How to use getSD method in autotest

Best Python code snippet using autotest_python

Task_1.py

Source:Task_1.py

1import CarRental2import datetime3import re4monthName = ['January', 'February', 'March', 'April', 'May', 'June', 'July', 'August', 'September', 'October',5             'November', 'December']6#modifying date format function7def modifyDate(entry):8    # We will be modifying:9    # 1)The date of birth of each object10    flag = 011    object = re.search(r"[-/][0-9]*[-/]", entry.getDob(),re.M | re.S)  # if the date has the format of "/digit/" or "-digit-" it should be modified12    if object:13        replaceString = monthName[int(object.group()[1:len(object.group()) - 1]) - 1]  # the replace string is the monthName element indexed by the digit14        entry.setDob(re.sub(r"[-/][0-9]*[-/]", " " + replaceString + " ", entry.getDob()))15        flag = 116    # 2)The start rental date of each object17    object = re.search(r"[-/][0-9]*[-/]", entry.getSd(), re.M | re.S)18    if object:19        replaceString = monthName[int(object.group()[1:len(object.group()) - 1]) - 1]20        entry.setSd(re.sub(r"[-/][0-9]*[-/]", " " + replaceString + " ", entry.getSd()))21        flag= 122    # 3)The end rental date of each object23    object = re.search(r"[-/][0-9]*[-/]", entry.getEd(), re.M | re.S)24    if object:25        replaceString = monthName[int(object.group()[1:len(object.group()) - 1]) - 1]26        entry.setEd(re.sub(r"[-/][0-9]*[-/]", " " + replaceString + " ", entry.getEd()))27        flag = 128    return flag29# function to try and complete the missing information30def completeMissing(list):31    missingList=[] # this is a list to put the elements which can't be completed32    completeList=[] # this is a list to put the elements which are completed33    printList1 = [0,0,0,0,0,0,0,0,0,0]   #this list will be counting data for printing summary for completed/recovered entries34    printList2 = [0,0,0,0,0,0,0,0,0,0]   #this list will be counting data for printing summary for uncompleted entries(either missing cl, or missing more than a field so that it can not be filled35    for i in list:36        countList = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0] #this list will be couting the data for printing summary for each entry seperately37        flag = modifyDate(i)    #if any date in the entry is modified, flag is set to one38        countList[1] = flag    #countList[1] represents if entry is with wrong date format39        if(i.getCl()!=""):      #if cl is missing, then this entry can not be completed40            if (i.getId() == "" or i.getName() == "" or i.getDob() == "" or i.getMobile() == "" or i.getCm() == "" or41                    i.getYear() == "" or i.getSd() == "" or i.getEd() == "" or i.getRb() == ""):42                for j in list:   #start searching the list, to fill the incompleted entry43                    if (i.getCl() == j.getCl()):44                        # get the missing cm from the j.getCm is it's exist45                        if (i.getCm() == ""):46                            countList[7] = 1   #countList[7] states whether a missing cm or not47                            if(j.getCm() != ""):48                              i.setCm(j.getCm())49                        # get the missing year from the j.getYear is it's exist50                        if (i.getYear() == ""):51                            countList[9] = 1   #countList[9] states whether the year is missing in this entry or not52                            if(j.getYear() != ""):53                              i.setYear(j.getYear())54                        if (i.getSd() == "" and j.getSd() != "" and i.getEd() != "" and compareDates(i.getEd(),j.getEd())==1): #trying to fill the start date,55                        #if missing start date, then need to check that end date is the same,56                        #if both dates are missing, then entry can not be completed57                            i.setSd(j.getSd())58                        if (i.getEd() == "" and j.getEd() != "" and i.getSd() != "" and compareDates(i.getSd(),j.getSd())==1): #trying to fill the end date59                        #if missing end  date, then start date should be checked before completing entry60                            i.setEd(j.getEd())61                        # get the missing rb from the j.getRb is it's exist62                        if (i.getRb() == "" and j.getRb() != "" and ( (i.getEd() != "" and compareDates(i.getEd(),j.getEd())==1)63                            or (i.getSd() != "" and compareDates(i.getSd(),j.getSd())==1) ) ):64                        #before completing the Rb entry, need to check the start or end date, to make sure we are dealing with same entries65                        #note: no two cars with same Cl and same start date and end date are not duplicates66                            i.setRb(j.getRb())67                        if (i.getId() == ""):68                            countList[3] = 1  #countList[3] states wether id is missing in the given entry69                            #if missing and before filling it, need to check that the cl and start date and end date are the same for this person70                            if(j.getId() != "" and i.getCl().upper() == j.getCl().upper() and i.getEd() != "" and compareDates(i.getEd(),j.getEd())==171                                and i.getSd() != "" and compareDates(i.getSd(),j.getSd())==1):72                                i.setId(j.getId())73                    if (i.getName() == ""):74                            countList[2] = 1  #countList[2] states wether name is missing in the given entry75                            #if name is missing, check same id ( as cl is already checked) before filling,smae concept is used for Dob and mobile76                            if(j.getName() != "" and (i.getId()==j.getId())):77                              i.setName(j.getName())78                            # get the missing id from the j.getId if it's exist79                    if (i.getDob() == ""):80                            countList[4] = 1  #countList[4] states wether Dob is missing in the given entry81                            if(j.getDob() != "" and (i.getId()==j.getId())):82                               i.setDob(j.getDob())83                            # get the missing mobile from the j.getMobile if it's exist84                    if (i.getMobile() == ""):85                            countList[5] = 1  #countList[5] states wether id is missing in the given entry86                            if(j.getMobile() != ""  and (i.getId() == j.getId())):87                              i.setMobile(j.getMobile())88        else:89            if (i.getCm() == ""):90                countList[7] = 191            if (i.getYear() == ""):92                countList[9] = 193            if (i.getId() == ""):94                countList[3] = 195            if (i.getName() == ""):96                countList[2] = 197            if (i.getDob() == ""):98                countList[4] = 199            if (i.getMobile() == ""):100                countList[5] = 1101            countList[8] = 1   #countList[8] states wether cl is missing in the given entry102        # now if there are still missing fields then move that element with missing fields into a list called missingList103        if (i.getCl() == "" or i.getId() == "" or i.getName() == "" or i.getDob() == "" or i.getMobile() == "" or i.getCm() == "" or i.getYear() == ""104            or i.getSd() == "" or i.getEd() == "" or i.getRb() == ""):105            if(i.getId() == "" or i.getName() == "" or i.getDob() == "" or i.getMobile() == ""):106               countList[6] = 1 #countList[6] states wether the personal information in this entry can't be recovered107            missingList.append(i)108            for k in range(0,10):109                printList2[k] += countList[k]110        # if the current entry dosn't have any missing fields then mve it into a list called completeList111        else:112            completeList.append(i)113            for k in range(0, 10):114                printList1[k] += countList[k]115    printList2[0] = calcNumOfDuplicates(list)116    #moving all not comlete entries to a new text file called(âCarRentalMissing.txtâ)117    f=open("CarRentalMissing.txt","w")118    for i in missingList:119        f.write(str(i.printFormatedInfo()))120        f.write("\n")121    f.close()122    # moving all comlete entries to a new text file called(âCarRentalCompleted.txtâ123    f=open("CarRentalCompleted.txt","w")124    for i in completeList:125        f.write(str(i.printFormatedInfo()))126        f.write("\n")127    f.close()128    l = removeDuplicate(completeList)129    completeList = l[0]130    printList1[0] = l[1]131    #printSummary(printList1, printList2)132    return [completeList,printList1,printList2]133def printSummary(printList1,printList2):134    #printing summary before recovering, requires printing the summation of printList1[i]+printList2[i] in most cases135    print("Summary of data missing in the database:")136    print("Number of duplicate entries in the database = " , printList2[0] )137    print("Number of entries with wrong date format in the database = " , (printList1[1] + printList2[1]))138    print("Number of entries where names are dropped from the database = " ,(printList1[2] + printList2[2]))139    print("Number of entries where Ids are dropped from the database = " , (printList1[3] + printList2[3]))140    print("Number of entries where dob are dropped from the database = ", (printList1[4] + printList2[4]))141    print("Number of entries where mobile numbers are dropped from the database = " , (printList1[5] + printList2[5]))142    print("Number of entries where personal entry can not be completed = " , printList2[6])143    print("Number of entries where car make is dropped from the database = " , (printList1[7] + printList2[7]))144    print("Number of entries where car Ids are dropped from the database = ", (printList2[8]))145    print("Number of entries where car models (year) are dropped from the database = " , (printList1[9] + printList2[9]))146    print("")147    #printing summary after recovery, requires printing the printList1 elements148    print("Summary of data recovered from the database:")149    print("Number of duplicate entries removed from the new database = " , printList1[0])150    print("Number of entries with wrong date format fixed in the new database = " , printList1[1])151    print("Number of entries with names recovered in the new database = " , printList1[2])152    print("Number of entries with Ids recovered in the new database = " , printList1[3])153    print("Number of entries with dob recovered in the new database = " , printList1[4])154    print("Number of entries with mobile numbers recovered in the new database = " , printList1[5])155    print("Number of entries with car make recovered in the new database = " , printList1[7])156    print("Number of entries with car models (year) recovered in the new database = " , printList1[9])157#This function will encounter the number of duplicates in the whole database158def calcNumOfDuplicates(list):159    # this list will be a flag to help as know wether this entry is encountered as a duplicates or not160    # so we have initailzed it with zeros161    flagList = []162    for i in range(len(list)):163        flagList.append(0)164    # sum variable will contains the number of duplicates in the whole database165    sum = 0166    for i in range(len(list)):167        # if this entry is considered as a duplicate of anther antry or it's cl is not exist or bot the start and end dats are not exist168        # then we can't know if it have a duplicates or not so continue looping169        if(flagList[i]==0 and ( list[i].getCl()=="" or (list[i].getSd()=="" and list[i].getEd()=="") ) ):170            continue171        # this loop will check the duplicate of the current entry starting from the next of this current entry172        for j in range(i+1,len(list)):173            # if this entry is not a duplicate of another entry , and the cars ids are identical and some of the start or end dates174            # are identical and not empty then this entry is a duplicate of the current entry175            if(flagList[j]==0 and list[i].getCl()==list[j].getCl() and176            ((list[i].getSd()!="" and list[i].getSd()==list[j].getSd()) or (list[i].getEd()!="" and list[i].getEd()==list[j].getEd())) ):177                sum += 1178                flagList[j] = 1179    return sum180# function to remove the duplicates from the completed database181def removeDuplicate(list):182    i=0183    sum=0184    while (i < len(list)): # loops through the list185        j=i+1186        # loops through the list starting from the first element in the list after the element obtained from the first loop187        while (j < len(list)):188            #if the ids are idenetical then cheack the other field and if they are all identical then remove the second element189            if (list[i].getCl() == list[j].getCl() and compareDates(list[i].getSd(),list[j].getSd())==1 and compareDates(list[i].getEd(),list[j].getEd())==1 and190                list[i].getName().lower() == list[j].getName().lower() and compareDates(list[j].getDob(),list[i].getDob()) ==1191                 and list[i].getMobile() == list[j].getMobile() and list[i].getCm().lower() == list[j].getCm().lower()192                 and list[i].getYear() == list[j].getYear() and list[i].getRb() == list[j].getRb()):193                    sum += 1194                    list.pop(j)195                    j-=1196            j+=1197        i+=1198    return [list , sum ]199def compareDates(date1, date2):200    # if the date has the format of "/digit/" or "-digit-" it should be modified201    object1 = re.search(r"[-/][0-9]*[-/]", date1, re.M | re.S)202    if object1:203        # the replace string is the monthName element indexed by the digit204        replaceString = monthName[int(object1.group()[1:len(object1.group()) - 1]) - 1]205        date1 = re.sub(r"[-/][0-9]*[-/]", " " + replaceString + " ", date1)206    object2 = re.search(r"[-/][0-9]*[-/]", date2, re.M | re.S)207    if object2:208        # the replace string is the monthName element indexed by the digit209        replaceString = monthName[int(object2.group()[1:len(object2.group()) - 1]) - 1]210        date2 = re.sub(r"[-/][0-9]*[-/]", " " + replaceString + " ", date2)211    date1 = datetime.datetime.strptime(date1,"%d %B %Y")212    # we have created a date object to comaper the dates , because maybe date1 = 1 May 2020 and date2 = 01 May 2020213    # then comparing them as string will yield to be not identical , so using date objects will solve the problem214    date2 = datetime.datetime.strptime(date2,"%d %B %Y")215    if (date1 == date2):216        return 1217    else:...

initialize.py

Source:initialize.py

1'''2This module will read3Created on 19 Jun 20174@author: Amaurys Ãvila Ibarra5'''6from configparser import ConfigParser, ExtendedInterpolation7import os, errno, stat8from shutil import copy29__config_file = "%s/.budeAlaScan.ini" % os.path.expanduser("~")10# Ini file sections11__exe_sect = 'Executables'12__dir_sect = 'Directories'13__names_sect = 'File Names'14__general_sect = 'General'15# Ini file General options.16__gen_max_auto_num_opt = "MaxAutoNumber"17__gen_max_auto_num_val = '20'18# ini file dir options19__dir_wrk_opt = "Work"20__dir_wrk_val = "%s/budeAlaScan" % (os.path.expanduser("~"))21__dir_scan_opt = "Scan"22__dir_scan_val = "alaScan"23__dir_blibs_opt = "BudeLibs"24__dir_blibs_val = "libs"25__dir_rslt_opt = "BudeResults"26__dir_rslt_val = "results"27__dir_src_opt = "PdbSources"28__dir_src_val = "sources"29__dir_seq_opt = "BudeSeqs"30__dir_seq_val = "budeSeqs"31__dir_chi_opt = "Chimera"32__dir_chi_val = "chimeraScripts"33__dir_l_src_opt = "LongPdbSources"34__dir_l_src_val = "${%s}/${%s}" % (__dir_scan_opt, __dir_src_opt)35__dir_l_seq_opt = "LongBudeSeqs"36__dir_l_seq_val = "${%s}/${%s}" % (__dir_scan_opt, __dir_seq_opt)37__dir_l_blibs_opt = "LongBudeLibs"38__dir_l_blibs_val = "${%s}/${%s}" % (__dir_scan_opt, __dir_blibs_opt)39__dir_l_rslt_opt = "LongResults"40__dir_l_rslt_val = "${%s}/${%s}" % (__dir_scan_opt, __dir_rslt_opt)41__dir_l_chi_opt = "LongChimera"42__dir_l_chi_val = "${%s}/${%s}" % (__dir_scan_opt, __dir_chi_opt)43__dir_cpp_opt = "CppCode"44__dir_cpp_val = "cppCode"45__dir_bude_opt = "BUDE"46__dir_bude_val = "${%s}/%s/%s/bin" % (__dir_cpp_opt, "BUDE-1.2.9", "build")47__dir_getsd_opt = "GetSD"48__dir_getsd_val = "${%s}/%s" % (__dir_cpp_opt, "getSD")49__dir_colsd_opt = "ColourBySD"50__dir_colsd_val = "${%s}/%s" % (__dir_cpp_opt, "colourBySD")51__dir_msrc_opt = "MutationSources"52__dir_mrslt_opt = "mut_rslt"53# Ini file executable options54__exe_bude_opt = "BUDE"55__exe_bude_val = "budeScan"56__exe_bseq_opt = "BudeSeq"57__exe_bseq_val = "bude_sequence"58__exe_colsd_opt = "ColouBySD"59__exe_colsd_val = "colourBySD"60__exe_getsd_opt = "GetSD"61__exe_getsd_val = "getSD"62__exe_fbude_opt = "FullBude"63__exe_fbude_val = "${%s:%s}/${%s}" % (__dir_sect, __dir_bude_opt, __exe_bude_opt)64__exe_fbseq_opt = "FullBseq"65__exe_fbseq_val = "${%s:%s}/${%s}" % (__dir_sect, __dir_bude_opt, __exe_bseq_opt)66__exe_fcolsd_opt = "FullColourSD"67__exe_fcolsd_val = "${%s:%s}/${%s}" % (__dir_sect, __dir_colsd_opt, __exe_colsd_opt)68__exe_fgetsd_opt = "FullGetSD"69__exe_fgetsd_val = "${%s:%s}/${%s}" % (__dir_sect, __dir_getsd_opt, __exe_getsd_opt)70# Ini file names options71__names_b_bmc_opt = "BudeBMC"72__names_b_bmc_val = "budeAlaScan.bemc"73__names_b_ctrl_opt = "BudeCtrl"74__names_b_ctrl_val = "alaScan.bctl"75__names_b_gen_zero_opt = "BudeGenZero"76__names_b_gen_zero_val = "zeroGeneration.bzgn"77__names_b_ff_opt = "BudeForcefield"78__names_b_ff_val = "forcefield.bhff"79__names_b_transf_opt = "BudeTransformations"80__names_b_transf_val = "transformations.bltr"81__names_b_rot_choice_opt = "BudeRotamerChoice"82__names_b_rot_choice_val = "rotamer_choice.brch"83__names_b_rot_lib_opt = "BudeRotamerLibrary"84__names_b_rot_lib_val = "rotamer_library.brot"85__names_ligs_list_opt = "LigandsList"86__names_ligs_list_val = "myLigands.list"87__names_rcpts_list_opt = "ReceptorsList"88__names_rcpts_list_val = "myReceptors.list"89__names_rslt_lig_list_opt = "LigandResultsList"90__names_rslt_lig_list_val = "resultsLigands.list"91__names_rslt_rcpt_list_opt = "ReceptorResultsList"92__names_rslt_rcpt_list_val = "resultsReceptors.list"93__names_lig_sd_opt = "LigandsAvgSD"94__names_lig_sd_val = "ligandsAvgSD.bals"95__names_rcpt_sd_opt = "ReceptorsAvgSD"96__names_rcpt_sd_val = "receptorsAvgSD.bals"97__config_sections = {98    __general_sect:99     {100        __gen_max_auto_num_opt: __gen_max_auto_num_val101     }102    ,103    __exe_sect:104     {105        __exe_bude_opt: __exe_bude_val,106        __exe_bseq_opt: __exe_bseq_val,107        __exe_colsd_opt: __exe_colsd_val,108        __exe_getsd_opt: __exe_getsd_val,109        __exe_fbude_opt: __exe_fbude_val,110        __exe_fbseq_opt: __exe_fbseq_val,111        __exe_fcolsd_opt: __exe_fcolsd_val,112        __exe_fgetsd_opt: __exe_fgetsd_val113     }114    ,115    __dir_sect:116     {117        __dir_wrk_opt: __dir_wrk_val,118        __dir_scan_opt: __dir_scan_val,119        __dir_blibs_opt: __dir_blibs_val,120        __dir_rslt_opt: __dir_rslt_val,121        __dir_src_opt: __dir_src_val,122        __dir_seq_opt: __dir_seq_val,123        __dir_chi_opt: __dir_chi_val,124        __dir_l_src_opt: __dir_l_src_val,125        __dir_l_seq_opt: __dir_l_seq_val,126        __dir_l_blibs_opt: __dir_l_blibs_val,127        __dir_l_rslt_opt: __dir_l_rslt_val,128        __dir_l_chi_opt: __dir_l_chi_val,129        __dir_cpp_opt: __dir_cpp_val,130        __dir_bude_opt: __dir_bude_val,131        __dir_getsd_opt: __dir_getsd_val,132        __dir_colsd_opt: __dir_colsd_val133     }134     ,135    __names_sect:136     {137        __names_b_bmc_opt: __names_b_bmc_val,138        __names_b_ctrl_opt: __names_b_ctrl_val,139        __names_b_gen_zero_opt: __names_b_gen_zero_val,140        __names_b_ff_opt: __names_b_ff_val,141        __names_b_transf_opt: __names_b_transf_val,142        __names_b_rot_choice_opt: __names_b_rot_choice_val,143        __names_b_rot_lib_opt: __names_b_rot_lib_val,144        __names_ligs_list_opt: __names_ligs_list_val,145        __names_rcpts_list_opt: __names_rcpts_list_val,146        __names_rslt_lig_list_opt: __names_rslt_lig_list_val,147        __names_rslt_rcpt_list_opt: __names_rslt_rcpt_list_val,148        __names_lig_sd_opt: __names_lig_sd_val,149        __names_rcpt_sd_opt: __names_rcpt_sd_val150     }151    }152def __create_cfg():153    '''154    Create configuration by adding all sections and options to it.155    '''156    my_cfg = ConfigParser(interpolation=ExtendedInterpolation())157    my_cfg.optionxform = str158    for a_section in __config_sections:159        my_cfg.add_section(a_section)160        for an_option in __config_sections[a_section]:161            my_cfg.set(a_section, an_option, __config_sections[a_section][an_option])162    return my_cfg163def __read_cfg():164    '''165    Read config file, add missing configuration parameters and update166    config file if any section or option was added. 167    '''168    my_cfg = ConfigParser(interpolation=ExtendedInterpolation())169    my_cfg.optionxform = str170    my_cfg.read(__config_file, encoding='utf-8')171    if __did_add_missing_conf(my_cfg):172        copy2(__config_file, (__config_file + ".backup"))173        cfg = open(__config_file, 'w')174        my_cfg.write(cfg)175        cfg.close()176    return my_cfg177def __did_add_missing_conf(my_cfg):178    '''179    Add missing section or option and return true if any change is made.180    '''181    addition_was_made = False182    for a_section in __config_sections:183        if not my_cfg.has_section(a_section):184            my_cfg.add_section(a_section)185            addition_was_made = True186        for an_option in __config_sections[a_section]:187            if not my_cfg.has_option(a_section, an_option):188                my_cfg.set(a_section, an_option, __config_sections[a_section][an_option])189                addition_was_made = True190    return addition_was_made191def create_configuration():192    '''193    Creates configuration or reads it from file.194    '''195    try:196        flags = os.O_EXCL | os.O_WRONLY | os.O_CREAT197        mode = stat.S_IREAD | stat.S_IWRITE | stat.S_IRGRP | stat.S_IROTH198        ini_file = os.open(__config_file, flags, mode)199        os.close(ini_file)200    except OSError as e:201        if e.errno == errno.EEXIST:202            my_config = __read_cfg()203        else:204            raise205    else:206        cfg = open(__config_file, 'w')207        my_config = __create_cfg()208        my_config.write(cfg)209        cfg.close()...

delete.py

Source:delete.py

1import argparse2import time3import requests4def getSD(SDtoken, urlpart):5    url = 'https://api.serverdensity.io{}'.format(urlpart)6    r = requests.get(url, params={'token': SDtoken})7    j = r.json()8    time.sleep(0.1)9    return j10def delete(sdid, SDtoken, urlpart):11    url = 'https://api.serverdensity.io{0}/{sdid}'.format(urlpart, sdid=sdid)12    r = requests.delete(url, params={'token': SDtoken})13    time.sleep(0.1)14    return r.status_code15def delete_list(items, SDtoken, urlpart):16    for item in items:17        if '@' in str(item.get('login')):18            delete(item['_id'], SDtoken, urlpart)19            print "Item with id: {} has been deleted".format(item['_id'])20        else:21            print "Saving users that don't have an email as username"22if __name__ == '__main__':23    parser = argparse.ArgumentParser()24    parser.add_argument("SDtoken",25                        help="the api token you get from Server Density")26    args = parser.parse_args()27    SDtoken = args.SDtoken28    users = getSD(SDtoken, '/users/users')29    devices = getSD(SDtoken, '/inventory/devices')30    services = getSD(SDtoken, '/inventory/services')31    tags = getSD(SDtoken, '/inventory/tags')32    notifications = getSD(SDtoken, '/notifications/recipients')33    delete_list(users, SDtoken, '/users/users')34    delete_list(devices, SDtoken, '/inventory/devices')35    delete_list(services, SDtoken, '/inventory/services')36    delete_list(tags, SDtoken, '/inventory/tags')...

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