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_list_cluster_experiment_processes(): ''' List the processes of an experiment in the cluster. ''' # initialize the control variable OK = True # print the header clib.clear_screen() clib.print_headers_with_environment('Logs - List experiment processes in the cluster') # get the cluster 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) else: print('WARNING: There is not any running cluster.') OK = False # create the SSH client connection if OK: (OK, error_list, ssh_client) = xssh.create_ssh_client_connection(cluster_name, 'master') for error in error_list: log.write('{0}\n'.format(error)) # get experiment identification if OK: experiment_id = cinputs.input_experiment_id(ssh_client, help=True) if experiment_id == '': print('WARNING: The cluster {0} has not experiment data.'.format(cluster_name)) OK = False # get the result dataset list of the experiment if OK: command = 'cd {0}/{1}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;'.format(xlib.get_cluster_result_dir(), experiment_id) (OK, stdout, stderr) = xssh.execute_cluster_command(ssh_client, command) if OK: result_dataset_id_list = [] for line in stdout: line = line.rstrip('\n') if line != 'lost+found': result_dataset_id_list.append(line) # print the result dataset identification list of the experiment if OK: print(xlib.get_separator()) if result_dataset_id_list == []: print('*** WARNING: There is not any result dataset of the experiment {0}.'.format(experiment_id)) else: result_dataset_id_list.sort() # set data width result_dataset_width = 25 bioinfo_app_width = 25 # set line template line_template = '{0:' + str(result_dataset_width) + '} {1:' + str(bioinfo_app_width) + '}' # print header print(line_template.format('Result dataset', 'Bioinfo app / Utility')) print(line_template.format('=' * result_dataset_width, '=' * bioinfo_app_width)) # print detail lines for result_dataset_id in result_dataset_id_list: if result_dataset_id.startswith(xlib.get_bedtools_code()+'-'): bioinfo_app_name = xlib.get_bedtools_name() elif result_dataset_id.startswith(xlib.get_blastplus_code()+'-'): bioinfo_app_name = xlib.get_blastplus_name() elif result_dataset_id.startswith(xlib.get_bowtie2_code()+'-'): bioinfo_app_name = xlib.get_bowtie2_name() elif result_dataset_id.startswith(xlib.get_busco_code()+'-'): bioinfo_app_name = xlib.get_busco_name() elif result_dataset_id.startswith(xlib.get_cd_hit_code()+'-'): bioinfo_app_name = xlib.get_cd_hit_est_name() elif result_dataset_id.startswith(xlib.get_cd_hit_code()+'-'): bioinfo_app_name = xlib.get_cd_hit_est_name() elif result_dataset_id.startswith(xlib.get_detonate_code()+'-'): bioinfo_app_name = xlib.get_detonate_name() elif result_dataset_id.startswith(xlib.get_emboss_code()+'-'): bioinfo_app_name = xlib.get_emboss_name() elif result_dataset_id.startswith(xlib.get_fastqc_code()+'-'): bioinfo_app_name = xlib.get_fastqc_name() elif result_dataset_id.startswith(xlib.get_gmap_code()+'-'): bioinfo_app_name = xlib.get_gmap_name() elif result_dataset_id.startswith(xlib.get_gmap_gsnap_code()+'-'): bioinfo_app_name = xlib.get_gmap_gsnap_name() elif result_dataset_id.startswith(xlib.get_gzip_code()+'-'): bioinfo_app_name = xlib.get_gzip_name() elif result_dataset_id.startswith(xlib.get_insilico_read_normalization_code()+'-'): bioinfo_app_name = xlib.get_insilico_read_normalization_name() elif result_dataset_id.startswith(xlib.get_miniconda3_code()+'-'): bioinfo_app_name = xlib.get_miniconda3_name() elif result_dataset_id.startswith(xlib.get_ngshelper_code()+'-'): bioinfo_app_name = xlib.get_ngshelper_name() elif result_dataset_id.startswith(xlib.get_quast_code()+'-'): bioinfo_app_name = xlib.get_quast_name() elif result_dataset_id.startswith(xlib.get_r_code()+'-'): bioinfo_app_name = xlib.get_r_name() elif result_dataset_id.startswith(xlib.get_ref_eval_code()+'-'): bioinfo_app_name = xlib.get_ref_eval_name() elif result_dataset_id.startswith(xlib.get_rnaquast_code()+'-'): bioinfo_app_name = xlib.get_rnaquast_name() elif result_dataset_id.startswith(xlib.get_rsem_code()+'-'): bioinfo_app_name = xlib.get_rsem_name() elif result_dataset_id.startswith(xlib.get_rsem_eval_code()+'-'): bioinfo_app_name = xlib.get_rsem_eval_name() elif result_dataset_id.startswith(xlib.get_samtools_code()+'-'): bioinfo_app_name = xlib.get_samtools_name() elif result_dataset_id.startswith(xlib.get_soapdenovotrans_code()+'-'): bioinfo_app_name = xlib.get_soapdenovotrans_name() elif result_dataset_id.startswith(xlib.get_star_code()+'-'): bioinfo_app_name = xlib.get_star_name() elif result_dataset_id.startswith(xlib.get_transabyss_code()+'-'): bioinfo_app_name = xlib.get_transabyss_name() elif result_dataset_id.startswith(xlib.get_transcript_filter_code()+'-'): bioinfo_app_name = xlib.get_transcript_filter_name() elif result_dataset_id.startswith(xlib.get_transcriptome_blastx_code()+'-'): bioinfo_app_name = xlib.get_transcriptome_blastx_name() elif result_dataset_id.startswith(xlib.get_transrate_code()+'-'): bioinfo_app_name = xlib.get_transrate_name() elif result_dataset_id.startswith(xlib.get_trimmomatic_code()+'-'): bioinfo_app_name = xlib.get_trimmomatic_name() elif result_dataset_id.startswith(xlib.get_trinity_code()+'-'): bioinfo_app_name = xlib.get_trinity_name() else: bioinfo_app_name = 'xxx' print(line_template.format(result_dataset_id, bioinfo_app_name)) # 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_view_cluster_experiment_process_log(): ''' View the log of an experiment process in the cluster. ''' # initialize the control variable OK = True # print the header clib.clear_screen() clib.print_headers_with_environment('Logs - View an experiment process log in the cluster') # get the clustner name if OK: print(xlib.get_separator()) if xec2.get_running_cluster_list(volume_creator_included=False) != []: cluster_name = cinputs.input_cluster_name(volume_creator_included=False, help=True) else: print('WARNING: There is not any running cluster.') OK = False # create the SSH client connection if OK: (OK, error_list, ssh_client) = xssh.create_ssh_client_connection(cluster_name, 'master') for error in error_list: log.write('{0}\n'.format(error)) # create the SSH transport connection if OK: (OK, error_list, ssh_transport) = xssh.create_ssh_transport_connection(cluster_name, 'master') for error in error_list: log.write('{0}\n'.format(error)) # create the SFTP client if OK: sftp_client = xssh.create_sftp_client(ssh_transport) # get the experiment identification if OK: experiment_id = cinputs.input_experiment_id(ssh_client, help=True) if experiment_id == '': print('WARNING: The cluster has not experiment data.') OK = False # get the result_dataset identification if OK: result_dataset_id = cinputs.input_result_dataset_id('uncompressed', ssh_client, experiment_id, help=True) if result_dataset_id == '': print('WARNING: The experiment {0} has not result datasets.'.format(experiment_id)) OK = False # create the local path if not os.path.exists(xlib.get_temp_dir()): os.makedirs(xlib.get_temp_dir()) # get the log file name and build local and cluster paths if OK: log_file = xlib.get_cluster_log_file() local_path = '{0}/{1}'.format(xlib.get_temp_dir(), log_file) cluster_path = '{0}/{1}/{2}'.format(xlib.get_cluster_experiment_result_dir(experiment_id), result_dataset_id, log_file) # download the log file from the cluster if OK: print(xlib.get_separator()) print('The file {0} is being downloaded from {1} ...'.format(log_file, cluster_path)) OK = xssh.get_file(sftp_client, cluster_path, local_path) if OK: print('The file has been uploaded.') # close the SSH transport connection if OK: xssh.close_ssh_transport_connection(ssh_transport) # close the SSH client connection if OK: xssh.close_ssh_client_connection(ssh_client) # view the log file if OK: text = 'Logs - View an experiment process log in the cluster' OK = clib.view_file(local_path, text) # show continuation message print(xlib.get_separator()) input('Press [Intro] to continue ...')
def form_list_cluster_experiment_processes(): ''' List the processes of an experiment in the cluster. ''' # initialize the control variable OK = True # print the header clib.clear_screen() clib.print_headers_with_environment( 'Logs - List experiment processes in the cluster') # get the cluster name print(xlib.get_separator()) if xec2.get_running_cluster_list(only_environment_cluster=True, volume_creator_included=False) != []: cluster_name = cinputs.input_cluster_name( volume_creator_included=False, help=True) else: print('WARNING: There is not any running cluster.') OK = False # create the SSH client connection if OK: (OK, error_list, ssh_client) = xssh.create_ssh_client_connection(cluster_name) for error in error_list: print(error) # get experiment identification if OK: experiment_id = cinputs.input_experiment_id(ssh_client, help=True) if experiment_id == '': print( f'WARNING: The cluster {cluster_name} does not have experiment data.' ) OK = False # get the result dataset list of the experiment if OK: command = f'cd {xlib.get_cluster_result_dir()}/{experiment_id}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;' (OK, stdout, _) = xssh.execute_cluster_command(ssh_client, command) if OK: result_dataset_id_list = [] for line in stdout: line = line.rstrip('\n') if line != 'lost+found': result_dataset_id_list.append(line) # print the result dataset identification list of the experiment if OK: print(xlib.get_separator()) if result_dataset_id_list == []: print( f'*** WARNING: There is not any result dataset of the experiment {experiment_id}.' ) else: result_dataset_id_list.sort() # set data width result_dataset_width = 30 bioinfo_app_width = 25 # set line line = '{0:' + str(result_dataset_width) + '} {1:' + str( bioinfo_app_width) + '}' # print header print(line.format('Result dataset', 'Bioinfo app / Utility')) print( line.format('=' * result_dataset_width, '=' * bioinfo_app_width)) # print detail lines for result_dataset_id in result_dataset_id_list: if result_dataset_id.startswith(xlib.get_bedtools_code() + '-'): bioinfo_app_name = xlib.get_bedtools_name() elif result_dataset_id.startswith(xlib.get_blastplus_code() + '-'): bioinfo_app_name = xlib.get_blastplus_name() elif result_dataset_id.startswith(xlib.get_bcftools_code() + '-'): bioinfo_app_name = xlib.get_bcftools_name() elif result_dataset_id.startswith(xlib.get_bowtie2_code() + '-'): bioinfo_app_name = xlib.get_bowtie2_name() elif result_dataset_id.startswith(xlib.get_busco_code() + '-'): bioinfo_app_name = xlib.get_busco_name() elif result_dataset_id.startswith(xlib.get_cd_hit_code() + '-'): bioinfo_app_name = xlib.get_cd_hit_name() elif result_dataset_id.startswith(xlib.get_cd_hit_est_code() + '-'): bioinfo_app_name = xlib.get_cd_hit_est_name() elif result_dataset_id.startswith(xlib.get_cuffdiff_code() + '-'): bioinfo_app_name = xlib.get_cuffdiff_name() elif result_dataset_id.startswith(xlib.get_cufflinks_code() + '-'): bioinfo_app_name = xlib.get_cufflinks_name() elif result_dataset_id.startswith( xlib.get_cufflinks_cuffmerge_code() + '-'): bioinfo_app_name = xlib.get_cufflinks_cuffmerge_name() elif result_dataset_id.startswith(xlib.get_cuffnorm_code() + '-'): bioinfo_app_name = xlib.get_cuffnorm_name() elif result_dataset_id.startswith(xlib.get_cuffquant_code() + '-'): bioinfo_app_name = xlib.get_cuffquant_name() elif result_dataset_id.startswith(xlib.get_cutadapt_code() + '-'): bioinfo_app_name = xlib.get_cutadapt_name() elif result_dataset_id.startswith( xlib.get_ddradseq_simulation_code() + '-'): bioinfo_app_name = xlib.get_ddradseq_simulation_name() elif result_dataset_id.startswith( xlib.get_ddradseqtools_code() + '-'): bioinfo_app_name = xlib.get_ddradseqtools_name() elif result_dataset_id.startswith(xlib.get_detonate_code() + '-'): bioinfo_app_name = xlib.get_detonate_name() elif result_dataset_id.startswith(xlib.get_diamond_code() + '-'): bioinfo_app_name = xlib.get_diamond_name() elif result_dataset_id.startswith(xlib.get_emboss_code() + '-'): bioinfo_app_name = xlib.get_emboss_name() elif result_dataset_id.startswith( xlib.get_entrez_direct_code() + '-'): bioinfo_app_name = xlib.get_entrez_direct_name() elif result_dataset_id.startswith(xlib.get_express_code() + '-'): bioinfo_app_name = xlib.get_express_name() elif result_dataset_id.startswith(xlib.get_fastqc_code() + '-'): bioinfo_app_name = xlib.get_fastqc_name() elif result_dataset_id.startswith(xlib.get_ggtrinity_code() + '-'): bioinfo_app_name = xlib.get_ggtrinity_name() elif result_dataset_id.startswith(xlib.get_gmap_gsnap_code() + '-'): bioinfo_app_name = xlib.get_gmap_gsnap_name() elif result_dataset_id.startswith(xlib.get_gmap_code() + '-'): bioinfo_app_name = xlib.get_gmap_name() elif result_dataset_id.startswith(xlib.get_gsnap_code() + '-'): bioinfo_app_name = xlib.get_gsnap_name() elif result_dataset_id.startswith(xlib.get_gzip_code() + '-'): bioinfo_app_name = xlib.get_gzip_name() elif result_dataset_id.startswith(xlib.get_hisat2_code() + '-'): bioinfo_app_name = xlib.get_hisat2_name() elif result_dataset_id.startswith(xlib.get_htseq_code() + '-'): bioinfo_app_name = xlib.get_htseq_name() elif result_dataset_id.startswith(xlib.get_htseq_count_code() + '-'): bioinfo_app_name = xlib.get_htseq_count_name() elif result_dataset_id.startswith( xlib.get_insilico_read_normalization_code() + '-'): bioinfo_app_name = xlib.get_insilico_read_normalization_name( ) elif result_dataset_id.startswith(xlib.get_ipyrad_code() + '-'): bioinfo_app_name = xlib.get_ipyrad_name() elif result_dataset_id.startswith(xlib.get_kallisto_code() + '-'): bioinfo_app_name = xlib.get_kallisto_name() elif result_dataset_id.startswith(xlib.get_miniconda3_code() + '-'): bioinfo_app_name = xlib.get_miniconda3_name() elif result_dataset_id.startswith(xlib.get_ngshelper_code() + '-'): bioinfo_app_name = xlib.get_ngshelper_name() elif result_dataset_id.startswith(xlib.get_quast_code() + '-'): bioinfo_app_name = xlib.get_quast_name() elif result_dataset_id.startswith(xlib.get_r_code() + '-'): bioinfo_app_name = xlib.get_r_name() elif result_dataset_id.startswith(xlib.get_raddesigner_code() + '-'): bioinfo_app_name = xlib.get_raddesigner_name() elif result_dataset_id.startswith(xlib.get_ref_eval_code() + '-'): bioinfo_app_name = xlib.get_ref_eval_name() elif result_dataset_id.startswith(xlib.get_rnaquast_code() + '-'): bioinfo_app_name = xlib.get_rnaquast_name() elif result_dataset_id.startswith(xlib.get_rsem_code() + '-'): bioinfo_app_name = xlib.get_rsem_name() elif result_dataset_id.startswith(xlib.get_rsem_eval_code() + '-'): bioinfo_app_name = xlib.get_rsem_eval_name() elif result_dataset_id.startswith(xlib.get_rsitesearch_code() + '-'): bioinfo_app_name = xlib.get_rsitesearch_name() elif result_dataset_id.startswith(xlib.get_samtools_code() + '-'): bioinfo_app_name = xlib.get_samtools_name() elif result_dataset_id.startswith(xlib.get_soapdenovo2_code() + '-'): bioinfo_app_name = xlib.get_soapdenovo2_name() elif result_dataset_id.startswith( xlib.get_soapdenovotrans_code() + '-'): bioinfo_app_name = xlib.get_soapdenovotrans_name() elif result_dataset_id.startswith(xlib.get_star_code() + '-'): bioinfo_app_name = xlib.get_star_name() elif result_dataset_id.startswith(xlib.get_starcode_code() + '-'): bioinfo_app_name = xlib.get_starcode_name() elif result_dataset_id.startswith(xlib.get_toa_code() + '-'): bioinfo_app_name = xlib.get_toa_name() elif result_dataset_id.startswith( xlib.get_toa_process_download_basic_data_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_basic_data_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_dicots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_dicots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_gene_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_gene_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_go_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_go_name() elif result_dataset_id.startswith( xlib.get_toa_process_download_gymno_01_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_gymno_01_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_interpro_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_interpro_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_monocots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_monocots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_taxonomy_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_taxonomy_name( ) elif result_dataset_id.startswith( xlib. get_toa_process_gilist_viridiplantae_nucleotide_gi_code( ) + '-'): bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_nucleotide_gi_name( ) elif result_dataset_id.startswith( xlib. get_toa_process_gilist_viridiplantae_protein_gi_code() + '-'): bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_protein_gi_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_basic_data_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_basic_data_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_dicots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_dicots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_gene_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_gene_name() elif result_dataset_id.startswith( xlib.get_toa_process_load_go_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_go_name() elif result_dataset_id.startswith( xlib.get_toa_process_load_gymno_01_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_gymno_01_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_interpro_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_interpro_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_monocots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_monocots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_merge_annotations_code() + '-'): bioinfo_app_name = xlib.get_toa_process_merge_annotations_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_nr_blastplus_db_code() + '-'): bioinfo_app_name = xlib.get_toa_process_nr_blastplus_db_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_nr_diamond_db_code() + '-'): bioinfo_app_name = xlib.get_toa_process_nr_diamond_db_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_nt_blastplus_db_code() + '-'): bioinfo_app_name = xlib.get_toa_process_nt_blastplus_db_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_pipeline_aminoacid_code() + '-'): bioinfo_app_name = xlib.get_toa_process_pipeline_aminoacid_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_pipeline_nucleotide_code() + '-'): bioinfo_app_name = xlib.get_toa_process_pipeline_nucleotide_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_dicots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_dicots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_gymno_01_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_gymno_01_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_monocots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_monocots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_refseq_plant_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_refseq_plant_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_rebuild_toa_database_code() + '-'): bioinfo_app_name = xlib.get_get_toa_process_rebuild_toa_database_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_recreate_toa_database_code() + '-'): bioinfo_app_name = xlib.get_get_toa_process_recreate_toa_database_name( ) elif result_dataset_id.startswith(xlib.get_tophat_code() + '-'): bioinfo_app_name = xlib.get_tophat_name() elif result_dataset_id.startswith(xlib.get_transabyss_code() + '-'): bioinfo_app_name = xlib.get_transabyss_name() elif result_dataset_id.startswith( xlib.get_transcript_filter_code() + '-'): bioinfo_app_name = xlib.get_transcript_filter_name() elif result_dataset_id.startswith( xlib.get_transcriptome_blastx_code() + '-'): bioinfo_app_name = xlib.get_transcriptome_blastx_name() elif result_dataset_id.startswith( xlib.get_transdecoder_code() + '-'): bioinfo_app_name = xlib.get_transdecoder_name() elif result_dataset_id.startswith(xlib.get_transrate_code() + '-'): bioinfo_app_name = xlib.get_transrate_name() elif result_dataset_id.startswith(xlib.get_trimmomatic_code() + '-'): bioinfo_app_name = xlib.get_trimmomatic_name() elif result_dataset_id.startswith(xlib.get_trinity_code() + '-'): bioinfo_app_name = xlib.get_trinity_name() elif result_dataset_id.startswith( xlib.get_variant_calling_code() + '-'): bioinfo_app_name = xlib.get_variant_calling_name() elif result_dataset_id.startswith(xlib.get_vcftools_code() + '-'): bioinfo_app_name = xlib.get_vcftools_name() elif result_dataset_id.startswith( xlib.get_vcftools_perl_libraries_code() + '-'): bioinfo_app_name = xlib.get_vcftools_perl_libraries_name() elif result_dataset_id.startswith(xlib.get_vsearch_code() + '-'): bioinfo_app_name = xlib.get_vsearch_name() else: bioinfo_app_name = 'xxx' print(line.format(result_dataset_id, bioinfo_app_name)) # 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_results_logs(): ''' List the processes of an experiment in the cluster. ''' # initialize the control variable OK = True # print the header clib.clear_screen() clib.print_headers_with_environment('Logs - List result logs') # get experiment identification experiment_id = cinputs.input_experiment_id() if experiment_id == '': print('WARNING: There is not any experiment/process run.') OK = False # get the dictionary of TOA configuration. if OK: toa_config_dict = xtoa.get_toa_config_dict() # get the result dataset list of the experiment if OK: experiment_dir = f'{toa_config_dict["RESULT_DIR"]}/{experiment_id}' subdir_list = [ subdir for subdir in os.listdir(experiment_dir) if os.path.isdir(os.path.join(experiment_dir, subdir)) ] result_dataset_id_list = [] for subdir in subdir_list: result_dataset_id_list.append(subdir) # print the result dataset identification list of the experiment if OK: print(xlib.get_separator()) if result_dataset_id_list == []: print( f'*** WARNING: There is not any result dataset of the experiment/process {experiment_id}.' ) else: result_dataset_id_list.sort() # set data width result_dataset_width = 25 bioinfo_app_width = 25 # set line template line_template = '{0:' + str( result_dataset_width) + '} {1:' + str( bioinfo_app_width) + '}' # print header print( line_template.format('Result dataset', 'Bioinfo app / Utility')) print( line_template.format('=' * result_dataset_width, '=' * bioinfo_app_width)) # print detail lines for result_dataset_id in result_dataset_id_list: if result_dataset_id.startswith(xlib.get_blastplus_code() + '-'): bioinfo_app_name = xlib.get_blastplus_name() elif result_dataset_id.startswith(xlib.get_diamond_code() + '-'): bioinfo_app_name = xlib.get_diamond_name() elif result_dataset_id.startswith( xlib.get_entrez_direct_code() + '-'): bioinfo_app_name = xlib.get_entrez_direct_name() elif result_dataset_id.startswith(xlib.get_miniconda3_code() + '-'): bioinfo_app_name = xlib.get_miniconda3_name() elif result_dataset_id.startswith(xlib.get_r_code() + '-'): bioinfo_app_name = xlib.get_r_name() elif result_dataset_id.startswith( xlib.get_toa_process_download_basic_data_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_basic_data_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_dicots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_dicots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_gene_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_gene_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_go_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_go_name() elif result_dataset_id.startswith( xlib.get_toa_process_download_gymno_01_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_gymno_01_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_interpro_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_interpro_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_monocots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_monocots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_download_taxonomy_code() + '-'): bioinfo_app_name = xlib.get_toa_process_download_taxonomy_name( ) elif result_dataset_id.startswith( xlib. get_toa_process_gilist_viridiplantae_nucleotide_gi_code( ) + '-'): bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_nucleotide_gi_name( ) elif result_dataset_id.startswith( xlib. get_toa_process_gilist_viridiplantae_protein_gi_code() + '-'): bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_protein_gi_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_basic_data_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_basic_data_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_dicots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_dicots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_gene_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_gene_name() elif result_dataset_id.startswith( xlib.get_toa_process_load_go_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_go_name() elif result_dataset_id.startswith( xlib.get_toa_process_load_gymno_01_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_gymno_01_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_interpro_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_interpro_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_load_monocots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_load_monocots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_merge_annotations_code() + '-'): bioinfo_app_name = xlib.get_toa_process_merge_annotations_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_nr_blastplus_db_code() + '-'): bioinfo_app_name = xlib.get_toa_process_nr_blastplus_db_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_nr_diamond_db_code() + '-'): bioinfo_app_name = xlib.get_toa_process_nr_diamond_db_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_nt_blastplus_db_code() + '-'): bioinfo_app_name = xlib.get_toa_process_nt_blastplus_db_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_pipeline_aminoacid_code() + '-'): bioinfo_app_name = xlib.get_toa_process_pipeline_aminoacid_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_pipeline_nucleotide_code() + '-'): bioinfo_app_name = xlib.get_toa_process_pipeline_nucleotide_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_dicots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_dicots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_gymno_01_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_gymno_01_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_monocots_04_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_monocots_04_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_proteome_refseq_plant_code() + '-'): bioinfo_app_name = xlib.get_toa_process_proteome_refseq_plant_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_rebuild_toa_database_code() + '-'): bioinfo_app_name = xlib.get_get_toa_process_rebuild_toa_database_name( ) elif result_dataset_id.startswith( xlib.get_toa_process_recreate_toa_database_code() + '-'): bioinfo_app_name = xlib.get_get_toa_process_recreate_toa_database_name( ) elif result_dataset_id.startswith( xlib.get_transdecoder_code() + '-'): bioinfo_app_name = xlib.get_transdecoder_name() else: bioinfo_app_name = 'xxx' print(line_template.format(result_dataset_id, bioinfo_app_name)) # show continuation message print(xlib.get_separator()) input('Press [Intro] to continue ...')