def restart_cluster(cluster_name, log, function=None):
'''
Restart a cluster.
'''
# initialize the control variable
OK = True
# warn that the log window must not be closed
if not isinstance(log, xlib.DevStdOut):
log.write(
'This process might take several minutes. Do not close this window, please wait!\n'
)
# warn that the requirements are being verified
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Verifying process requirements ...\n')
# verify the master is stopped
if OK:
(master_state_code,
master_state_name) = xec2.get_node_state(cluster_name, 'master')
if master_state_code != 80:
log.write(
'*** ERROR: The cluster {0} is not stopped. Its state is {1} ({2}).\n'
.format(cluster_name, master_state_code, master_state_name))
OK = False
# warn that the requirements are OK
if OK:
log.write('Process requirements are OK.\n')
# restart the cluster
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Restarting cluster {0} using StarCluster ...\n'.format(
cluster_name))
log.write('\n')
command = '{0} start --no-create {1}'.format(xlib.get_starcluster(),
cluster_name)
rc = xlib.run_command(command, log)
log.write('\n')
if rc == 0:
log.write('The cluster is restarted.\n')
else:
log.write('*** ERROR: Return code {0} in command -> {1}\n'.format(
rc, command))
OK = False
# warn that the log window can be closed
if not isinstance(log, xlib.DevStdOut):
log.write('{0}\n'.format(xlib.get_separator()))
log.write('You can close this window now.\n')
# execute final function
if function is not None:
function()
# return the control variable
return OK
def form_create_keypairs():
'''
Create the key pairs of a region.
'''
# initialize the control variable
OK = True
# print the header and get the cluster name
clib.clear_screen()
clib.print_headers_with_environment('Security - Create key pairs')
# get current region name
region_name = xconfiguration.get_current_region_name()
# confirm the creation of the key pairs
print(xlib.get_separator())
OK = clib.confirm_action('The key pairs of the region {0} are going to be created.'.format(region_name))
# create key pairs
if OK:
print(xlib.get_separator())
print('The key pairs of the region {0} are been created ...'.format(region_name))
(OK, error_list) = xec2.create_keypairs(region_name)
if OK:
print('The key pairs and their corresponding local files have been created.')
else:
for error in error_list:
print(error)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_list_keypairs():
'''
List the key pairs of a region.
'''
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Security - List key pairs')
# get the key pair dictionary and the keypair names list
keypairs_dict = xec2.get_keypair_dict(region_name)
keypair_keys_list = sorted(keypairs_dict.keys())
# list keypairs
print(xlib.get_separator())
if keypair_keys_list == []:
print('WARNING: There is not any keypair created in the region {0}.'.format(region_name))
else:
# set data width
keypair_name_width = 25
fingerprint_width = 59
# set line template
line_template = '{0:' + str(keypair_name_width) + '} {1:' + str(fingerprint_width) + '}'
# print header
print(line_template.format('Key Pair Name', 'Fingerprint'))
print(line_template.format('=' * keypair_name_width, '=' * fingerprint_width))
# print detail lines
for keypair_key in keypair_keys_list:
keypair_name = keypairs_dict[keypair_key]['keypair_name']
fingerprint = keypairs_dict[keypair_key]['fingerprint']
print(line_template.format(keypair_name, fingerprint))
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_manage_toa_database(process_type):
'''
Manage the TOA database.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
if process_type == xlib.get_toa_type_recreate():
clib.print_headers_with_environment(
f'{xlib.get_toa_name()} - Recreate database')
elif process_type == xlib.get_toa_type_rebuild():
clib.print_headers_with_environment(
f'{xlib.get_toa_name()} - Rebuild database')
# confirm the process run
if OK:
print(xlib.get_separator())
OK = clib.confirm_action(
f'The {xlib.get_toa_name()} database is going to be {process_type}.'
)
# run the process
if OK:
devstdout = xlib.DevStdOut(xtoa.manage_toa_database.__name__)
OK = xtoa.manage_toa_database(process_type, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_edit_pipeline_config_file(pipeline_type):
'''
Edit a pipeline config file to change the parameters of each process.
'''
# initialize the control variable
OK = True
# set the pipeline name
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
name = xlib.get_toa_process_pipeline_nucleotide_name()
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
name = xlib.get_toa_process_pipeline_aminoacid_name()
elif pipeline_type == xlib.get_toa_process_merge_annotations_code():
name = xlib.get_toa_process_merge_annotations_name()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{name} - Edit config file')
# get the config file
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
config_file = xtoa.get_nucleotide_pipeline_config_file()
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
config_file = xtoa.get_aminoacid_pipeline_config_file()
elif pipeline_type == xlib.get_toa_process_merge_annotations_code():
config_file = xtoa.get_annotation_merger_config_file()
# edit the read transfer config file
print(xlib.get_separator())
print(f'Editing the {name} config file ...')
command = f'{xlib.get_editor()} {config_file}'
rc = subprocess.call(command, shell=True)
if rc != 0:
print(f'*** ERROR: RC {rc} in command -> {command}')
OK = False
# check the config file
if OK:
print(xlib.get_separator())
print(f'Checking the {name} config file ...')
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
(OK, error_list) = xtoa.check_pipeline_config_file(pipeline_type,
strict=False)
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
(OK, error_list) = xtoa.check_pipeline_config_file(pipeline_type,
strict=False)
elif pipeline_type == xlib.get_toa_process_merge_annotations_code():
(OK, error_list) = xtoa.check_annotation_merger_config_file(
strict=False)
if OK:
print('The file is OK.')
else:
print()
for error in error_list:
print(error)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_restart_cluster():
'''
Restart a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Restart cluster')
# get the cluster name
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
# confirm the restarting of the cluster
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The cluster is going to be restarted.')
# stop the cluster
if OK:
devstdout = xlib.DevStdOut(xcluster.restart_cluster.__name__)
OK = xcluster.restart_cluster(cluster_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_show_cluster_composing():
'''
Show cluster information of every node: OS, CPU number and memory.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Show cluster composing')
# get the cluster name
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
# show the status of batch jobs
if OK:
devstdout = xlib.DevStdOut(xcluster.show_cluster_composing.__name__)
xcluster.show_cluster_composing(cluster_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_remove_volume():
'''
Remove a volume in the current zone.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Remove volume')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the volume name
print(xlib.get_separator())
volume_name = cinputs.input_volume_name(zone_name, template_name='', help=True, help_type='created')
# confirm the removal of the volume
print(xlib.get_separator())
OK = clib.confirm_action('The volume is going to be removed.')
# remove the volume
if OK:
devstdout = xlib.DevStdOut(xvolume.remove_volume.__name__)
OK = xvolume.remove_volume(volume_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_open_terminal():
'''
Open a terminal windows of a cluster node.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cloud control - Open a terminal')
# get the cluster name and node name
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)
node_name = cinputs.input_node_name(cluster_name, new=False, is_master_valid=True, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# confirm the terminal opening
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The terminal is going to be opened using StarCluster.')
# open de terminal
if OK:
xcluster.open_terminal(cluster_name, node_name)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def kill_batch_job(cluster_name, job_id, log, function=None):
'''
Kill a batch job in the cluster.
'''
# initialize the control variable
OK = True
# create the SSH client connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Establishing connection with cluster {0} ...\n'.format(
cluster_name))
(OK, error_list, ssh_client) = xssh.create_ssh_client_connection(
cluster_name, 'master')
if OK:
log.write('The connection is established.\n')
else:
for error in error_list:
log.write('{0}\n'.format(error))
# kill the job in the cluster
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
sge_env = get_sge_env()
command = '{0}; qdel {1}'.format(sge_env, job_id)
(OK, stdout,
stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
if len(stdout) > 0:
for line in stdout:
log.write('{0}\n'.format(line))
else:
log.write('The job is been killed.\n')
if len(stderr) > 0:
for line in stderr:
log.write('{0}\n'.format(line))
else:
log.write('*** ERROR: Wrong command ---> {0}.\n'.format(command))
# close the SSH client connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write(
'Closing connection with cluster {0} ...\n'.format(cluster_name))
xssh.close_ssh_client_connection(ssh_client)
log.write('The connection is closed.\n')
# warn that the log window can be closed
if not isinstance(log, xlib.DevStdOut):
log.write('{0}\n'.format(xlib.get_separator()))
log.write('You can close this window now.\n')
# execute final function
if function is not None:
function()
# return the control variable
return OK
def remove_node(cluster_name, node_name, log, function=None):
'''
Remove a node in a cluster.
'''
# initialize the control variable
OK = True
# warn that the requirements are being verified
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Verifying process requirements ...\n')
# verify the master is running
if OK:
(master_state_code,
master_state_name) = xec2.get_node_state(cluster_name, 'master')
if master_state_code != 16:
log.write(
'*** ERROR: The cluster {0} is not running. Its state is {1} ({2}).'
.format(cluster_name, master_state_code, master_state_name))
OK = False
# verify the node is running
if OK:
pass
# warn that the requirements are OK
if OK:
log.write('Process requirements are OK.\n')
# remove node
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write(
'Removing node {0} in cluster {1} using StarCluster ...\n'.format(
node_name, cluster_name))
log.write('\n')
command = '{0} removenode --confirm {1} --alias={2}'.format(
xlib.get_starcluster(), cluster_name, node_name)
rc = xlib.run_command(command, log)
log.write('\n')
if rc == 0:
log.write('The node is removed.\n')
else:
log.write('*** ERROR: Return code {0} in command -> {1}\n'.format(
rc, command))
OK = False
# warn that the log window can be closed
if not isinstance(log, xlib.DevStdOut):
log.write('{0}\n'.format(xlib.get_separator()))
log.write('You can close this window now.\n')
# execute final function
if function is not None:
function()
# return the control variable
return OK
def form_update_connection_data():
'''
Update the user id, access key id, secret access key and contact e-mail address
in the NGScloud config file corresponding to the environment.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Configuration - Update connection data')
# get basic AWS data and contact e-mail address from NGScloud config file
(user_id, access_key_id, secret_access_key) = xconfiguration.get_basic_aws_data()
email = xconfiguration.get_contact_data()
# input the new AWS data and the contact e-mail address
print(xlib.get_separator())
user_id = cinputs.input_user_id(user_id)
access_key_id = cinputs.input_access_key_id(access_key_id)
secret_access_key = cinputs.input_secret_access_key(secret_access_key)
email = cinputs.input_email(email)
# verify the AWS access key identification and the AWS secret access key
print(xlib.get_separator())
print('Verifying the AWS access key identification and the AWS secret access key')
OK = xec2.verify_aws_credentials(access_key_id, secret_access_key)
if OK:
print('The credentials are OK.')
else:
print('ERROR: The credentials are wrong. Please review your access key identification and secret access key in the AWS web.')
# get the NGScloud config file
if OK:
ngscloud_config_file = xconfiguration.get_ngscloud_config_file()
# confirm the connection data update in the NGScloud config file
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The file {0} is going to be update with the new connection data.'.format(ngscloud_config_file))
# save the options dictionary in the NGScloud config file
if OK:
print(xlib.get_separator())
print('The file {0} is being update with the new connection data ...'.format(ngscloud_config_file))
(OK, error_list) = xconfiguration.update_connection_data(user_id, access_key_id, secret_access_key)
if OK:
(OK, error_list) = xconfiguration.update_contact_data(email)
if OK:
print('The config file has been update.')
else:
for error in error_list:
print(error)
raise xlib.ProgramException('C001')
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def show_cluster_composing(cluster_name, log, function=None):
'''
Show cluster information of every node: OS, CPU number and memory.
'''
# initialize the control variable
OK = True
# create the SSH client connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Establishing connection with cluster {0} ...\n'.format(
cluster_name))
(OK, error_list, ssh_client) = xssh.create_ssh_client_connection(
cluster_name, 'master')
if OK:
log.write('The connection is established.\n')
else:
for error in error_list:
log.write('{0}\n'.format(error))
# show the cluster composing
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
sge_env = get_sge_env()
command = '{0}; qhost'.format(sge_env)
(OK, stdout,
stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
if len(stdout) > 0:
for line in stdout:
log.write('{0}\n'.format(line))
else:
log.write('Cluster composing not found.\n')
else:
log.write('*** ERROR: Wrong command ---> {0}.\n'.format(command))
# close the SSH client connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write(
'Closing connection with cluster {0} ...\n'.format(cluster_name))
xssh.close_ssh_client_connection(ssh_client)
log.write('The connection is closed.\n')
# warn that the log window can be closed
if not isinstance(log, xlib.DevStdOut):
log.write('{0}\n'.format(xlib.get_separator()))
log.write('You can close this window now.\n')
# execute final function
if function is not None:
function()
# return the control variable
return OK
def list_clusters(log, function=None):
'''
List clusters.
'''
# initialize the control variable
OK = True
# get current region
region_name = xconfiguration.get_current_region_name()
# warn that the log window must not be closed
if not isinstance(log, xlib.DevStdOut):
log.write(
'This process might take a few minutes. Do not close this window, please wait!\n'
)
# warn that the requirements are being verified
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Verifying process requirements ...\n')
# verify if there are some running clusters
if xec2.get_running_cluster_list(volume_creator_included=True) == []:
log.write('WARNING: There is not any running cluster.\n')
OK = False
# warn that the requirements are OK
if OK:
log.write('Process requirements are OK.\n')
# list clusters
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Listing clusters using StarCluster ...\n')
log.write('\n')
command = '{0} --region={1} listclusters'.format(
xlib.get_starcluster(), region_name)
rc = xlib.run_command(command, log)
if rc != 0:
log.write('*** ERROR: Return code {0} in command -> {1}\n'.format(
rc, command))
OK = False
# warn that the log window can be closed
if not isinstance(log, xlib.DevStdOut):
log.write('{0}\n'.format(xlib.get_separator()))
log.write('You can close this window now.\n')
# execute final function
if function is not None:
function()
# return the control variable
return OK
def form_run_pipeline_process(pipeline_type):
'''
Run a pipeline process with the parameters in the corresponding config file.
'''
# initialize the control variable
OK = True
# set the pipeline name
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
name = xlib.get_toa_process_pipeline_nucleotide_name()
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
name = xlib.get_toa_process_pipeline_aminoacid_name()
elif pipeline_type == xlib.get_toa_process_merge_annotations_code():
name = xlib.get_toa_process_merge_annotations_name()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{name} - Run process')
# confirm the process run
if OK:
print(xlib.get_separator())
OK = clib.confirm_action(f'The {name} process is going to be run.')
# run the process
if OK:
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
devstdout = xlib.DevStdOut(xtoa.run_pipeline_process.__name__)
OK = xtoa.run_pipeline_process(pipeline_type,
devstdout,
function=None)
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
devstdout = xlib.DevStdOut(xtoa.run_pipeline_process.__name__)
OK = xtoa.run_pipeline_process(pipeline_type,
devstdout,
function=None)
elif pipeline_type == xlib.get_toa_process_merge_annotations_code():
devstdout = xlib.DevStdOut(
xtoa.run_annotation_merger_process.__name__)
OK = xtoa.run_annotation_merger_process(devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_kill_batch_job():
'''
Kill a batch job in the cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Kill batch job')
# get the cluster name, experiment identification, read dataset identification and the file pattern
print(xlib.get_separator())
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
# 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:
print(error)
# get the batch job identificaction
if OK:
batch_job_id = cinputs.input_batch_job_id(ssh_client, help=True)
if batch_job_id == '':
print('WARNING: There is not any batch job.')
OK = False
# confirm the kill of the batch job
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The batch job {0} is going to be killed.'.format(batch_job_id))
# kill the batch job
if OK:
devstdout = xlib.DevStdOut(xcluster.kill_batch_job.__name__)
xcluster.kill_batch_job(cluster_name, batch_job_id, devstdout, function=None)
# close the SSH client connection
if OK:
xssh.close_ssh_client_connection(ssh_client)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_list_templates():
'''
List the characteristics of the cluster templates.
'''
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Configuration - List cluster templates')
# get the cluster template dictionary and the template name list
template_dict = xconfiguration.get_template_dict()
template_name_list = xconfiguration.get_template_name_list(volume_creator_included=False)
# list cluster templates
print(xlib.get_separator())
if template_name_list == []:
print('WARNING: There is not any cluster template defined.')
else:
# set data width
template_width = 30
instance_type_width = 13
vcpu_width = 5
memory_width = 12
use_width = 17
generation_width = 10
# set line template
line_template = '{0:' + str(template_width) + '} {1:' + str(instance_type_width) + '} {2:>' + str(vcpu_width) + '} {3:>' + str(memory_width) + '} {4:' + str(use_width) + '} {5:' + str(generation_width) + '}'
# print header
print(line_template.format('Template name', 'Instance type', 'vCPUs', 'Memory (GiB)', 'Use', 'Generation'))
print(line_template.format('=' * template_width, '=' * instance_type_width, '=' * vcpu_width, '=' * memory_width, '=' * use_width, '=' * generation_width))
# print detail lines
for template_name in template_name_list:
instance_type = template_dict[template_name]['master_instance_type']
vcpu = template_dict[template_name]['vcpu']
memory = template_dict[template_name]['memory']
use = template_dict[template_name]['use']
generation = template_dict[template_name]['generation']
print(line_template.format(template_name, instance_type, vcpu, memory, use, generation))
# show warnings about characteristics and pricing
print(xlib.get_separator())
print('You can consult the characteristics of the EC2 intance types in:')
print(' https://aws.amazon.com/ec2/instance-types/')
print('and the EC2 pricing is detailed in:')
print(' https://aws.amazon.com/ec2/pricing/')
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_edit_data_file(data_file):
'''
Edit a data file.
'''
# initialize the control variable
OK = True
# get the head
if data_file == xtoa.get_dataset_file():
head = f'{xlib.get_toa_name()} - Edit the file of genomic dataset'
elif data_file == xtoa.get_species_file():
head = f'{xlib.get_toa_name()} - Edit the file of species'
# print the header
clib.clear_screen()
clib.print_headers_with_environment(head)
# edit the read transfer config file
print(xlib.get_separator())
print(f'Editing the file {data_file} ...')
command = f'{xlib.get_editor()} {data_file}'
rc = subprocess.call(command, shell=True)
if rc != 0:
print(f'*** ERROR: Return code {rc} in command -> {command}')
OK = False
# check the data file
if OK:
print(xlib.get_separator())
print(f'Checking the file {data_file} ...')
if data_file == xtoa.get_dataset_file():
(OK, error_list) = xtoa.check_dataset_file(strict=False)
elif data_file == xtoa.get_species_file():
(OK, error_list) = xtoa.check_species_file(strict=False)
if OK:
print('The file is OK.')
else:
print()
for error in error_list:
print(error)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_delink_volume_from_template():
'''
Delink a volume from a cluster template
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Configuration - Delink volume in a cluster template')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the template name and the volume name
print(xlib.get_separator())
template_name = cinputs.input_template_name(volume_creator_included=False, help=True, is_all_possible=True)
volume_name = cinputs.input_volume_name(zone_name, template_name, help=True, help_type='linked')
# verify there is some volume linked to the cluster template
if volume_name == '':
print(xlib.get_separator())
print('*** WARNING: There is not any volume linked to the cluster template.')
OK = False
# confirm the exclusion of the volume
if OK:
print(xlib.get_separator())
if template_name == 'all':
OK = clib.confirm_action('The volume {0} is going to be delinked from every template.'.format(volume_name))
else:
OK = clib.confirm_action('The volume {0} is going to be delinked from the template {0}.'.format(volume_name, template_name))
# delink a volume in a cluster template
if OK:
print(xlib.get_separator())
print('The volume {0} is being delinked from the cluster template {1}.'.format(volume_name, template_name))
devstdout = xlib.DevStdOut(xconfiguration.delink_volume_from_template.__name__)
(OK, error_list) = xconfiguration.delink_volume_from_template(template_name, volume_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_mount_volume():
'''
Mount a volume in a node.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Mount volume in a node')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the cluster name and node name
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)
node_name = cinputs.input_node_name(cluster_name, new=False, is_master_valid=True, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# get the volume name, AWS device file and directory path
if OK:
volume_name = cinputs.input_volume_name(zone_name, template_name='', help=True, help_type='created')
aws_device_file = cinputs.input_device_file(node_name, volume_name)
mounting_path = cinputs.input_mounting_path(node_name, aws_device_file)
# confirm the mounting of the volume
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The volume is going to be mounted.')
# mount the volume in the node
if OK:
devstdout = xlib.DevStdOut(xvolume.mount_volume.__name__)
xvolume.mount_volume(cluster_name, node_name, volume_name, aws_device_file, mounting_path, devstdout, function=None, is_menu_call=True)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_restart_pipeline_process(pipeline_type):
'''
Restart a pipeline process from the last step ended OK.
'''
# initialize the control variable
OK = True
# set the pipeline name
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
name = xlib.get_toa_process_pipeline_nucleotide_name()
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
name = xlib.get_toa_process_pipeline_aminoacid_name()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{name} - Run process')
# get the pipeline dataset identification
app_list = [pipeline_type]
pipeline_dataset_id = cinputs.input_result_dataset_id(
xlib.get_toa_result_pipeline_dir(), app_list)
if pipeline_dataset_id == '':
print(f'WARNING: There are not any {pipeline_type} result datasets.')
OK = False
# confirm the process run
if OK:
print(xlib.get_separator())
OK = clib.confirm_action(f'The {name} process is going to be run.')
# run the process
if OK:
devstdout = xlib.DevStdOut(xtoa.restart_pipeline_process.__name__)
OK = xtoa.restart_pipeline_process(pipeline_type,
pipeline_dataset_id,
devstdout,
function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_list_volumes():
'''
List volumes created.
'''
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - List volumes')
# get the volume dictionary and volume key list
volumes_dict = xec2.get_volume_dict()
volume_keys_list = sorted(volumes_dict.keys())
# list volume
print(xlib.get_separator())
if volume_keys_list == []:
print('WARNING: There is not any volume created.')
else:
# set data width
zone_name_width = 20
volume_name_width = 20
volume_id_width = 21
size_width = 10
state_width = 10
attachments_number_width = 11
# set line template
line_template = '{0:' + str(zone_name_width) + '} {1:' + str(volume_name_width) + '} {2:' + str(volume_id_width) + '} {3:' + str(size_width) + '} {4:' + str(state_width) + '} {5:' + str(attachments_number_width) + '}'
# print header
print(line_template.format('Zone', 'Volume Name', 'Volume Id', 'Size (GiB)', 'State', 'Attachments'))
print(line_template.format('=' * zone_name_width, '=' * volume_name_width, '=' * volume_id_width, '=' * size_width, '=' * state_width, '=' * attachments_number_width))
# print detail lines
for volume_key in volume_keys_list:
zone_name = volumes_dict[volume_key]['zone_name']
volume_name = volumes_dict[volume_key]['volume_name']
volume_id = volumes_dict[volume_key]['volume_id']
size = volumes_dict[volume_key]['size']
state = volumes_dict[volume_key]['state']
attachments_number = volumes_dict[volume_key]['attachments_number']
print(line_template.format(zone_name, volume_name, volume_id, size, state, attachments_number))
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_review_volume_links():
'''
Review linked volumes of cluster templates in order to remove linked volumes
that do not currently exist.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Configuration - Review volumes linked to cluster templates')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# get the NGScloud confign file
ngscloud_config_file = xconfiguration.get_ngscloud_config_file()
# verify if there are any volumes linked
if xconfiguration.get_volumes_dict() == {}:
print(xlib.get_separator())
print('WARNING: There is not any volume linked.')
OK = False
# confirm the review of volumes links
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The file {0} is going to be reviewed in order to remove volumes linked which are not currently created in the zone {1}.'.format(ngscloud_config_file, zone_name))
# review volumen link
if OK:
devstdout = xlib.DevStdOut(xconfiguration.review_volume_links.__name__)
(OK, error_list) = xconfiguration.review_volume_links(zone_name, devstdout, function=None)
# show continuation message or exit of application
print(xlib.get_separator())
if not OK and error_list != []:
raise xlib.ProgramException('C001')
else:
input('Press [Intro] to continue ...')
def form_terminate_cluster(force):
'''
Terminate a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
if not force:
clib.print_headers_with_environment('Cluster operation - Terminate cluster')
else:
clib.print_headers_with_environment('Cluster operation - Force termination of a cluster')
# get the cluster name that must be terminated
print(xlib.get_separator())
if not force:
if xec2.get_running_cluster_list(volume_creator_included=False) == []:
print('WARNING: There is not any running cluster.')
OK = False
else:
cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True)
else:
cluster_name = cinputs.input_template_name(volume_creator_included=False, help=False, is_all_possible=False)
# confirm the termination of the cluster
if OK:
print(xlib.get_separator())
if not force:
OK = clib.confirm_action('The cluster is going to be terminated.')
else:
OK = clib.confirm_action('The cluster is going to be forced to terminate.')
# terminate the cluster
if OK:
devstdout = xlib.DevStdOut(xcluster.terminate_cluster.__name__)
OK = xcluster.terminate_cluster(cluster_name, force, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_create_volume():
'''
Create a volume in the current zone.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Create volume')
# get current zone name
zone_name = xconfiguration.get_current_zone_name()
# show sites related to EBS volumes
print(xlib.get_separator())
print('You can consult the characteristics of the EBS volumes in:')
print(' https://aws.amazon.com/ebs/details/')
print('and the EBS pricing is detailed in:')
print(' https://aws.amazon.com/ebs/pricing/')
# get the cluster name, node name, volume name, volume type and volume size
print(xlib.get_separator())
volume_name = cinputs.input_volume_name(zone_name, template_name='', help=False, help_type='created')
volume_type = cinputs.input_volume_type()
volume_size = cinputs.input_volume_size(volume_type)
terminate_indicator = cinputs.input_terminate_indicator()
# confirm the creation of the volume
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The volume is going to be created.')
# create the volume
if OK:
devstdout = xlib.DevStdOut(xvolume.create_volume.__name__)
OK = xvolume.create_volume(volume_name, volume_type, volume_size, terminate_indicator, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_list_nodes():
'''
List nodes running.
'''
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Node operation - List nodes')
# get the node dictionary and node key list
node_dict = xec2.get_node_dict()
node_key_list = sorted(node_dict.keys())
# list nodes
print(xlib.get_separator())
if node_key_list == []:
print('WARNING: There is not any node running.')
else:
# set data width
security_group_name_width = 28
zone_name_width = 20
node_name_width = 20
node_id_width = 19
state_width = 20
# set line template
line_template = '{0:' + str(security_group_name_width) + '} {1:' + str(zone_name_width) + '} {2:' + str(node_name_width) + '} {3:' + str(node_id_width) + '} {4:' + str(state_width) + '}'
# print header
print(line_template.format('Security Group', 'Zone', 'Node Name', 'Node Id', 'State'))
print(line_template.format('=' * security_group_name_width, '=' * zone_name_width, '=' * node_name_width, '=' * node_id_width, '=' * state_width))
# print detail lines
for node_key in node_key_list:
security_group_name = node_dict[node_key]['security_group_name']
zone_name = node_dict[node_key]['zone_name']
node_name = node_dict[node_key]['node_name']
node_id = node_dict[node_key]['node_id']
state = node_dict[node_key]['state']
print(line_template.format(security_group_name, zone_name, node_name, node_id, state))
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_create_cluster():
'''
Create a cluster from a template name.
'''
# initialize the control variable
OK = True
# initialize the state variables
master_state_code = ''
master_state_name = ''
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Cluster operation - Create cluster')
# show sites related to EBS volumes
print(xlib.get_separator())
print('You can consult the characteristics of the EC2 intance types in:')
print(' https://aws.amazon.com/ec2/instance-types/')
print('and the EC2 pricing is detailed in:')
print(' https://aws.amazon.com/ec2/pricing/')
print()
# get the template name and set the cluster name
print(xlib.get_separator())
template_name = cinputs.input_template_name(volume_creator_included=False, help=True, is_all_possible=False)
cluster_name = template_name
# confirm the creation of the cluster
print(xlib.get_separator())
OK = clib.confirm_action('The cluster is going to be created.')
# create the cluster
if OK:
devstdout = xlib.DevStdOut(xcluster.create_cluster.__name__)
(OK, master_state_code, master_state_name) = xcluster.create_cluster(template_name, cluster_name, devstdout, function=None, is_menu_call=True)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_update_region_zone():
'''
Update the current region and zone names in the NGScloud config file
corresponding to the envoronment.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Configuration - Update region and zone')
# input new current region and zone
print(xlib.get_separator())
region_name = cinputs.input_region_name(region_name, help=True)
zone_name = cinputs.input_zone_name(region_name, zone_name, help=True)
# get the NGScloud config file
ngscloud_config_file = xconfiguration.get_ngscloud_config_file()
# confirm the region and zone update in the NGScloud config file
print(xlib.get_separator())
OK = clib.confirm_action('The file {0} is going to be update with the new region and zone.'.format(ngscloud_config_file))
# save the options dictionary in the NGScloud config file
if OK:
print(xlib.get_separator())
print('The file {0} is being update with the new region and zone ...'.format(ngscloud_config_file))
(OK, error_list) = xconfiguration.update_region_zone_data(region_name, zone_name)
if OK:
print('The config file has been update.')
else:
for error in error_list:
print(error)
raise xlib.ProgramException('C001')
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_add_node():
'''
Add a node in a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Node operation - Add node in a cluster')
# get the cluster name and node name
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)
if len(xec2.get_cluster_node_list(cluster_name)) >= xec2.get_max_node_number():
print('WARNING: The maximum number ({0}) of instances is already running.'.format(xec2.get_max_node_number()))
OK = False
else:
node_name = cinputs.input_node_name(cluster_name, new=True, is_master_valid=False, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# confirm the addition of the node in the cluster
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The node is going to be added.')
# add node in cluster
if OK:
devstdout = xlib.DevStdOut(xnode.add_node.__name__)
xnode.add_node(cluster_name, node_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_remove_node():
'''
Remove a node in a cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Node operation - Remove node in a cluster')
# get the cluster name and node name
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)
node_name = cinputs.input_node_name(cluster_name, new=False, is_master_valid=False, help=True)
if node_name == []:
print('WARNING: There is not any running node besides the master.')
OK = False
else:
print('WARNING: There is not any running cluster.')
OK = False
# confirm the removal of the node in the cluster
if OK:
print(xlib.get_separator())
OK = clib.confirm_action('The node is going to be removed.')
# remove node
if OK:
devstdout = xlib.DevStdOut(xnode.remove_node.__name__)
xnode.remove_node(cluster_name, node_name, devstdout, function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
