OrgSimProcessor

#!/usr/bin/python3
# Model Configuration
# Include standard modules
import argparse
import os  # directory navigation
import glob  # file search
import re  # re for partial name changes.
import fileinput  # file readin and replacement
from datetime import datetime
import pandas as pd

import shutil #moving files

from sys import argv
import fnmatch


def ModelConfiguration(
    workingFolder_config,
    sourceFolder_config,
    outputFolder_config,
    titleDetected,
    titleReplacement,
    phraseDetected,
    phraseReplacement,
    fileCompared1,
    fileCompared2,
):
    # File List, and command List

    # create parser
    # parser = argparse.ArgumentParser()

    # add arguments to the parser
    # parser.add_argument("sourceFolder")
    # parser.add_argument("workingFolder")
    # parser.add_argument("titleDetected")
    # parser.add_argument("titleReplacement")
    # parser.add_argument("phraseDetected")
    # parser.add_argument("phraseReplacement")
    # parser.add_argument("fileCompared1")
    # parser.add_argument("fileCompared2")

    # args = parser.parse_args()
    selection = 0

    while selection < 9:

        print("1. Transfer Files")
        print("2. Delete Files")
        print("3. Filename Change: " + titleDetected + " " + titleReplacement)
        print("4. Parameter Change: " + phraseDetected + " " + phraseReplacement)
        print(
            "5. Change Source and Working Folder: "
            + sourceFolder_config
            + " "
            + outputFolder_config
        )
        print("6. Working Folder Contents")
        print("7. Model Consistency: " + fileCompared1 + " " + fileCompared2)
        print("8. Annotation")
        print("9. Go back")

        selection = int(input())

        if selection == 1:

            print(
                "Source and Working Folder:"
                + sourceFolder_config
                + workingFolder_config
            )  # transfer files
            os.chdir(sourceFolder_config)
            if not os.path.exists(outputFolder_config):
                os.makedirs(outputFolder_config)
            for file in glob.glob("*.model"):
                shutil.copy(sourceFolder_config + file, outputFolder_config + file)
            print("Transfer completed")

        elif selection == 2:
            # Delete Files unfinished
            os.chdir(outputFolder_config)
            for file in glob.glob("*.model"):
                print(file)

        elif selection == 3:
            # Date/title change
            titleSelection = 0
            while titleSelection < 3:
                print("Rename Model Files")
                print("Output Folder: " + outputFolder_config)
                print("1. Process Title Change")
                print(
                    "2. Change Title to Detect and Replace: "
                    + titleDetected
                    + " "
                    + titleReplacement
                )
                print("3. Go back")

                titleSelection = int(input())
                if titleSelection == 1:
                    # process title change
                    os.chdir(outputFolder_config)
                    for file in glob.glob("*.model"):
                        titleAltered = re.sub(titleDetected, titleReplacement, file)
                        print("words" + titleDetected + " " + titleReplacement + " " + file + " " + titleAltered)
                        os.rename(file, titleAltered)
                    print("Title Change completed")
                elif titleSelection == 2:  # title replacement values
                    titleDetected, titleReplacement = input(
                        "Enter the title you wish to replace and its replacement title: "
                    ).split()

        elif selection == 4:
            # Parameter change
            parameterSelection = 0
            while parameterSelection < 5:
                print("Output Directory: " + outputFolder_config)
                print("1. Change Parameter")
                print("2. List Model File")
                print(
                    "3. Change Detected and Replacement Phrase: "
                    + phraseDetected
                    + " "
                    + phraseReplacement
                )
                print("4. Parameter Presence Check: " + phraseReplacement)
                print("5. Go back")

                parameterSelection = int(input())

                if parameterSelection == 1:  # change parameter
                    os.chdir(outputFolder_config)
                    for file in glob.glob("*.model"):
                        # Read in the file
                        with fileinput.FileInput(file, inplace = True, backup = '.bak' ) as file:
                            # Replace the target string
                            for line in file: 
                                print(line.replace(phraseDetected, phraseReplacement), end = '')

                elif parameterSelection == 2:  # list model file
                    fileSelected = input("Enter the file you want to look at: ")
                    for line in fileSelected:
                        print(line)

                elif parameterSelection == 3:  # change parameter to find and change
                    phraseDetected, phraseReplacement = input(
                        "Enter the parameterline you wish to replace and its replacement line: "
                    ).split()

                elif parameterSelection == 4:  # parameter presence check

                    print("Looking for " + phraseReplacement)
                    os.chdir(outputFolder_config)
                    for file in glob.glob("*.model"):
                        with open(file) as f:
                            if phraseReplacement in f.read():
                                print(file + "phrase found")
                            else:
                                print(file + "nothing found")

        elif selection == 5:
            # Folder change
            sourceFolder_config, workingFolder_config = input(
                "Enter your source and working folders: "
            ).split()

        elif selection == 6:  # List output folder contents
            print(os.listdir(outputFolder_config))
            print("Done listing folder contents")

        elif selection == 7:
            # Model consistency check
            print("Model file consistency Check")
            print("Files to be compared: " + fileCompared1 + fileCompared2)
            changeComparison = input(
                "Do you wish to change the file comparison? Y or N : "
            )

            if changeComparison == "Y":
                fileCompared1, fileCompared2 = input(
                    "Enter files you wish to compare: "
                ).split()


            os.chdir(outputFolder_config)

            # reading files
            f1 = open(fileCompared1, "r")
            f2 = open(fileCompared2, "r")

            i = 0

            for line1 in f1:
                i += 1

                for line2 in f2:

                    # matching line1 from both files
                    if line1 == line2:
                        # print IDENTICAL if similar
                        print("Line ", i, ": IDENTICAL")
                    else:
                        # print("Line ", i, ":")
                        # else print that line from both files
                        print("\tFile 1:", line1, end='')
                        print("\tFile 2:", line2, end='')
                    break

                    # closing files
            f1.close()
            f2.close()

        elif selection == 8:
            # Model Annotation
            os.chdir(outputFolder_config)


            fileAnnotation = open("annotation.txt", "a")
            annotation = input("Annotate the changes you are making: ")
            now = datetime.now()
            dt_string = now.strftime("%d/%m/%Y %H:%M:%S")
            combinedAnnotation = dt_string + annotation
            fileAnnotation.writelines(combinedAnnotation)
            fileAnnotation.close()


# Parameter File Restructure Agnostic


def SimCommandGenerator(outputFolder_config):

    selection = 0
    while selection < 3:
        print("Generate Command List ")
        print("1. Generate List")
        print("2. Change working folder" + outputFolder_config)
        print("3. Go back")

        selection = int(input())
        if selection == 1:
            # process title change
            os.chdir(outputFolder_config)
            print("test")
            print(outputFolder_config)

            j = 0
            k = 0
            frozenList = []
            dynamicList = []

            for file in glob.glob("*.model"):
                dynamicflag = 0
                choppedfile = file[13:]  # remove parameterlist
                if choppedfile[0] == "_":
                    dynamicflag = 1
                    choppedfile = choppedfile.split(
                        "_"
                    )  # remove _ in those that need it
                    choppedfile = choppedfile[1]

                choppedfile_datesettingextension = choppedfile.split(".")  # remove .model
                choppedfile_datesetting = choppedfile_datesettingextension[0]
                choppedfile_date = choppedfile_datesetting[0:6]
                print(choppedfile_date)
                # chunk size
                #n = 6

                #chunks = [choppedfile2[i : i + n] for i in range(0, len(choppedfile2), n)]

                if dynamicflag == 0:
                    frozenEntry = "sbatch mersimCommandScriptRemote.sh ./parameterfiles/{1}/parameterlist{0}.model StandardSteadyStateWUSGradient01272A.init results{0} {0}".format(choppedfile_datesetting, choppedfile_date)
                    frozenList.append(frozenEntry)
                    j = j + 1
                    

                else:
                    dynamicEntry = "sbatch mersimCommandScriptRemote.sh ./parameterfiles/{1}/parameterlist_{0}.model StandardSteadyStateWUSGradientEmpty.init results{0} {0}".format(choppedfile_datesetting, choppedfile_date)
                    dynamicList.append(dynamicEntry)
                    k = k + 1
            if j > 0:
                   for entry in frozenList:
                        print(entry)
            if k > 0:
                   for entry in dynamicList:
                        print(entry)

        elif selection == 2:
            outputFolder_config = input("Enter the folder you want to look at: ")

        else:
            print("blah")
            print(selection)
            break

import csv


def SeriesGenerator(outputFolder_series):

    selection = 0
    
    while selection < 4:
        print("1. Process Raw Results Files into Series Files")
        print("2. Change output folder" + outputFolder_series)
        print("3. Go back")

        selection = int(input())
        os.chdir(workingFolder_config)

        titleline = "x y z radius WUSRNA WUSNuc_WS WUSCyto CLV3Sig1 CLV3_Peptide StochasticTimeOverFlow CLV3Sig2 MarkerOverFlow Monomer Dimer MonomerMarker DimerMarker ckReceptor ckLigand ckComplex WExport neighbors?"

        for file in glob.glob("results*"): #will process and overwrite all results files
            #print(file)  
            #print(os.getcwd())
            os.chdir(workingFolder_config)
            with open(file,'r') as sourcefile:
                 lines = sourcefile.readlines()

            seriesFileCount = 1
            lineCount = 2 # to skip beginning lines of result file

            choppedname = file[7:19]  # remove results and date from input file to create a destination folder
            
            path = outputFolder_series + "wtresults" + choppedname + "/"

            if os.path.exists(path) == False:
                os.mkdir(path)


            while seriesFileCount < 100:
                print(file)
                print(lineCount)



                if seriesFileCount < 10:
                    seriesFileName = "pararesults00" + str(seriesFileCount) + ".csv"

                elif seriesFileCount == 10 or seriesFileCount < 100:
                    seriesFileName = "pararesults0" + str(seriesFileCount) + ".csv"
                 
                os.chdir(path)

                with open(seriesFileName,'w') as writefile:
                    writefile.write(titleline + "\n")
                    for line in lines[lineCount:(lineCount + 1366)]:
                        writefile.write(line)
                

                os.chdir(outputFolder_series)
                lineCount = lineCount + 1366 + 2 #remove section header 
                seriesFileCount = seriesFileCount + 1
             
            shutil.move(workingFolder_config + file, outputFolder_series + file)



def ParaviewLoader(
    date_paraview,
    inputFolder_paraview,
    clv3aMax,
    clv3bMax,
    clv3pMax,
    dimerMax,
    monomerMax,
    wusCMax,
    wusNMax,
    wusRMax,
):

    # Alters Pic taking scripts with rescaling factors and date

    # Prep for image taking

    clv3ARescale = "RescaleTransferFunction(0.0" + clv3aMax + ")"

    clv3BRescale = "RescaleTransferFunction(0.0" + clv3bMax + ")"

    clv3PRescale = "RescaleTransferFunction(0.0" + clv3pMax + ")"

    dimerRescale = "RescaleTransferFunction(0.0" + dimerMax + ")"

    monomerRescale = "RescaleTransferFunction(0.0" + monomerMax + ")"

    wusCRescale = "RescaleTransferFunction(0.0" + wusCMax + ")"

    wusNRescale = "RescaleTransferFunction(0.0" + wusNMax + ")"

    wusRRescale = "RescaleTransferFunction(0.0" + wusRMax + ")"

    inputfile = "paraviewAutoM7.py"

    # Read in the file
    with open(inputfile, "r") as file:
        filedata = file.read()

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 1.0)", clv3ARescale)

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 2.0)", clv3BRescale)

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 3.0)", clv3PRescale)

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 4.0)", dimerRescale)

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 5.0)", monomerRescale)

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 6.0)", wusCRescale)

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 7.0)", wusNRescale)

    # Replace the target string
    filedata = filedata.replace("RescaleTransferFunction(0.0, 8.0)", wusRRescale)

    for file in inputFolder_paraview:

        if fnmatch.fnmatch(file, "date_paraview*"):
            modelName = file[0:5]
            modelDate = file[6:11]

            # Read in the file
            with open(inputfile, "r") as file:
                filedata = file.read()

            # Replace the target string
            filedata = filedata.replace("021121DcTrWt", modelName + modelDate)
            filedata = filedata.replace("021121FcAcWt", modelName + modelDate)

            outputfile = "paraviewAutoM7Temp.py"

            # Write the file out again
            with open(outputfile, "w+") as file:
                file.write(filedata)

            os.system("pvpython paraviewAutoM7Temp.py")


def Grapher(datemodel, sourceFolder_graph, outputFolder_graph, speciesGraphList):

    os.chdir(sourceFolder_graph)
    for file in glob.glob("datemodel*"):

        choppedname = file[0:5]  # remove results and date

        if choppedname == "FcAcWt":
            outputFile = "FWT.csv"

        elif choppedname == "FcAcMd":
            outputFile = "FMD.csv"

        elif choppedname == "FcAcM4":
            outputFile = "FM4.csv"

        elif choppedname == "FcAcTm":
            outputFile = "FTM.csv"

        elif choppedname == "FcAc9i":
            outputFile = "F9I.csv"

        elif choppedname == "FcAc5i":
            outputFile = "F5I.csv"

        elif choppedname == "FcAc5i":
            outputFile = "FMI.csv"

        elif choppedname == "FcAcCm":
            outputFile = "FCM.csv"

        if choppedname == "DcTrWt":
            outputFile = "DWT.csv"

        elif choppedname == "DcTrMd":
            outputFile = "DMD.csv"

        elif choppedname == "DcTrM4":
            outputFile = "DM4.csv"

        elif choppedname == "DcTrTm":
            outputFile = "DTM.csv"

        elif choppedname == "DcTr9i":
            outputFile = "D9I.csv"

        elif choppedname == "DcTr5i":
            outputFile = "D5I.csv"

        elif choppedname == "DcTr5i":
            outputFile = "DMI.csv"

        elif choppedname == "DcTrCm":
            outputFile = "DCM.csv"

        else:
            print("invalid name")

        modelName = datemodel + choppedName

        os.rename(
            workingFolder + "/" + modelName + "/" + "pararesults099.csv",
            outputFolder_graph + outputFile,
        )

        outputFolder_graph_quoted = '"' + outputFolder_graph + '"'

        if speciesGraph == 1:
            os.system("Rscript --vanilla ./clv3Graph.R " + outputFolder_graph_quoted)
        # os.system("Rscript --vanilla ./clv3Graph.R "./Results/Raw_DataFiles/results$2" "./Results/Raw_DataFiles/wtresults$2"")










configFile = pd.read_csv("mersimconfig", sep=": ", engine = 'python')

workingFolder_config = configFile.iat[0, 1]
sourceFolder_config = configFile.iat[1, 1]
outputFolder_config = configFile.iat[2, 1]
titleDetected = configFile.iat[3, 1]
titleReplacement = configFile.iat[4, 1]
phraseDetected = configFile.iat[5, 1]
phraseReplacement = configFile.iat[6, 1]
fileCompared1 = configFile.iat[7, 1]
fileCompared2 = configFile.iat[8, 1]

outputFolder_series = configFile.iat[9, 1]

datemodel = configFile.iat[10, 1]
inputFolder_paraview = configFile.iat[11, 1]
clv3aMax = configFile.iat[12, 1]
clv3bMax = configFile.iat[13, 1]
clv3pMax = configFile.iat[14, 1]
monomerMax = configFile.iat[15, 1]
dimerMax = configFile.iat[16, 1]
wusCMax = configFile.iat[17, 1]
wusNMax = configFile.iat[18, 1]
wusRMax = configFile.iat[19, 1]

sourceFolder_graph = configFile.iat[20, 1]
outputFolder_graph = configFile.iat[21, 1]
speciesGraphList = configFile.iat[22, 1]

selection = 0


while selection < 6:

    print("1. ModelConfiguration")
    print("2. Simulation Command Generator")
    print("3. Time Series Generation")
    print("4. Paraview Loader")
    print("5. Grapher")

    selection = int(input())
    os.chdir(workingFolder_config)

    if selection == 1:
        ModelConfiguration(
            workingFolder_config,
            sourceFolder_config,
            outputFolder_config,
            titleDetected,
            titleReplacement,
            phraseDetected,
            phraseReplacement,
            fileCompared1,
            fileCompared2,
        )

    elif selection == 2:
        SimCommandGenerator(outputFolder_config)

    elif selection == 3:
        SeriesGenerator(outputFolder_series)

    elif selection == 4:
        ParaviewLoader(
            date_paraview,
            inputFolder_paraview,
            clv3aMax,
            clv3bMax,
            clv3pMax,
            dimerMax,
            monomerMax,
            wusCMax,
            wusNMax,
            wusRMax,
        )

    elif selection == 5:
        Grapher(datemodel, sourceFolder_graph, outputFolder_graph, speciesGraphList)