def get_quast_process_starter():
'''
Get the QUAST process starter path in the local computer.
'''
# assign the QUAST process starter path
quast_process_starter = '{0}/{1}-process-starter.sh'.format(xlib.get_temp_dir(), xlib.get_quast_code())
# return the QUAST starter path
return quast_process_starter
def get_gmap_process_starter():
'''
Get the GMAP process starter path in the local computer.
'''
# assign the GMAP process starter path
gmap_process_starter = '{0}/{1}-process-starter.sh'.format(xlib.get_temp_dir(), xlib.get_gmap_code())
# return the GMAP starter path
return gmap_process_starter
def get_busco_process_starter():
'''
Get the BUSCO process starter path in the local computer.
'''
# assign the BUSCO process starter path
busco_process_starter = '{0}/{1}-process-starter.sh'.format(xlib.get_temp_dir(), xlib.get_busco_code())
# return the BUSCO starter path
return busco_process_starter
def get_gzip_process_starter(dataset_type):
'''
Get the gzip process starter path in the local computer.
'''
# assign the gzip process starter path
name = 'result' if dataset_type == 'whole-result' else dataset_type
gzip_process_starter = '{0}/{1}-{2}-starter.sh'.format(xlib.get_temp_dir(), xlib.get_gzip_code(), name)
# return the gzip starter path
return gzip_process_starter
def get_infrastructure_software_installation_script():
'''
Get the infrastructure software installation script path in the local computer.
'''
# assign infrastructure software installation script path
infrastructure_software_installation_script = '{0}/{1}'.format(
xlib.get_temp_dir(), 'infrastructure_software_installation.sh')
# return the infrastructure software installation script path
return infrastructure_software_installation_script
def get_fastqc_process_starter():
'''
Get the FastQC process starter path in the local computer.
'''
# assign the FastQC process starter path
fastqc_process_starter = '{0}/{1}-process-starter.sh'.format(
xlib.get_temp_dir(), xlib.get_fastqc_code())
# return the FastQC starter path
return fastqc_process_starter
def get_cd_hit_est_process_starter():
'''
Get the CD-HIT-EST process starter path in the local computer.
'''
# assign the CD-HIT-EST process starter path
cd_hit_est_process_starter = '{0}/{1}-process-starter.sh'.format(
xlib.get_temp_dir(), xlib.get_cd_hit_est_code())
# return the CD-HIT-EST starter path
return cd_hit_est_process_starter
def open_terminal(cluster_name, node_name):
'''
Open a terminal window in a node of the cluster.
'''
# get the keypair file
keypair_file = xconfiguration.get_keypair_file()
# get the public IP address corresponding to the cluster node
public_ip_address = xec2.get_node_data_dict(cluster_name,
node_name)['public_ip_address']
# set the command to start the terminal window and run ssh script
if sys.platform.startswith('linux'):
command = 'x-terminal-emulator -e ./sshinstance.sh {0} {1} {2}'.format(
keypair_file, 'root', public_ip_address).split()
elif sys.platform.startswith('darwin'):
open_terminal_script = '{0}/open_terminal.sh'.format(
xlib.get_temp_dir())
try:
if not os.path.exists(os.path.dirname(open_terminal_script)):
os.makedirs(os.path.dirname(open_terminal_script))
with open(open_terminal_script,
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('cd {0}'.format(os.getcwd())))
file_id.write('{0}\n'.format(
'./sshinstance.sh {0} {1} {2}'.format(
keypair_file, 'root', public_ip_address)))
except Exception as e:
print('*** ERROR: The file {0} can not be created'.format(
open_terminal_script))
os.chmod(open_terminal_script, 0o744)
command = 'open -a Terminal.app {0}'.format(
open_terminal_script).split()
elif sys.platform.startswith('win32') or sys.platform.startswith('cygwin'):
command = 'cmd.exe /c start .\sshinstance.bat {0} {1} {2}'.format(
keypair_file, 'root', public_ip_address).split()
# open the new terminal
process = subprocess.Popen(command)
def get_starcluster_dir():
'''
Get the directory where StarCluster is installed.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# initialize the StarCluster directory
starcluster_dir = ''
# set the path of the file used to store the StarCluster information
sci_file_path = '{0}/sci.txt'.format(xlib.get_temp_dir())
# store the StarCluster information
if OK:
command = '{0} {1}'.format(xlib.get_sci(), sci_file_path)
rc = xlib.run_command(command, sys.stdout)
if rc != 0:
error_list.append('*** ERROR: Return code {0} in command -> {1}\n'.format(rc, command))
OK = False
# find the StarCluster path
if OK:
try:
file_id = open(sci_file_path, mode='r', encoding='iso-8859-1', newline='\n')
except Exception as e:
error_list.append('*** ERROR: The file {0} can not be opened.\n'.format(sci_file_path))
OK = False
else:
OK = False
record = file_id.readline()
while record != '':
if record.startswith('FILE'):
record = file_id.readline().strip()
starcluster_dir = record[:record.find('__init__.py')]
OK = True
break
record = file_id.readline()
# return the control variable, error list and StarCluster directory
return (OK, error_list, starcluster_dir)
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 ...')
def form_view_cluster_start_log():
'''
View the cluster start log.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Logs - View the cluster start log')
# get the clustner name
if OK:
print(xlib.get_separator())
if xec2.get_running_cluster_list(only_environment_cluster=True,
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)
for error in error_list:
print(error)
# create the SSH transport connection
if OK:
(OK, error_list,
ssh_transport) = xssh.create_ssh_transport_connection(cluster_name)
for error in error_list:
print(error)
# create the SFTP client
if OK:
sftp_client = xssh.create_sftp_client(ssh_transport)
# 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:
local_path = f'{xlib.get_temp_dir()}/{os.path.basename(xinstance.get_infrastructure_software_installation_log())}'
cluster_path = f'/home/ubuntu/{os.path.basename(xinstance.get_infrastructure_software_installation_log())}'
# download the log file from the cluster
if OK:
print(xlib.get_separator())
print(
f'The file {os.path.basename(xinstance.get_infrastructure_software_installation_log())} is being downloaded from {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 the cluster start log'
OK = clib.view_file(local_path, text)
# show continuation message
input('Press [Intro] to continue ...')