in compartments:
        # if len(reactants) < 2:
        #    tmp = re.sub('^{0}\s*[*]'.format(compartment[0]),'',tmp)
        #    tmp = re.sub('([*]\s*{0})$'.format(compartment[0]),'',tmp)

        if compartment[0] in tmp:
            tmp = re.sub(
                r"(\W|^)({0})(\W|$)".format(compartment[0]),
                r"\1 {0} \3".format(str(compartment[1])),
                tmp,
            )
            # tmp = re.sub(r'(\W)({0})(\W)'.format(compartment[0]),r'\1%s\3' % str(compartment[1]),tmp)
            # logMess('INFO:MSC005','Exchanging reference to compartment %s for its dimensions' % compartment[0])

    # change references to time for time()
    # tmp =re.sub(r'(\W|^)(time)(\W|$)',r'\1time()\3',tmp)
    # tmp =re.sub(r'(\W|^)(Time)(\W|$)',r'\1time()\3',tmp)
    while re.search(r"(\W|^)inf(\W|$)", tmp) != None:
        tmp = re.sub(r"(\W|^)(inf)(\W|$)", r"\1 1e20 \3", tmp)
    # BNGL has ^ for power.
    if flag:
        finalString = "%s = %s" % (functionTitle, tmp)
    else:
        finalString = tmp
    # change references to local parameters
    for parameter in parameterDict:
        finalString = re.sub(
            r"(\W|^)({0})(\W|$)".format(parameter),
            r"\g<1>{0}\g<3>".format(parameterDict[parameter]),
            finalString,
        )
    # change references to reaction Id's to their netflux equivalent
    for reaction in reactionDict:
        if reaction in finalString:
            finalString = re.sub(
                r"(\W|^)({0})(\W|$)".format(reaction),
                r"\g<1>{0}\g<3>".format(reactionDict[reaction]),
                finalString,
            )

    # combinations '+ -' break ibonetgen
    finalString = re.sub(r"(\W|^)([-])(\s)+", r"\1-", finalString)
    # changing reference of 't' to time()
    # finalString = re.sub(r'(\W|^)(t)(\W|$)',r'\1time()\3',finalString)
    # pi
    finalString = re.sub(r"(\W|^)(pi)(\W|$)", r"\g<1>3.1415926535\g<3>", finalString)
    # print(reactants,finalString)
    # log for log 10
    finalString = re.sub(r"(\W|^)log\(", r"\1 ln(", finalString)
    # reserved keyword: e
    finalString = re.sub(r"(\W|^)(e)(\W|$)", r"\g<1>__e__\g<3>", finalString)
    # changing ceil
    # avoiding variables whose name starts with a number

    # removing mass-action elements

    tmp = finalString

    # print(finalString,reactants)
    # for reactant in reactants:
    #    finalString = re.sub(r'(\W|^)({0}\s+\*)'.format(reactant[0]),r'\1',finalString)
    #    finalString = re.sub(r'(\W|^)(\*\s+{0}(\s|$))'.format(reactant[0]),r'\1',finalString)
    # print(finalString)

    # if finalString != tmp:
    #    logMess('WARNING','Removed mass action elements from )
    return finalString


def curateParameters(param):
    """
    The objective of this function is to remove elements extraneous to bionetgen
    """
    for element in range(0, len(param)):
        tmp = param[element]
        while re.search(r"(\W|^)inf(\W|$)", tmp) != None:
            tmp = re.sub(r"(\W|^)(inf)(\W|$)", r"\g<1>1e20\g<3>", tmp)
        param[element] = tmp
    return param


def finalText(
    comments,
    param,
    molecules,
    species,
    observables,
    rules,
    functions,
    compartments,
    annotations,
    fileName,
):
    # output = open(fileName,'w')
    output = StringIO()
    # output.write(comments.decode('ascii','ignore'))
    output.write(comments)
    output.write("begin model\n")
    param = curateParameters(param)
    output.write(sectionTemplate("parameters", param))
    if len(compartments) > 0:
        output.write(sectionTemplate("compartments", compartments))
    output.write(
        sectionTemplate("molecule types", molecules, annotations["moleculeTypes"])
    )
    output.write(sectionTemplate("seed species", species))
    output.write(sectionTemplate("observables", observables))
    if len(functions) > 0:
        output.write(sectionTemplate("functions", functions))
    output.write(sectionTemplate("reaction rules", rules))
    output.write("end model\n")
    # output.write('generate_network({overwrite=>1})\n')
    # output.write('simulate({method=>"ode",t_end=>100,n_steps=>100})')
    # output.write('writeXML()\n')
    # with open(fileName,'w') as outputFile:
    #    outputFile.write(output.getvalue())
    # output.close()

    return output.getvalue()


def sectionTemplate(name, content, annotations={}):
    section = "begin %s\n" % name
    temp = []
    for line in content:
        if line in annotations:
            for ann in annotations[line]:
                temp.append("\t%s\n" % ann)
        temp.append("\t%s\n" % line)
    # temp = ['\t%s\n' % line for line in content]
    section += "".join(temp)
    section += "end %s\n" % name
    return section


# 341,6,12


def extendFunction(function, subfunctionName, subfunction):
    def constructFromList(argList, optionList, subfunctionParam, subfunctionBody):
        parsedString = ""
        idx = 0
        while idx < len(argList):
            if type(argList[idx]) is list:
                parsedString += (
                    "("
                    + constructFromList(
                        argList[idx], optionList, subfunctionParam, subfunctionBody
                    )
                    + ")"
                )
            elif argList[idx] in optionList:
                tmp = subfunctionBody
                commaIndexes = [0]
                commaIndexes.extend(
                    [i for i, x in enumerate(argList[idx + 1]) if x == ","]
                )
                commaIndexes.append(len(argList[idx + 1]))
                instancedParameters = [
                    argList[idx + 1][commaIndexes[i] : commaIndexes[i + 1]]
                    for i in range(0, len(commaIndexes) - 1)
                ]
                for parameter, instance in zip(subfunctionParam, instancedParameters):
                    if "," in instance:
                        instance.remove(",")
                    parsedParameter = (
                        " ( "
                        + constructFromList(
                            instance, optionList, subfunctionParam, subfunctionBody
                        )
                        + " ) "
                    )
                    tmp = re.sub(
                        r"(\W|^)({0})(\W|$)".format(parameter.strip()),
                        r"\1{0} \3".format(parsedParameter),
                        tmp,
                    )
                parsedString += " " + tmp + " "
                idx += 1
            else:
                if argList[idx] == "=":
                    parsedString += " " + argList[idx] + " "
                else:
                    parsedString += argList[idx]
            idx += 1
        return parsedString

    param = subfunction.split(" = ")[0][len(subfunctionName) + 1 : -1]
    # ASS2019: There are cases where the fuction doesn't have a definition and the
    # following line errors out with IndexError, let's handle it.
    try:
        body = subfunction.split(" = ")[1]
    except IndexError as e:
        logMess(
            "ERROR:TRS002",
            "This function doesn't have a definition, note that atomizer doesn't allow for function linking: {}".format(
                subfunction
            ),
        )
        raise e
    while (
        re.search(r"(\W|^){0}\([^)]*\)(\W|$)".format(subfunctionName), function) != None
    ):
        contentRule = (
            pyparsing.Word(pyparsing.alphanums + "_.")
            | ","
            | "+"
            | "-"
            | "*"
            | "/"
            | "^"
            | "&"
            | ">"
            | "<"
            | "="
            | "|"
        )
        parens = pyparsing.nestedExpr("(", ")", content=contentRule)
        subfunctionList = parens.parseString("(" + function + ")").asList()
        function = constructFromList(
            subfunctionList[0], [subfunctionName], param.split(","), body
        )
    return function

#!/usr/bin/env python

# import sys
# from importlib import reload
# reload(sys)
# sys.setdefaultencoding("ISO-8859-1")

import re
from copy import deepcopy
from bionetgen.atomizer.utils.util import logMess
import string

try:
    # 3.0.0 and above
    from pyparsing import pyparsing_common

    csl = pyparsing_common.comma_separated_list
except ImportError:
    # below 3.0.0
    from pyparsing import commaSeparatedList as csl
import pyparsing
from itertools import dropwhile

# import StringIO
from io import StringIO
import pyparsing as pyp


def evaluatePiecewiseFunction(function):
    pass


def bnglReaction(
    reactant,
    product,
    rate,
    tags,
    translator=[],
    isCompartments=False,
    reversible=True,
    comment="",
    reactionName=None,
):
    finalString = ""
    # if translator != []:
    #    translator = balanceTranslator(reactant,product,translator)
    if len(reactant) == 0 or (len(reactant) == 1 and reactant[0][1] == 0):
        finalString += "0 "
    for index in range(0, len(reactant)):
        tag = ""
        if reactant[index][2] in tags and isCompartments:
            tag = tags[reactant[index][2]]
        translated = printTranslate(reactant[index], tag, translator)
        finalString += translated
        if index < len(reactant) - 1:
            finalString += " + "

    if reversible:
        finalString += " <-> "
    else:
        finalString += " -> "
    if len(product) == 0:
        finalString += "0 "

    for index in range(0, len(product)):
        tag = ""
        if isCompartments:
            if len(product[index]) > 2 and product[index][2] in tags:
                tag = tags[product[index][2]]
        translated = printTranslate(product[index], tag, translator)

        finalString += translated
        if index < len(product) - 1:
            finalString += " + "
    finalString += " " + rate + " " + comment
    finalString = re.sub(r"(\W|^)0\(\)", "0", finalString)
    if reactionName:
        finalString = "{0}: {1}".format(reactionName, finalString)
    return finalString


def printTranslate(chemical, tags, translator={}):
    tmp = []
    if chemical[0] not in translator:
        app = chemical[0] + "()" + tags
    else:
        translator[chemical[0]].addCompartment(tags)
        app = str(translator[chemical[0]])
    if float(int(chemical[1])) == chemical[1]:
        for item in range(0, int(chemical[1])):
            tmp.append(app)
    else:
        idx = logMess(
            "ERROR:SIM205",
            "Cannot deal with non integer stoicheometries: {0}* {1}".format(
                chemical[1], chemical[0]
            ),
        )
        tmp.append(app)
    return " + ".join(tmp)


def balanceTranslator(reactant, product, translator):
    rMolecules = []
    pMolecules = []
    newTranslator = {}
    for species in reactant:
        if species[0] in translator:
            newTranslator[species[0]] = deepcopy(translator[species[0]])
            rMolecules.extend(newTranslator[species[0]].molecules)
    for species in product:
        if species[0] in translator:
            newTranslator[species[0]] = deepcopy(translator[species[0]])
            pMolecules.extend(newTranslator[species[0]].molecules)

    for rMolecule in rMolecules:
        for pMolecule in pMolecules:
            if rMolecule.name == pMolecule.name:
                overFlowingComponents = [
                    x
                    for x in rMolecule.components
                    if x.name not in [y.name for y in pMolecule.components]
                ]
                overFlowingComponents.extend(
                    [
                        x
                        for x in pMolecule.components
                        if x.name not in [y.name for y in rMolecule.components]
                    ]
                )
                rMolecule.removeComponents(overFlowingComponents)
                pMolecule.removeComponents(overFlowingComponents)
    return newTranslator


def rindex(lst, item):
    """
    returns the last ocurrence of an element in alist
    """
    try:
        return next(dropwhile(lambda x: lst[x] != item, reversed(range(len(lst)))))
    except StopIteration:
        raise ValueError("rindex(lst, item): item not in list")


def bnglFunction(
    rule, functionTitle, reactants, compartments=[], parameterDict={}, reactionDict={}
):
    def powParse(match):
        if match.group(1) == "root":
            exponent = "(1/%s)" % match.group(3)
        else:
            exponent = match.group(3)
        if match.group(1) in ["root", "pow"]:
            operator = "^"
        return "({0}){1}({2})".format(match.group(2), operator, exponent)

    def compParse(match):
        translator = {
            "gt": ">",
            "lt": "<",
            "and": "&&",
            "or": "||",
            "geq": ">=",
            "leq": "<=",
            "eq": "==",
            "neq": "!=",
        }
        exponent = match.group(3)
        operator = translator[match.group(1)]
        return "{0} {1} {2}".format(match.group(2), operator, exponent)

    def ceilfloorParse(math):
        flag = False
        if math.group(1) == "ceil":
            flag = True
        if flag:
            return "min(rint({0}+0.5),rint({0} + 1))".format(math.group(2))
        else:
            return "min(rint({0}-0.5),rint({0}+0.5))".format(math.group(2))

    def parameterRewrite(match):
        return match.group(1) + "param_" + match.group(2) + match.group(3)

    def constructFromList(argList, optionList):
        parsedString = ""
        idx = 0
        translator = {
            "gt": ">",
            "lt": "<",
            "and": "&&",
            "or": "||",
            "geq": ">=",
            "leq": "<=",
            "eq": "==",
        }
        while idx < len(argList):
            if type(argList[idx]) is list:
                parsedString += "(" + constructFromList(argList[idx], optionList) + ")"
            elif argList[idx] in optionList:
                if argList[idx] == "ceil":
                    parsedString += "min(rint(({0}) + 0.5),rint(({0}) + 1))".format(
                        constructFromList(argList[idx + 1], optionList)
                    )
                    idx += 1
                elif argList[idx] == "floor":
                    parsedString += "min(rint(({0}) -0.5),rint(({0}) + 0.5))".format(
                        constructFromList(argList[idx + 1], optionList)
                    )
                    idx += 1
                elif argList[idx] in ["pow"]:
                    index = rindex(argList[idx + 1], ",")
                    parsedString += (
                        "(("
                        + constructFromList(argList[idx + 1][0:index], optionList)
                        + ")"
                    )
                    parsedString += (
                        " ^ "
                        + "("
                        + constructFromList(argList[idx + 1][index + 1 :], optionList)
                        + "))"
                    )
                    idx += 1
                elif argList[idx] in ["sqr", "sqrt"]:
                    tag = "1/" if argList[idx] == "sqrt" else ""
                    parsedString += (
                        "(("
                        + constructFromList(argList[idx + 1], optionList)
                        + ") ^ ({0}2))".format(tag)
                    )
                    idx += 1
                elif argList[idx] == "root":
                    index = rindex(argList[idx + 1], ",")
                    tmp = (
                        "1/("
                        + constructFromList(argList[idx + 1][0:index], optionList)
                        + "))"
                    )
                    parsedString += (
                        "(("
                        + constructFromList(argList[idx + 1][index + 1 :], optionList)
                        + ") ^ "
                        + tmp
                    )
                    idx += 1
                elif argList[idx] == "piecewise":
                    index1 = argList[idx + 1].index(",")
                    try:
                        index2 = argList[idx + 1][index1 + 1 :].index(",") + index1 + 1
                        try:
                            index3 = (
                                argList[idx + 1][index2 + 1 :].index(",") + index2 + 1
                            )
                        except ValueError:
                            index3 = -1
                    except ValueError:
                        parsedString += constructFromList(
                            [argList[idx + 1][index1 + 1 :]], optionList
                        )
                        index2 = -1
                    if index2 != -1:
                        condition = constructFromList(
                            [argList[idx + 1][index1 + 1 : index2]], optionList
                        )
                        result = constructFromList(
                            [argList[idx + 1][:index1]], optionList
                        )
                        if index3 == -1:
                            result2 = constructFromList(
                                [argList[idx + 1][index2 + 1 :]], optionList
                            )
                        else:
                            result2 = constructFromList(
                                ["piecewise", argList[idx + 1][index2 + 1 :]],
                                optionList,
                            )
                        parsedString += "if({0},{1},{2})".format(
                            condition, result, result2
                        )
                    idx += 1
                elif argList[idx] in ["and", "or"]:
                    symbolDict = {"and": " && ", "or": " || "}
                    indexArray = [-1]
                    elementArray = []
                    for idx2, element in enumerate(argList[idx + 1]):
                        if element == ",":
                            indexArray.append(idx2)
                    indexArray.append(len(argList[idx + 1]))
                    tmpStr = argList[idx + 1]
                    for idx2, _ in enumerate(indexArray[0:-1]):
                        elementArray.append(
                            constructFromList(
                                tmpStr[indexArray[idx2] + 1 : indexArray[idx2 + 1]],
                                optionList,
                            )
                        )
                    parsedString += symbolDict[argList[idx]].join(elementArray)
                    idx += 1
                elif argList[idx] == "lambda":

                    tmp = "("
                    # ASS2019 - I'm not sure if this is an actual solution or
                    # this should just never happen. argList[idx+1] sometimes
                    # returns _only_ ['0'] and thus the following call fails with
                    # ValueError. Not sure if the list is built wrong or this
                    # result is not handled correctly. Either way, this, for now,
                    # skirts the issue.
                    try:
                        upperLimit = rindex(argList[idx + 1], ",")
                    except ValueError:
                        idx += 1
                        continue
                    parsedParams = []
                    for x in argList[idx + 1][0:upperLimit]:
                        if x == ",":
                            tmp += ", "
                        else:
                            tmp += "param_" + x
                            parsedParams.append(x)

                    # tmp = ''.join([x for x in constructFromList(argList[idx+1][0:upperLimit])])
                    tmp2 = ") = " + constructFromList(
                        argList[idx + 1][rindex(argList[idx + 1], ",") + 1 :],
                        optionList,
                    )
                    for x in parsedParams:
                        while re.search(r"(\W|^)({0})(\W|$)".format(x), tmp2) != None:
                            tmp2 = re.sub(
                                r"(\W|^)({0})(\W|$)".format(x), r"\1param_\2 \3", tmp2
                            )
                    idx += 1
                    parsedString += tmp + tmp2
            else:
                parsedString += argList[idx]
            idx += 1
        return parsedString

    def changeToBNGL(functionList, rule, function):
        oldrule = ""
        # if the rule contains any mathematical function we need to reformat
        while any(
            [
                re.search(r"(\W|^)({0})(\W|$)".format(x), rule) != None
                for x in functionList
            ]
        ) and (oldrule != rule):
            oldrule = rule
            for x in functionList:
                rule = re.sub("({0})\(([^,]+),([^)]+)\)".format(x), function, rule)
            if rule == oldrule:
                logMess("ERROR:TRS001", "Malformed pow or root function %s" % rule)
                print("meep")
        return rule

    # rule = changeToBNGL(['pow','root'],rule,powParse)
    rule = changeToBNGL(["gt", "lt", "leq", "geq", "eq"], rule, compParse)
    # rule = changeToBNGL(['and','or'],rule,compParse)
    flag = True
    contentRule = (
        pyparsing.Word(pyparsing.alphanums + "_")
        | ","
        | "."
        | "+"
        | "-"
        | "*"
        | "/"
        | "^"
        | "&"
        | ">"
        | "<"
        | "="
        | "|"
    )
    parens = pyparsing.nestedExpr("(", ")", content=contentRule)
    finalString = ""
    # remove ceil,floor

    if any(
        [
            re.search(r"(\W|^)({0})(\W|$)".format(x), rule) != None
            for x in ["ceil", "floor", "pow", "sqrt", "sqr", "root", "and", "or"]
        ]
    ):
        argList = parens.parseString("(" + rule + ")").asList()
        rule = constructFromList(
            argList[0], ["floor", "ceil", "pow", "sqrt", "sqr", "root", "and", "or"]
        )

    while "piecewise" in rule:
        argList = parens.parseString("(" + rule + ")").asList()
        rule = constructFromList(argList[0], ["piecewise"])
    # remove references to lambda functions
    if "lambda(" in rule:
        lambdaList = parens.parseString("(" + rule + ")")
        functionBody = constructFromList(lambdaList[0].asList(), ["lambda"])
        flag = False
        rule = "{0}{1}".format(functionTitle, functionBody)

    tmp = rule
    # delete the compartment from the rate function since cBNGL already does it
    # this is not true as seen by the test
    for compartment in compartments:
        # if len(reactants) < 2:
        #    tmp = re.sub('^{0}\s*[*]'.format(compartment[0]),'',tmp)
        #    tmp = re.sub('([*]\s*{0})$'.format(compartment[0]),'',tmp)

        if compartment[0] in tmp:
            tmp = re.sub(
                r"(\W|^)({0})(\W|$)".format(compartment[0]),
                r"\1 {0} \3".format(str(compartment[1])),
                tmp,
            )
            # tmp = re.sub(r'(\W)({0})(\W)'.format(compartment[0]),r'\1%s\3' % str(compartment[1]),tmp)
            # logMess('INFO:MSC005','Exchanging reference to compartment %s for its dimensions' % compartment[0])

    # change references to time for time()
    # tmp =re.sub(r'(\W|^)(time)(\W|$)',r'\1time()\3',tmp)
    # tmp =re.sub(r'(\W|^)(Time)(\W|$)',r'\1time()\3',tmp)
    while re.search(r"(\W|^)inf(\W|$)", tmp) != None:
        tmp = re.sub(r"(\W|^)(inf)(\W|$)", r"\1 1e20 \3", tmp)
    # BNGL has ^ for power.
    if flag:
        finalString = "%s = %s" % (functionTitle, tmp)
    else:
        finalString = tmp
    # change references to local parameters
    for parameter in parameterDict:
        finalString = re.sub(
            r"(\W|^)({0})(\W|$)".format(parameter),
            r"\g<1>{0}\g<3>".format(parameterDict[parameter]),
            finalString,
        )
    # change references to reaction Id's to their netflux equivalent
    for reaction in reactionDict:
        if reaction in finalString:
            finalString = re.sub(
                r"(\W|^)({0})(\W|$)".format(reaction),
                r"\g<1>{0}\g<3>".format(reactionDict[reaction]),
                finalString,
            )

    # combinations '+ -' break ibonetgen
    finalString = re.sub(r"(\W|^)([-])(\s)+", r"\1-", finalString)
    # changing reference of 't' to time()
    # finalString = re.sub(r'(\W|^)(t)(\W|$)',r'\1time()\3',finalString)
    # pi
    finalString = re.sub(r"(\W|^)(pi)(\W|$)", r"\g<1>3.1415926535\g<3>", finalString)
    # print(reactants,finalString)
    # log for log 10
    finalString = re.sub(r"(\W|^)log\(", r"\1 ln(", finalString)
    # reserved keyword: e
    finalString = re.sub(r"(\W|^)(e)(\W|$)", r"\g<1>__e__\g<3>", finalString)
    # changing ceil
    # avoiding variables whose name starts with a number

    # removing mass-action elements

    tmp = finalString

    # print(finalString,reactants)
    # for reactant in reactants:
    #    finalString = re.sub(r'(\W|^)({0}\s+\*)'.format(reactant[0]),r'\1',finalString)
    #    finalString = re.sub(r'(\W|^)(\*\s+{0}(\s|$))'.format(reactant[0]),r'\1',finalString)
    # print(finalString)

    # if finalString != tmp:
    #    logMess('WARNING','Removed mass action elements from )
    return finalString


def curateParameters(param):
    """
    The objective of this function is to remove elements extraneous to bionetgen
    """
    for element in range(0, len(param)):
        tmp = param[element]
        while re.search(r"(\W|^)inf(\W|$)", tmp) != None:
            tmp = re.sub(r"(\W|^)(inf)(\W|$)", r"\g<1>1e20\g<3>", tmp)
        param[element] = tmp
    return param


def finalText(
    comments,
    param,
    molecules,
    species,
    observables,
    rules,
    functions,
    compartments,
    annotations,
    fileName,
):
    # output = open(fileName,'w')
    output = StringIO()
    # output.write(comments.decode('ascii','ignore'))
    output.write(comments)
    output.write("begin model\n")
    param = curateParameters(param)
    output.write(sectionTemplate("parameters", param))
    if len(compartments) > 0:
        output.write(sectionTemplate("compartments", compartments))
    output.write(
        sectionTemplate("molecule types", molecules, annotations["moleculeTypes"])
    )
    output.write(sectionTemplate("seed species", species))
    output.write(sectionTemplate("observables", observables))
    if len(functions) > 0:
        output.write(sectionTemplate("functions", functions))
    output.write(sectionTemplate("reaction rules", rules))
    output.write("end model\n")
    # output.write('generate_network({overwrite=>1})\n')
    # output.write('simulate({method=>"ode",t_end=>100,n_steps=>100})')
    # output.write('writeXML()\n')
    # with open(fileName,'w') as outputFile:
    #    outputFile.write(output.getvalue())
    # output.close()

    return output.getvalue()


def sectionTemplate(name, content, annotations={}):
    section = "begin %s\n" % name
    temp = []
    for line in content:
        if line in annotations:
            for ann in annotations[line]:
                temp.append("\t%s\n" % ann)
        temp.append("\t%s\n" % line)
    # temp = ['\t%s\n' % line for line in content]
    section += "".join(temp)
    section += "end %s\n" % name
    return section


# 341,6,12


def extendFunction(function, subfunctionName, subfunction):
    def constructFromList(argList, optionList, subfunctionParam, subfunctionBody):
        parsedString = ""
        idx = 0
        while idx < len(argList):
            if type(argList[idx]) is list:
                parsedString += (
                    "("
                    + constructFromList(
                        argList[idx], optionList, subfunctionParam, subfunctionBody
                    )
                    + ")"
                )
            elif argList[idx] in optionList:
                tmp = subfunctionBody
                commaIndexes = [0]
                commaIndexes.extend(
                    [i for i, x in enumerate(argList[idx + 1]) if x == ","]
                )
                commaIndexes.append(len(argList[idx + 1]))
                instancedParameters = [
                    argList[idx + 1][commaIndexes[i] : commaIndexes[i + 1]]
                    for i in range(0, len(commaIndexes) - 1)
                ]
                for parameter, instance in zip(subfunctionParam, instancedParameters):
                    if "," in instance:
                        instance.remove(",")
                    parsedParameter = (
                        " ( "
                        + constructFromList(
                            instance, optionList, subfunctionParam, subfunctionBody
                        )
                        + " ) "
                    )
                    tmp = re.sub(
                        r"(\W|^)({0})(\W|$)".format(parameter.strip()),
                        r"\1{0} \3".format(parsedParameter),
                        tmp,
                    )
                parsedString += " " + tmp + " "
                idx += 1
            else:
                if argList[idx] == "=":
                    parsedString += " " + argList[idx] + " "
                else:
                    parsedString += argList[idx]
            idx += 1
        return parsedString

    param = subfunction.split(" = ")[0][len(subfunctionName) + 1 : -1]
    # ASS2019: There are cases where the fuction doesn't have a definition and the
    # following line errors out with IndexError, let's handle it.
    try:
        body = subfunction.split(" = ")[1]
    except IndexError as e:
        logMess(
            "ERROR:TRS002",
            "This function doesn't have a definition, note that atomizer doesn't allow for function linking: {}".format(
                subfunction
            ),
        )
        raise e
    while (
        re.search(r"(\W|^){0}\([^)]*\)(\W|$)".format(subfunctionName), function) != None
    ):
        contentRule = (
            pyparsing.Word(pyparsing.alphanums + "_.")
            | ","
            | "+"
            | "-"
            | "*"
            | "/"
            | "^"
            | "&"
            | ">"
            | "<"
            | "="
            | "|"
        )
        parens = pyparsing.nestedExpr("(", ")", content=contentRule)
        subfunctionList = parens.parseString("(" + function + ")").asList()
        function = constructFromList(
            subfunctionList[0], [subfunctionName], param.split(","), body
        )
    return function
#!/usr/bin/env python # import sys # from importlib import reload # reload(sys) # sys.setdefaultencoding("ISO-8859-1") # 3.0.0 and above # below 3.0.0 # import StringIO # if translator != []: #    translator = balanceTranslator(reactant,product,translator) returns the last ocurrence of an element in alist # ASS2019 - I'm not sure if this is an actual solution or # this should just never happen. argList[idx+1] sometimes # returns _only_ ['0'] and thus the following call fails with # ValueError. Not sure if the list is built wrong or this # result is not handled correctly. Either way, this, for now, # skirts the issue. # tmp = ''.join([x for x in constructFromList(argList[idx+1][0:upperLimit])]) # if the rule contains any mathematical function we need to reformat # rule = changeToBNGL(['pow','root'],rule,powParse) # rule = changeToBNGL(['and','or'],rule,compParse) # remove ceil,floor # remove references to lambda functions # delete the compartment from the rate function since cBNGL already does it # this is not true as seen by the test # if len(reactants) < 2: #    tmp = re.sub('^{0}\s*[*]'.format(compartment[0]),'',tmp) #    tmp = re.sub('([*]\s*{0})$'.format(compartment[0]),'',tmp) # tmp = re.sub(r'(\W)({0})(\W)'.format(compartment[0]),r'\1%s\3' % str(compartment[1]),tmp) # logMess('INFO:MSC005','Exchanging reference to compartment %s for its dimensions' % compartment[0]) # change references to time for time() # tmp =re.sub(r'(\W|^)(time)(\W|$)',r'\1time()\3',tmp) # tmp =re.sub(r'(\W|^)(Time)(\W|$)',r'\1time()\3',tmp) # BNGL has ^ for power. # change references to local parameters # change references to reaction Id's to their netflux equivalent # combinations '+ -' break ibonetgen # changing reference of 't' to time() # finalString = re.sub(r'(\W|^)(t)(\W|$)',r'\1time()\3',finalString) # pi # print(reactants,finalString) # log for log 10 # reserved keyword: e # changing ceil # avoiding variables whose name starts with a number # removing mass-action elements # print(finalString,reactants) # for reactant in reactants: #    finalString = re.sub(r'(\W|^)({0}\s+\*)'.format(reactant[0]),r'\1',finalString) #    finalString = re.sub(r'(\W|^)(\*\s+{0}(\s|$))'.format(reactant[0]),r'\1',finalString) # print(finalString) # if finalString != tmp: #    logMess('WARNING','Removed mass action elements from ) The objective of this function is to remove elements extraneous to bionetgen # output = open(fileName,'w') # output.write(comments.decode('ascii','ignore')) # output.write('generate_network({overwrite=>1})\n') # output.write('simulate({method=>"ode",t_end=>100,n_steps=>100})') # output.write('writeXML()\n') # with open(fileName,'w') as outputFile: #    outputFile.write(output.getvalue()) # output.close() # temp = ['\t%s\n' % line for line in content] # 341,6,12 # ASS2019: There are cases where the fuction doesn't have a definition and the # following line errors out with IndexError, let's handle it.