How to use install_component method in localstack

Best Python code snippet using localstack_python

launcher.py

Source:launcher.py

...55        print(datahandling.get_connection_info())56    if args.info:57        show_info()58    elif args.install:59        install_component()60    elif args.sample_id is not None:61        run_sample(args)62def show_info():63    """64    Shows information about the component65    """66    message: str = (67        f"Component: {COMPONENT['name']}\n"68        f"Version: {COMPONENT['version']}\n"69        f"Details: {json.dumps(COMPONENT['details'], indent=4)}\n"70        f"Requirements: {json.dumps(COMPONENT['requirements'], indent=4)}\n"71        f"Output files: {json.dumps(COMPONENT['db_values_changes']['files'], indent=4)}\n"72    )73    print(message)74def install_component():75    component: list[dict] = datahandling.get_components(component_names=[COMPONENT['name']])76    # if len(component) == 1:77    #     print(f"Component has already been installed")78    if len(component) > 1:79        print(f"Component exists multiple times in DB, please contact an admin to fix this in order to proceed")80    else:81        #HACK: Installs based on your current directory currently. Should be changed to the directory your docker/singularity file is82        #HACK: Removed install check so you can reinstall the component. Should do this in a nicer way83        COMPONENT['install']['path'] = os.path.os.getcwd()84        datahandling.post_component(COMPONENT)85        component: list[dict] = datahandling.get_components(component_names=[COMPONENT['name']])86        if len(component) != 1:87            print(f"Error with installation of {COMPONENT['name']} {len(component)}\n")88            exit()89def run_sample(args: object):90    """91    Runs sample ID through snakemake pipeline92    """93    if not os.path.isdir(args.outdir):94        os.makedirs(args.outdir)95    os.chdir(args.outdir)96    sample: list[dict] = datahandling.get_samples(sample_ids=[args.sample_id])97    component: list[dict] = datahandling.get_components(component_names=[COMPONENT['name']])98    if len(component) == 0:99        print(f"component not found in DB, would you like to install it (Y/N)?:")100        install_component()101    if len(sample) == 0:102        # Invalid sample id103        print(f"sample_id not found in DB")104        pass105    elif len(sample) != 1:106        print(f"Error with sample_id")107    elif len(component) != 1:108        print(f"Error with component_id")109    else:110        print(f"snakemake -s /bifrost_{COMPONENT['display_name']}/bifrost_{COMPONENT['display_name']}/pipeline.smk --config sample_id={str(sample[0]['_id'])} component_id={str(component[0]['_id'])}")111        try:112            process: subprocess.Popen = subprocess.Popen(113                f"snakemake -s /bifrost_{COMPONENT['display_name']}/bifrost_{COMPONENT['display_name']}/pipeline.smk --config sample_id={str(sample[0]['_id'])} component_id={str(component[0]['_id'])}",114                stdout=sys.stdout,...

setmeup.py

Source:setmeup.py

1import os, platform, json, subprocess2from common_res.clc_tools import ColorPrint, get_distro, get_version, get_architecture3resdir = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'setmeup_res')4logname = 'setmeup_LOG.log'5with open(os.path.join(resdir, 'install_scripts_index.json'), 'r') as data_f, open(logname, 'w') as log_f:6    install_data = json.load(data_f)7    uname = platform.uname()8    this_distro = get_distro(uname)9    this_version = get_version(uname)10    this_arch = get_architecture(uname)11    os_id = None12    for osid in install_data['supported_os']:13        if osid['distro'] == this_distro and osid['version'] == this_version and osid['arch'] == this_arch:14            os_id = osid['id']15            break16    if os_id is None:17        ColorPrint.Fail('Current system %s - %s - %s not supported, sorry! =/' % (this_distro, this_version, this_arch))18        exit()19    ColorPrint.Bold('Components to be installed (Green = available):\n')20    install_components = list()21    for command_group in install_data['command_groups']:22        install_component = dict()23        install_component['name'] = command_group['name']24        install_component['active'] = False25        install_component['components'] = list()26        print('<%s>' % command_group['name'])27        for component in command_group['components']:28            script_id = '-'29            for script_info_set in component['script_info']:30                for script_os in script_info_set['os']:31                    if script_os['id'] == os_id:32                        script_id = script_info_set['script_id']33                        install_component['active'] = True34                        break35                if not script_id == '-':36                    break37            script_item = dict()38            script_item['name'] = component['name']39            script_item['script'] = os.path.join(resdir, 'scripts', command_group['code'], '%s-%s.sh' % (component['code'], script_id))40            script_item['active'] = (not script_id == '-')41            install_component['components'].append(script_item)42            if script_item['active']:43                ColorPrint.Green('  * %s' % script_item['name'])44            else:45                ColorPrint.Fail('  * %s' % script_item['name'])46        if install_component['active']:47            install_components.append(install_component)48    print()49    user_ack = input('Is this acceptable? [y]n: ')50    if not (user_ack.lower() == 'y' or user_ack == ''):51        print('Very well. Not proceeding.')52        exit()53    print('Proceeding...')54    print()55    for install_component in install_components:56        print('<%s>' % install_component['name'])57        components = [component for component in install_component['components'] if component['active']]58        for script in components:59            print('  * %s ... ' % script['name'], end='')60            try:61                n = len(script['script'])62                log_f.write('\n%s\n%s\n%s\n' % ('-'*n, script['script'], '='*n))63                output = subprocess.check_output([script['script']], stdin=subprocess.DEVNULL, stderr=log_f)64                log_f.write(output.decode("utf-8"))65                ColorPrint.Green('Success.')66            except subprocess.CalledProcessError as e:67                log_f.write(e.output.decode("utf-8"))68                ColorPrint.Fail('Failed.')69    print('Install script outputs written to logfile: ', end='')70    ColorPrint.Bold(logname)71        ...

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