def build_fastqc_process_starter(current_run_dir):
'''
Build the starter of the current FastQC process.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# write the FastQC process starter
try:
if not os.path.exists(os.path.dirname(get_fastqc_process_starter())):
os.makedirs(os.path.dirname(get_fastqc_process_starter()))
with open(get_fastqc_process_starter(),
mode='w',
encoding='utf8',
newline='\n') as file_id:
file_id.write('{0}\n'.format('#!/bin/bash'))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format('{0}/{1} &>{0}/{2}'.format(
current_run_dir, os.path.basename(get_fastqc_process_script()),
xlib.get_cluster_log_file())))
except:
error_list.append('*** ERROR: The file {0} can not be created'.format(
get_fastqc_process_starter()))
OK = False
# return the control variable and the error list
return (OK, error_list)
def build_gzip_process_starter(dataset_type, current_run_dir):
'''
Build the starter of the current gzip process.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the log file name
log_file = xlib.get_cluster_log_file()
# write the gzip process starter
try:
if not os.path.exists(os.path.dirname(get_gzip_process_starter(dataset_type))):
os.makedirs(os.path.dirname(get_gzip_process_starter(dataset_type)))
with open(get_gzip_process_starter(dataset_type), mode='w', encoding='iso-8859-1', newline='\n') as file_id:
file_id.write( '#!/bin/bash\n')
file_id.write( '#-------------------------------------------------------------------------------\n')
file_id.write( '{0}\n'.format('{0}/{1} &>>{0}/{2}'.format(current_run_dir, os.path.basename(get_gzip_process_script(dataset_type)), log_file)))
except Exception as e:
error_list.append(f'*** EXCEPTION: "{e}".')
error_list.append('*** ERROR: The file {0} can not be created'.format(get_gzip_process_starter(dataset_type)))
OK = False
# return the control variable and the error list
return (OK, error_list)
def form_view_cluster_experiment_process_log():
'''
View the log of an experiment process in the cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Logs - View an experiment process log in the cluster')
# get the clustner name
if OK:
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) != []:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# create the SSH client connection
if OK:
(OK, error_list, ssh_client) = xssh.create_ssh_client_connection(cluster_name, 'master')
for error in error_list:
log.write('{0}\n'.format(error))
# create the SSH transport connection
if OK:
(OK, error_list, ssh_transport) = xssh.create_ssh_transport_connection(cluster_name, 'master')
for error in error_list:
log.write('{0}\n'.format(error))
# create the SFTP client
if OK:
sftp_client = xssh.create_sftp_client(ssh_transport)
# get the experiment identification
if OK:
experiment_id = cinputs.input_experiment_id(ssh_client, help=True)
if experiment_id == '':
print('WARNING: The cluster has not experiment data.')
OK = False
# get the result_dataset identification
if OK:
result_dataset_id = cinputs.input_result_dataset_id('uncompressed', ssh_client, experiment_id, help=True)
if result_dataset_id == '':
print('WARNING: The experiment {0} has not result datasets.'.format(experiment_id))
OK = False
# create the local path
if not os.path.exists(xlib.get_temp_dir()):
os.makedirs(xlib.get_temp_dir())
# get the log file name and build local and cluster paths
if OK:
log_file = xlib.get_cluster_log_file()
local_path = '{0}/{1}'.format(xlib.get_temp_dir(), log_file)
cluster_path = '{0}/{1}/{2}'.format(xlib.get_cluster_experiment_result_dir(experiment_id), result_dataset_id, log_file)
# download the log file from the cluster
if OK:
print(xlib.get_separator())
print('The file {0} is being downloaded from {1} ...'.format(log_file, cluster_path))
OK = xssh.get_file(sftp_client, cluster_path, local_path)
if OK:
print('The file has been uploaded.')
# close the SSH transport connection
if OK:
xssh.close_ssh_transport_connection(ssh_transport)
# close the SSH client connection
if OK:
xssh.close_ssh_client_connection(ssh_client)
# view the log file
if OK:
text = 'Logs - View an experiment process log in the cluster'
OK = clib.view_file(local_path, text)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')