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_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 build_menu_toa_taxonomy():
'''
Build the menu NCBI Taxonomy.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_taxonomy_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Download taxonomy data from NCBI server')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_manage_genomic_database(xlib.get_toa_type_download_data(), xlib.get_toa_data_taxonomy_code())
elif option == 'X':
break
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_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_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 build_menu_toa_refseq_plant():
'''
Build the menu NCBI RefSeq Plant.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_refseq_plant_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Build proteome')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_manage_genomic_database(xlib.get_toa_type_build_proteome(), xlib.get_toa_data_refseq_plant_code())
elif option == 'X':
break
def build_menu_metacyc_stats():
'''
Build the menu Statistics - MetaCyc.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Statistics - MetaCyc')
# print the menu options
print( 'Options:')
print()
print( ' 1. Frecuency distribution data')
print( ' 2. # sequences per # ids data')
print()
print( ' X. Return to menu Statistics')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_view_ontologic_data_frecuency(stats_code='metacyc')
elif option == '2':
ctoa.form_view_x_per_y_data(stats_code='seq_per_metacyc')
elif option == 'X':
break
def build_menu_toa_go():
'''
Build the menu Gene Ontology.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_go_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Download functional annotations from Gene Ontology server')
print(f' 2. Load data into {xlib.get_toa_name()} database')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_manage_genomic_database(xlib.get_toa_type_download_data(), xlib.get_toa_data_go_code())
elif option == '2':
ctoa.form_manage_genomic_database(xlib.get_toa_type_load_data(), xlib.get_toa_data_go_code())
elif option == 'X':
break
def build_menu_toa_pipelines():
'''
Build the menu Pipelines.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Pipelines')
# print the menu options
print( 'Options:')
print()
print(f' 1. {xlib.get_toa_name()} {xlib.get_toa_process_pipeline_nucleotide_name()}')
print(f' 2. {xlib.get_toa_name()} {xlib.get_toa_process_pipeline_aminoacid_name()}')
print()
print(f' 3. Annotation merger of {xlib.get_toa_name()} pipelines')
print()
print( ' X. Return to menu Main')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
build_menu_toa_nucleotide_pipeline()
elif option == '2':
build_menu_toa_aminoacid_pipeline()
elif option == '3':
build_menu_toa_annotation_merger()
elif option == 'X':
break
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 build_menu_alignment_stats():
'''
Build the menu Statistics - Alignment.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Statistics - Alignment')
# print the menu options
print( 'Options:')
print()
print( ' 1. # HITs per # HSPs data')
print()
print( ' X. Return to menu Statistics')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_view_x_per_y_data(stats_code='hit_per_hsp')
elif option == 'X':
break
def build_menu_family_stats():
'''
Build the menu Statistics - Family.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Statistics - Family')
# print the menu options
print( 'Options:')
print()
print( ' 1. Frecuency distribution data')
print()
print( ' X. Return to menu Statistics')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_view_phylogenic_data_frecuency(stats_code='family')
elif option == 'X':
break
def build_menu_toa_annotation_merger():
'''
Build the menu annotation merger of TOA pipelines.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(f'Annotation merger of {xlib.get_toa_name()} pipelines')
# print the menu options
print( 'Options:')
print()
print( ' 1. Recreate config file')
print( ' 2. Edit config file')
print()
print( ' 3. Run process')
print()
print( ' X. Return to menu Pipelines')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_recreate_annotation_merger_config_file()
elif option == '2':
ctoa.form_edit_pipeline_config_file(xlib.get_toa_process_merge_annotations_code())
elif option == '3':
ctoa.form_run_pipeline_process(xlib.get_toa_process_merge_annotations_code())
elif option == 'X':
break
def build_menu_toa_stats():
'''
Build the menu Statistics.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Statistics')
# print the menu options
print( 'Options:')
print()
print( ' 1. Alignment')
print()
print( ' 2. Annotation datasets')
print()
print( ' 3. Species')
print( ' 4. Family')
print( ' 5. Phylum')
print()
print( ' 6. EC')
print( ' 7. Gene Ontology')
print( ' 8. InterPro')
print( ' 9. KEGG')
print( ' A. MapMan')
print( ' B. MetaCyc')
print()
print( ' X. Return to menu Main')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
build_menu_alignment_stats()
elif option == '2':
build_menu_annotation_dataset_stats()
elif option == '3':
build_menu_species_stats()
elif option == '4':
build_menu_family_stats()
elif option == '5':
build_menu_phylum_stats()
elif option == '6':
build_menu_ec_stats()
elif option == '7':
build_menu_go_stats()
elif option == '8':
build_menu_interpro_stats()
elif option == '9':
build_menu_kegg_stats()
elif option == 'A':
build_menu_mapman_stats()
elif option == 'B':
build_menu_metacyc_stats()
elif option == 'X':
break
def form_view_submission_log():
'''
View the log of a submission.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment('Logs - View a submission log')
# get the submission log
submission_log_file = cinputs.input_submission_log_file()
if submission_log_file == '':
print('WARNING: There is not any submission log.')
OK = False
# view the log file
if OK:
text = 'Logs - View a submission log'
OK = clib.view_file(
os.path.join(xlib.get_log_dir(), submission_log_file), text)
# show continuation message
input('Press [Intro] to continue ...')
def build_menu_go_stats():
'''
Build the menu Statistics - Gene Ontology.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Statistics - Gene Ontology')
# print the menu options
print( 'Options:')
print()
print( ' 1. Frecuency distribution data per term')
print( ' 2. Frecuency distribution data per namespace')
print( ' 3. # sequences per # terms data')
print()
print( ' X. Return to menu Statistics')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_view_go_data_frecuency()
elif option == '2':
ctoa.form_view_phylogenic_data_frecuency(stats_code='namespace')
elif option == '3':
ctoa.form_view_x_per_y_data(stats_code='seq_per_go')
elif option == 'X':
break
def build_menu_toa_protein_gi():
'''
Build the menu NCBI Protein GenInfo identifier lists.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_viridiplantae_protein_gi_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Build identifier list using NCBI server')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_manage_genomic_database(xlib.get_toa_type_build_gilist(), xlib.get_toa_data_viridiplantae_protein_gi_code())
elif option == 'X':
break
def build_menu_toa_nr():
'''
Build the menu NCBI BLAST database NR.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_nr_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Build database for BLAST+')
print( ' 2. Build database for DIAMOND')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
ctoa.form_manage_genomic_database(xlib.get_toa_type_build_blastplus_db(), xlib.get_toa_data_nr_code())
elif option == '2':
ctoa.form_manage_genomic_database(xlib.get_toa_type_build_diamond_db(), xlib.get_toa_data_nr_code())
elif option == 'X':
break
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_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 build_menu_main():
'''
Build the menu Main.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment('Main')
# print the menu options
print( 'Options:')
print()
print( ' 1. Configuration')
print()
print( ' 2. Genomic databases')
print()
print( ' 3. Annotation pipelines')
print()
print( ' 4. Statistics')
print()
print( ' 5. Logs')
print()
print(f' X. Exit {xlib.get_short_project_name()}')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
build_menu_toa_configuration()
elif option == '2':
build_menu_toa_databases()
elif option == '3':
build_menu_toa_pipelines()
elif option == '4':
build_menu_toa_stats()
elif option == '5':
build_menu_logs()
elif option == 'X':
sure = ''
print( '')
while sure not in ['Y', 'N']:
sure = input(f'Are you sure to exit {xlib.get_short_project_name()}? (y or n): ').upper()
if sure == 'Y':
break
def form_view_result_log():
'''
View the log of an experiment/process result.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment(
'Logs - View an experiment/process result log')
# get the experiment identification
if OK:
experiment_id = cinputs.input_experiment_id()
if experiment_id == '':
print('WARNING: There is not any experiment/process data.')
OK = False
# get the result_dataset identification
if OK:
result_dataset_id = cinputs.input_result_dataset_id(
experiment_id, xlib.get_all_applications_selected_code())
if result_dataset_id == '':
print(
f'WARNING: The experiment/process {experiment_id} does not have result datasets.'
)
OK = False
# get the dictionary of TOA configuration.
if OK:
toa_config_dict = xtoa.get_toa_config_dict()
# get the log file name and build local and cluster paths
if OK:
log_file = f'{toa_config_dict["RESULT_DIR"]}/{experiment_id}/{result_dataset_id}/{xlib.get_run_log_file()}'
# view the log file
if OK:
text = 'Logs - View an experiment/process log'
OK = clib.view_file(log_file, text)
# show continuation message
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 build_menu_toa_basic_data():
'''
Build the menu Basic data.
'''
while True:
# print headers
clib.clear_screen()
clib.print_headers_with_environment(xlib.get_toa_data_basic_data_name())
# print the menu options
print( 'Options:')
print()
print( ' 1. Recreate genomic dataset file')
print( ' 2. Edit genomic file')
print()
print( ' 3. Recreate species file')
print( ' 4. Edit species file')
print()
print( ' 5. Download other basic data')
print()
print(f' 6. Load data into {xlib.get_toa_name()} database')
print()
print( ' X. Return to menu Genomic databases')
print()
# get the selected option
option = input('Input the selected option: ').upper()
# process the selected option
if option == '1':
cbioinfoapp.form_recreate_data_file(xtoa.get_dataset_file())
elif option == '2':
cbioinfoapp.form_edit_data_file(xtoa.get_dataset_file())
elif option == '3':
cbioinfoapp.form_recreate_data_file(xtoa.get_species_file())
elif option == '4':
cbioinfoapp.form_edit_data_file(xtoa.get_species_file())
elif option == '5':
ctoa.form_manage_genomic_database(xlib.get_toa_type_download_data(), xlib.get_toa_data_basic_data_code())
elif option == '6':
ctoa.form_manage_genomic_database(xlib.get_toa_type_load_data(), xlib.get_toa_data_basic_data_code())
elif option == 'X':
break
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 ...')