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")
