dirs = Dirs(is_user_upload, data_object['run'], data_object['platform'],
data_object['lane_name'])
dirs.check_and_make_output_dir()
dirs.create_all_output_dirs()
data_object['output_dir'] = dirs.output_dir
##############
#
# VALIDATE THE INI FILE
#
##############
# print('do1',data_object)
del v
v = MetadataUtils(configuration_dictionary=data_object)
v.convert_and_save_ini(data_object['output_dir'])
data_object = v.validate(data_object['output_dir'])
#general_data = v.get_general_data()
answer = v.get_confirmation(args.steps, data_object['general'])
#print('do2',data_object)
if answer == 'q':
sys.exit()
elif answer == 'v':
# view CONFIG file contents
fh = open(
os.path.join(dirs.analysis_dir,
data_object['general']['run'] + '.ini'))
lines = fh.readlines()
logger.debug("\n=== START ===\n")
dirs = Dirs(is_user_upload, data_object['run'], data_object['platform'], data_object['lane_name'])
dirs.check_and_make_output_dir()
dirs.create_all_output_dirs()
data_object['output_dir'] = dirs.output_dir
##############
#
# VALIDATE THE INI FILE
#
##############
# print('do1',data_object)
del v
v = MetadataUtils( configuration_dictionary = data_object )
v.convert_and_save_ini(data_object['output_dir'])
data_object = v.validate(data_object['output_dir'])
#general_data = v.get_general_data()
answer = v.get_confirmation(args.steps, data_object['general'])
#print('do2',data_object)
if answer == 'q':
sys.exit()
elif answer == 'v':
# view CONFIG file contents
fh = open(os.path.join(dirs.analysis_dir, data_object['general']['run']+'.ini'))
lines = fh.readlines()
logger.debug("\n=== START ===\n")
for line in lines:
line = line.strip()
logger.debug("Creating output directory: "+outdir)
os.makedirs(outdir)
except:
sys.exit("Could not find or create the output_dir "+data_object['output_dir']+" - Exiting.")
data_object['output_dir'] = outdir
##############
#
# VALIDATE THE INI FILE
#
##############
#print 'do1',data_object
del v
v = MetadataUtils( configuration_dictionary = data_object )
v.convert_and_save_ini()
data_object = v.validate()
#general_data = v.get_general_data()
answer = v.get_confirmation(args.steps, data_object['general'])
#print 'do2',data_object
if answer == 'q':
sys.exit()
elif answer == 'v':
# view CONFIG file contents
fh = open(os.path.join(data_object['general']['output_dir'], data_object['general']['run']+'.ini'))
lines = fh.readlines()
print "\n=== START ===\n"
for line in lines:
line = line.strip()
print line
