def login_test(ele_dict, user_lst): wd = open_browser(ele_dict['chromedriver']) log = LogInfo() log.log_init('Username', 'Password', 'Result', 'Description') open_url(wd, ele_dict['url']) ele_tuple = find_elements(wd, ele_dict) for arg in user_lst: send_values(ele_tuple, arg) time.sleep(5) result = check_results(wd, ele_dict['err_xpath'], arg, log) if result: wd.find_element_by_xpath(ele_dict['Signout_xpath']).click() break time.sleep(10) log.log_close() wd.quit()
def run_selected_util(self, utiltorun, programparams): if self.upc.required_params_set(utiltorun, programparams): # Run the AcceptorCheck util. if utiltorun == "acceptorcheck": varcon_file = VariantContextFile(programparams['varcon']) bamread_list = varcon_file.get_all_variant_context_acceptor_read_ids() acheck = AcceptorCheck() acheck.main(bamread_list, programparams['vasefq1'], programparams['vasefq2']) # Run the AcceptorReadInfo util. if utiltorun == "acceptorreadinfo": ari = AcceptorReadInfo(self.vuh) ari.main(programparams['acceptorbam'], programparams['varcon'], programparams['samplefilter'], programparams['varconfilter'], programparams['readidfilter']) # Run the CheckFastQ util. if utiltorun == "checkfastq": varcon_file = VariantContextFile(programparams['varcon']) acceptorreadlist = varcon_file.get_all_variant_context_acceptor_read_ids() donorreadlist = varcon_file.get_all_variant_context_donor_read_ids() checkf = CheckVaSeFastq() checkf.main(programparams['templatefq1'], programparams['vasefq1'], programparams['templatefq2'], programparams['vasefq2'], acceptorreadlist, donorreadlist) # Run the CheckDonorFiles util if utiltorun == "checkdonorfiles": check_dfiles = CheckDonorFilesExist(self.vuh) check_dfiles.main(programparams['donorfiles'], programparams['samplefilter']) # Run the CompareAcceptorContexts util if utiltorun == "compareacceptor": cacs = CompareAcceptorContexts(self.vuh) cacs.main(programparams['infile1'], programparams['infile2'], programparams['samplefilter'], programparams['varconfilter'], programparams['chromfilter']) # Run the CompareDonorContexts util if utiltorun == "comparedonor": cdcs = CompareDonorContexts(self.vuh) cdcs.main(programparams['infile1'], programparams['infile2'], programparams['samplefilter'], programparams['varconfilter'], programparams['chromfilter']) # Run the CompareVariantContexts util if utiltorun == "comparevarcon": cvcs = CompareVarcon() cvcs.main(programparams['varcon'], programparams['varcon2'], programparams['samplefilter'], programparams['varconfilter'], programparams['chromfilter']) # Run the DonorCheck util. if utiltorun == "donorcheck": varcon_file = VariantContextFile(programparams['varcon']) bamread_list = varcon_file.get_all_variant_context_donor_read_ids() dcheck = DonorCheck() dcheck.main(bamread_list, programparams['vasefq1'], programparams['vasefq2']) # Run the DonorReadInfo util. if utiltorun == "donorreadinfo": dri = DonorReadInfo(self.vuh) dri.main(programparams['donorfiles'], programparams['varcon'], programparams['samplefilter'], programparams['varconfilter'], programparams['readidfilter']) # Run the LogInfo util. if utiltorun == "loginfo": li = LogInfo(self.vuh) li.main(programparams['vaselog'], programparams['logfilter']) # Subset a provided variant context file and write it to a new output file if utiltorun == "subsetvarcon": varcon_file = VariantContextFile(programparams["varcon"], programparams["samplefilter"], programparams["varconfilter"], programparams["chromfilter"]) varcon_file.write_variant_context_file(programparams["outfile"]) # Run the VarconData util if utiltorun == "varcondata": varconvcfdata = VarconVcfData() varconvcfdata.main(programparams['donorfiles'], programparams['varcon'], programparams['samplefilter'], programparams['varconfilter'], programparams['chromfilter']) # Run the VcfInVarcon util if utiltorun == "vcfinvarcon": varcon_file = VariantContextFile(programparams['varcon'], programparams['samplefilter'], programparams['varconfilter'], programparams['chromfilter']) vvivc = VcfVariantsInVariantContexts(self.vuh) vvivc.main(programparams['infile1'], varcon_file) else: self.vaseutillogger.warning("Not all parameters were set.") notsetparams = self.upc.get_not_set_parameters(utiltorun, programparams) self.vaseutillogger.warning("Parameter(s) " + ", ".join(notsetparams) + " are invalid") self.vaseutillogger.warning("Skipping selected util")