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 ...')