FinalProject/cli-launcher.py at develop · Vesemir/FinalProject · GitHub

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__copyright__ = """
Copyright © 2000 nnosko <shackaler@yandex.ru>
This work is free. You can redistribute it and/or modify it under the
terms of the Do What The Fuck You Want To Public License, Version 2,
as published by Sam Hocevar. See the COPYING file for more details.
"""
import os
import sys

import argparse
from argparse import RawTextHelpFormatter
from vbox.tools.vmrun_cycled import run_sample, run_cycled
from vbox.tools.PyCommands.settings import RAW_DIR
from lib.pander import process_all_logs
from lib.seq_analyzer.local_alignment import test_match

def main():
    parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter,
                                     description='Command line interface for '
                                     'invoking scan, parse, and analyze procedures'
                                     ' of current module.')
    parser.add_argument('-a', '--action', default='analyze_exe_sample',
                        help='Specify actions, one of: \n'
                        'analyze_exe_sample - default value, performs sample '
                        'scan, logs parsing and slow_comparison with kbase\n'
                        'analyze_seq - performs slow_comparison of ready '
                        'sequence with kbase and outputs html report\n\n'
                        'parse_log - performs parsing of ready log file, produced '
                        'by scan_exe, outputs npy which can later be used by '
                        'analyze_seq\n\n'
                        'scan_sample - performs launch in vbox and logs collection\n\n'
                        'add_to_kbase - performs scanning, parsing and add resulting'
                        ' sequence to current knowledge base\n\n'
                        'batch_scan - performs batch parallel scan of all samples in '
                        ' specified location, outputs to vbox/logs\n\n'
                        'batch_parse - performs batch parsing of all logs in target directory, '
                        'outputs to hdf5 file "test" directory\n\n'
                        'batch_analyze - performs fast_comparison of all sequences '
                        'in target directory with knowledge base')
    parser.add_argument('-t', '--target', required=True,
                        help='Select the target for specified action')
    args = parser.parse_args()
    action, target = args.action, args.target
    if action == 'analyze_seq':
        test_group = 'test'
        print('[!] Option analyze_seq was selected, processing specified sequence '
              'in "%s" directory.' % test_group)
        test_match(strategy='SLOW', test_group=test_group, match_one=target)
    elif action == 'parse_log':
        print('[!] Option parse_log was selected, processing specified log '
              'outputting to "test" directory of current hdf5 file')
        if not os.path.isfile(target):
            print('[-] Specified target file doesn\'t exist !')
            sys.exit(1)
        if not target.endswith('apicalls.log'):
            print('[-] Target file should be created by scan and it\'s usually'
                  ' named apicalls.log, if you renamed, please rename it back!')
            sys.exit(1)
        process_all_logs(source=target, target_group='test')
    elif action == 'scan_sample':
        print('[!] Option scan_exe was selected, collecting logs for specified '
              'sample zipped executable file.')
        if not os.path.isfile(target):
            print('[-] Specified target file doesn\'t exist !')
            sys.exit(1)
        if not target.endswith('.zip'):
            print('[-] Target file should be zipped!')
            sys.exit(1)
        target_logfile = run_sample(target)
        if not os.path.isfile(target_logfile):
            print('[-] Unfortunately, scanning produced no logs, terminating...')
            sys.exit(1)
        else:
            print('[+] Logs present in %s file.' % os.path.abspath(target_logfile))
    elif action == 'add_to_kbase':
        print('[!] Option add_to_kbase was selected, processing specified sample '
              'zipped executable file, parsing and adding result sequence into '
              'default knowledgebase file.')
        if not os.path.isfile(target):
            print('[-] Specified target file doesn\'t exist !')
            sys.exit(1)
        if not target.endswith('.zip'):
            print('[-] Target file should be zipped!')
            sys.exit(1)
        target_logfile = run_sample(target)
        if not os.path.isfile(target_logfile):
            print('[-] Unfortunately, scanning produced no logs, terminating...')
            sys.exit(1)
        process_all_logs(source=target_logfile, target_group='knowledgebase')
        print('[+] Succesfully added %s sequence to knowledgebase.' % target)
    elif action == 'batch_scan':
        print('[!] Option batch_scan selected, running scan of all samples in '
              'specified samples directory and outputting result into '
              'default logs directory vbox/logs...')
        if not os.path.isdir(target):
            print('[-] Specified target directory doesn\'t exist !')
            sys.exit(1)
        run_cycled(sample_dir=target)
        print('[+] Logs present in %s directory.' % RAW_DIR)
    elif action == 'batch_parse':
        print('[!]  Option batch_parse selected, running parse of all sample logs'
              ' in specified logs directory and outputting to "test" directory'
              ' of default knowledgebase file lib/seq_analyzer/datas/knowledgebase.hdf5')
        if not os.path.isdir(target):
            print('[-] Specified target directory doesn\'t exist !')
            sys.exit(1)
        process_all_logs(source=target, target_group='test')
    elif action == 'batch_analyze':
        print('[!] Option batch_analyze selected, running fast_comparison of '
              'all sequences in default "test" group of default knowledgebase '
              'file on current kbase')
        test_match(strategy='FAST', test_group=target)
    elif action == 'analyze_exe_sample':
        print('[!] Default option analyze_exe_sample selected, going to perform '
              'scan, parsing and analyze that sample on current knowledgebase.')
        if not os.path.isfile(target):
            print('[-] Specified target file doesn\'t exist !')
            sys.exit(1)
        if not target.endswith('.zip'):
            print('[-] Target file should be zipped!')
            sys.exit(1)
        target_logfile = run_sample(target)
        target_name = os.path.splitext(os.path.basename(target))[0]
        if not os.path.isfile(target_logfile):
            print('[-] Unfortunately, scanning produced no logs, terminating...')
            sys.exit(1)
        process_all_logs(source=target_logfile, target_group='test')
        test_match(strategy='SLOW',
                   test_group='test',
                   match_one=target_name)
    else:
        print('[-] Unknown action "%s" specified, terminating...' % action)
        sys.exit(1)


if __name__ == '__main__':
    main()