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_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 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_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_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_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 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_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_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_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_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_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_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_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 ...')
def form_terminate_volume_creator():
'''
Terminate de volume creator of the current zone.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Volume operation - Terminate volume creator')
# confirm the termination of the volume creator
print(xlib.get_separator())
OK = clib.confirm_action('The volume creator is going to be terminated.')
# terminate the volume creator
if OK:
devstdout = xlib.DevStdOut(xcluster.terminate_cluster.__name__)
xcluster.terminate_cluster(xlib.get_volume_creator_name(), True, devstdout, function=None, is_menu_call=False)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_recreate_data_file(data_file):
'''
Recreate a data file.
'''
# get the head
if data_file == xtoa.get_dataset_file():
head = f'{xlib.get_toa_name()} - Recreate the file of genomic dataset'
elif data_file == xtoa.get_species_file():
head = f'{xlib.get_toa_name()} - Recreate the file of species'
# print the header
clib.clear_screen()
clib.print_headers_with_environment(head)
# confirm the creation of the data file
print(xlib.get_separator())
OK = clib.confirm_action(
f'The file {data_file} is going to be recreated. The previous files will be lost.'
)
# recreate the config file
if OK:
if data_file == xtoa.get_dataset_file():
(OK, error_list) = xtoa.create_dataset_file()
elif data_file == xtoa.get_species_file():
(OK, error_list) = xtoa.create_species_file()
if OK:
print('The file is recreated.')
else:
for error in error_list:
print(error)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_manage_genomic_database(process_type, genomic_database):
'''
Manage processes of genomic database.
'''
# initialize the control variable
OK = True
# set the genomica database name
if genomic_database == xlib.get_toa_data_basic_data_code():
name = xlib.get_toa_data_basic_data_name()
elif genomic_database == xlib.get_toa_data_gymno_01_code():
name = xlib.get_toa_data_gymno_01_name()
elif genomic_database == xlib.get_toa_data_dicots_04_code():
name = xlib.get_toa_data_dicots_04_name()
elif genomic_database == xlib.get_toa_data_monocots_04_code():
name = xlib.get_toa_data_monocots_04_name()
elif genomic_database == xlib.get_toa_data_refseq_plant_code():
name = xlib.get_toa_data_refseq_plant_name()
elif genomic_database == xlib.get_toa_data_taxonomy_code():
name = xlib.get_toa_data_taxonomy_name()
elif genomic_database == xlib.get_toa_data_nt_code():
name = xlib.get_toa_data_nt_name()
elif genomic_database == xlib.get_toa_data_viridiplantae_nucleotide_gi_code(
):
name = xlib.get_toa_data_viridiplantae_nucleotide_gi_name()
elif genomic_database == xlib.get_toa_data_nr_code():
name = xlib.get_toa_data_nr_name()
elif genomic_database == xlib.get_toa_data_viridiplantae_protein_gi_code():
name = xlib.get_toa_data_viridiplantae_protein_gi_name()
elif genomic_database == xlib.get_toa_data_gene_code():
name = xlib.get_toa_data_gene_name()
elif genomic_database == xlib.get_toa_data_interpro_code():
name = xlib.get_toa_data_interpro_name()
elif genomic_database == xlib.get_toa_data_go_code():
name = xlib.get_toa_data_go_name()
# print the header
clib.clear_screen()
if process_type == xlib.get_toa_type_build_blastplus_db():
clib.print_headers_with_environment(f'Build {name} for BLAST+')
elif process_type == xlib.get_toa_type_build_diamond_db():
clib.print_headers_with_environment(f'Build {name} for DIAMOND')
elif process_type == xlib.get_toa_type_build_gilist():
clib.print_headers_with_environment(f'Build {name}')
elif process_type == xlib.get_toa_type_build_proteome():
clib.print_headers_with_environment(f'Build {name} proteome')
elif process_type == xlib.get_toa_type_download_data():
clib.print_headers_with_environment(
f'Download {name} functional annotations')
elif process_type == xlib.get_toa_type_load_data():
clib.print_headers_with_environment(
f'Load {name} data in {xlib.get_toa_name()} database')
print(xlib.get_separator())
# confirm the process run
if OK:
OK = clib.confirm_action(f'The {name} process is going to be run.')
# run the process
if OK:
devstdout = xlib.DevStdOut(xtoa.manage_genomic_database.__name__)
OK = xtoa.manage_genomic_database(process_type,
genomic_database,
devstdout,
function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_recreate_pipeline_config_file(pipeline_type):
'''
Recreate a pipeline 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()
# set 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()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{name} - Recreate config file')
print(xlib.get_separator())
# get the transcriptome directory
transcriptome_dir = ''
while transcriptome_dir == '':
transcriptome_dir = input('Enter transcriptome directory: ')
if not os.path.isdir(transcriptome_dir):
print(f'***ERROR: The directory {transcriptome_dir} is not valid.')
transcriptome_dir = ''
# get the transcriptome file
transcriptome_file = ''
while transcriptome_file == '':
transcriptome_file = input('Enter transcriptome file: ')
print(f'transcriptome_file: {transcriptome_file}')
if not os.path.isfile(f'{transcriptome_dir}/{transcriptome_file}'):
print(f'***ERROR: The file {transcriptome_file} is not valid.')
transcriptome_file = ''
# get the database list
if OK:
# nucleotide pipelines
if pipeline_type == xlib.get_toa_process_pipeline_nucleotide_code():
database_list = cinputs.input_database_list(
xtoa.get_nucleotide_annotation_database_code_list(), 'nt')
# amino acid pipelines
elif pipeline_type == xlib.get_toa_process_pipeline_aminoacid_code():
database_list = cinputs.input_database_list(
xtoa.get_aminoacid_annotation_database_code_list(), 'nr')
# recreate the pipeline config file
if OK:
# confirm the creation of the config file
print(xlib.get_separator())
OK = clib.confirm_action(
f'The file {config_file} is going to be recreated. The previous files will be lost.'
)
# recreate the config file
if OK:
(OK, error_list) = xtoa.create_pipeline_config_file(
pipeline_type, transcriptome_dir, transcriptome_file,
database_list)
if OK:
print('The file is recreated.')
else:
for error in error_list:
print(error)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_recreate_annotation_merger_config_file():
'''
Recreate the annotation merger config file.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment(
f'{xlib.get_toa_process_merge_annotations_name()} - Recreate config file'
)
# get the identification of the first pipeline dataset
app_list = [
xlib.get_toa_process_pipeline_nucleotide_code(),
xlib.get_toa_process_pipeline_aminoacid_code(),
xlib.get_toa_process_merge_annotations_code()
]
print('First pipeline ...')
pipeline_dataset_id_1 = cinputs.input_result_dataset_id(
xlib.get_toa_result_pipeline_dir(), app_list)
if pipeline_dataset_id_1 == '':
print('WARNING: There are not any pipeline datasets.')
OK = False
# get the identification of the second pipeline dataset
app_list = [
xlib.get_toa_process_pipeline_nucleotide_code(),
xlib.get_toa_process_pipeline_aminoacid_code(),
xlib.get_toa_process_merge_annotations_code()
]
print('Second pipeline ...')
pipeline_dataset_id_2 = cinputs.input_result_dataset_id(
xlib.get_toa_result_pipeline_dir(), app_list)
if pipeline_dataset_id_2 == '':
print('WARNING: There are not any pipeline datasets.')
OK = False
elif pipeline_dataset_id_1 == pipeline_dataset_id_2:
print('ERROR: The first pipeline dataset is equal to the second one.')
OK = False
# get the merger operation
if OK:
merger_operation = cinputs.input_code(
text='Merger operation',
code_list=xlib.get_annotation_merger_operation_code_list(),
default_code=None).upper()
# recreate the pipeline config file
if OK:
# confirm the creation of the config file
print(xlib.get_separator())
OK = clib.confirm_action(
f'The file {xtoa.get_annotation_merger_config_file()} is going to be recreated. The previous files will be lost.'
)
# recreate the config file
if OK:
(OK, error_list) = xtoa.create_annotation_merger_config_file(
pipeline_dataset_id_1, pipeline_dataset_id_2, merger_operation)
if OK:
print('The file is recreated.')
else:
for error in error_list:
print(error)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_create_toa_config_file():
'''
Create the TOA config file.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment(
f'{xlib.get_toa_name()} - Recreate config file')
print(xlib.get_separator())
# get the HOME directory
home_dir = str(pathlib.Path.home())
# set the TOA directory
toa_dir = os.path.dirname(os.path.abspath(__file__))
print(f'TOA directory: {toa_dir}')
# set the Miniconda3 directory
miniconda3_dir = cinputs.input_directory(
directory_name='Miniconda3',
default_directory=f'{home_dir}/{xlib.get_miniconda_dir()}',
is_created=False)
# set the database directory
db_dir = cinputs.input_directory(
directory_name='database',
default_directory=f'{home_dir}/{xlib.get_toa_database_dir()}',
is_created=False)
# set the result directory
result_dir = cinputs.input_directory(
directory_name='result',
default_directory=f'{home_dir}/{xlib.get_toa_result_dir()}',
is_created=False)
# create the TOA config file
if OK:
# confirm the creation of the config file
print(xlib.get_separator())
OK = clib.confirm_action(
f'The file {xtoa.get_toa_config_file()} is going to be recreated. The previous files will be lost.'
)
# recreate the config file
if OK:
(OK,
error_list) = xtoa.create_toa_config_file(toa_dir, miniconda3_dir,
db_dir, result_dir)
if OK:
print('The file is recreated.')
else:
for error in error_list:
print(error)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_install_bioinfo_app(app_code):
'''
Install the bioinfo application software in the cluster.
'''
# initialize the control variable
OK = True
# set the bioinfo application name
if app_code == xlib.get_blastplus_code():
app_name = xlib.get_blastplus_name()
elif app_code == xlib.get_diamond_code():
app_name = xlib.get_diamond_name()
elif app_code == xlib.get_entrez_direct_code():
app_name = xlib.get_entrez_direct_name()
elif app_code == xlib.get_miniconda3_code():
app_name = xlib.get_miniconda3_name()
elif app_code == xlib.get_r_code():
app_name = xlib.get_r_name()
elif app_code == xlib.get_transdecoder_code():
app_name = xlib.get_transdecoder_name()
# print the header
clib.clear_screen()
clib.print_headers_with_environment(f'{app_name} - Install software')
# confirm the software installation
print(xlib.get_separator())
if app_code == xlib.get_miniconda3_code():
OK = clib.confirm_action(
f'{app_name} (Conda infrastructure) is going to be installed. All Conda packages previously installed will be lost and they have to be reinstalled.'
)
elif app_code == xlib.get_r_code():
OK = clib.confirm_action(
f'{app_name} and analysis packages are going to be installed. The previous version will be lost, if it exists.'
)
else:
OK = clib.confirm_action(
f'The {app_name} Conda package is going to be installed. The previous version will be lost, if it exists.'
)
# install the software
if OK:
# install the BLAST+ software
if app_code == xlib.get_blastplus_code():
# -- package_code_list = [(xlib.get_blastplus_conda_code(), 'last')]
package_code_list = [(xlib.get_blastplus_conda_code(), '2.9.0')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# install the DIAMOND software
elif app_code == xlib.get_diamond_code():
# -- package_code_list = [(xlib.get_diamond_conda_code(), 'last')]
package_code_list = [(xlib.get_diamond_conda_code(), '0.9.34')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# install the Entrez Direct software
elif app_code == xlib.get_entrez_direct_code():
package_code_list = [(xlib.get_entrez_direct_conda_code(), 'last')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# install the Miniconda3 software
elif app_code == xlib.get_miniconda3_code():
devstdout = xlib.DevStdOut(xbioinfoapp.install_miniconda3.__name__)
OK = xbioinfoapp.install_miniconda3(devstdout, function=None)
# install R and analysis packages
elif app_code == xlib.get_r_code():
devstdout = xlib.DevStdOut(xbioinfoapp.install_r.__name__)
OK = xbioinfoapp.install_r(devstdout, function=None)
# install the TransDecoder software
elif app_code == xlib.get_transdecoder_code():
package_code_list = [(xlib.get_transdecoder_conda_code(), 'last')]
devstdout = xlib.DevStdOut(
xbioinfoapp.install_conda_package_list.__name__)
OK = xbioinfoapp.install_conda_package_list(app_code,
app_name,
package_code_list,
devstdout,
function=None)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
def form_create_ngscloud_config_file(is_menu_call):
'''
Create the NGScloud config file corresponding to the environment.
'''
# initialize the control variable
OK = True
# print the header
if is_menu_call:
clib.clear_screen()
clib.print_headers_with_environment('Configuration - Recreate TransciptomeCloud config file')
# get current region and zone names
region_name = xconfiguration.get_current_region_name()
zone_name = xconfiguration.get_current_zone_name()
# 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()
# confirm or change the AWS data and 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.')
if not is_menu_call:
raise xlib.ProgramException('EXIT')
# confirm the creation of the NGScloud config file
if OK:
if is_menu_call:
print(xlib.get_separator())
OK = clib.confirm_action('The {0} config file is going to be created. The previous files will be lost.'.format(xlib.get_project_name()))
# create the NGScloud config file corresponding to the environment
if OK:
print(xlib.get_separator())
print('The file {0} is being created ...'.format(xconfiguration.get_ngscloud_config_file()))
(OK, error_list) = xconfiguration.create_ngscloud_config_file(user_id, access_key_id, secret_access_key, email)
if OK:
print('The config file is created with default values.')
print()
print('You can modify the conection data and contact e-mail address in:')
print(' "Cloud control" -> "Configuration" -> "Update connection data and contact e-mail"')
print('The assigned region and zone are {0} and {1}, respectively. You can modify them in:'.format(xconfiguration.get_default_region_name(), xconfiguration.get_default_zone_name()))
print(' "Cloud control" -> "Configuration" -> "Update region and zone data"')
else:
for error in error_list:
print(error)
raise xlib.ProgramException('C001')
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
