def __init__(self, config=None, read_config_files=None): if config is None: config = read_config() self._read_cfg_files = read_config_files self._cfg_obj = config self._used_var = {}
metavar="FILE", required=False, help='config file (highest priority value of settings; this overrides the '\ 'setting values found in the peyotl config and the values in the config '\ 'specified by the GCMDR_CONFIG_FILE env var (if used).') args = parser.parse_args() cmd = args.command.lower() if cmd not in lc_commands: sys.exit('Expecting the command to be one of: {}'.format(', '.join(commands))) cfg_filepaths = [None] # always read the default peyotl config ecfg = os.environ.get('GCMDR_CONFIG_FILE') if ecfg is not None: cfg_filepaths.append(ecfg) if args.config: cfg_filepaths.append(args.config) cfg, read_cfg_files = read_config(cfg_filepaths) _LOG.debug('read configuration in lowest->highest priority from: "{}"'.format('", "'.join(read_cfg_files))) if cmd in requires_studies: if args.studies is None: sys.exit('A list of trees in studies (--studies arg) must be specified when using the "{}" command'.format(cmd)) tree_list = parse_study_tree_list(args.studies) gcmdr = GraphCommander(config=cfg, read_config_files=read_cfg_files) if cmd == 'taxonomy': gcmdr.load_taxonomy() elif cmd == 'fetchnexsons': gcmdr.fetch_nexsons(tree_list, download=args.download) elif cmd == 'loadgraph': gcmdr.load_graph(tree_list, reinitialize=args.reinitialize) elif cmd == 'synthesize': gcmdr.synthesize() elif cmd == 'extractsynthesis':
delete_study, \ GitWorkflowError, \ merge_from_master from peyotl.phylesystem.phylesystem_umbrella import Phylesystem from peyotl.utility.input_output import read_as_json from peyotl.utility import get_logger, read_config, _replace_default_config import unittest import codecs import json import copy import sys from peyotl.test.support import pathmap _LOG = get_logger(__name__) config, cfg_filename = read_config() COMMITS_SHOULD_FAIL_ARG = 'tiny_max_file_size' COMMITS_SHOULD_FAIL = COMMITS_SHOULD_FAIL_ARG in sys.argv if COMMITS_SHOULD_FAIL: sys.argv.remove(COMMITS_SHOULD_FAIL_ARG) if 'phylesystem' not in config.sections(): config.add_section('phylesystem') config.set('phylesystem', 'max_file_size', '10') # ten bytes is not large _replace_default_config(config) phylesystem = Phylesystem(pathmap.get_test_repos(), ) _MINI_PHYL_SHA1 = '2d59ab892ddb3d09d4b18c91470b8c1c4cca86dc' _SID = 'xy_10' _AUTH = { 'name': 'test_name',
required=False, help='config file (highest priority value of settings; this overrides the '\ 'setting values found in the peyotl config and the values in the config '\ 'specified by the GCMDR_CONFIG_FILE env var (if used).') args = parser.parse_args() cmd = args.command.lower() if cmd not in lc_commands: sys.exit('Expecting the command to be one of: {}'.format( ', '.join(commands))) cfg_filepaths = [None] # always read the default peyotl config ecfg = os.environ.get('GCMDR_CONFIG_FILE') if ecfg is not None: cfg_filepaths.append(ecfg) if args.config: cfg_filepaths.append(args.config) cfg, read_cfg_files = read_config(cfg_filepaths) _LOG.debug( 'read configuration in lowest->highest priority from: "{}"'.format( '", "'.join(read_cfg_files))) if cmd in requires_studies: if args.studies is None: sys.exit( 'A list of trees in studies (--studies arg) must be specified when using the "{}" command' .format(cmd)) tree_list = parse_study_tree_list(args.studies) gcmdr = GraphCommander(config=cfg, read_config_files=read_cfg_files) if cmd == 'taxonomy': gcmdr.load_taxonomy() elif cmd == 'fetchnexsons': gcmdr.fetch_nexsons(tree_list, download=args.download) elif cmd == 'loadgraph':
commit_and_try_merge2master, \ delete_study, \ GitWorkflowError, \ merge_from_master from peyotl.phylesystem.phylesystem_umbrella import Phylesystem from peyotl.utility.input_output import read_as_json from peyotl.utility import get_logger, read_config, _replace_default_config import unittest import codecs import json import copy import sys from peyotl.test.support import pathmap _LOG = get_logger(__name__) config, cfg_filename = read_config() COMMITS_SHOULD_FAIL_ARG = 'tiny_max_file_size' COMMITS_SHOULD_FAIL = COMMITS_SHOULD_FAIL_ARG in sys.argv if COMMITS_SHOULD_FAIL: sys.argv.remove(COMMITS_SHOULD_FAIL_ARG) if 'phylesystem' not in config.sections(): config.add_section('phylesystem') config.set('phylesystem', 'max_file_size', '10') # ten bytes is not large _replace_default_config(config) phylesystem = Phylesystem(pathmap.get_test_repos(), ) _MINI_PHYL_SHA1 = '2d59ab892ddb3d09d4b18c91470b8c1c4cca86dc' _SID = 'xy_10' _AUTH = {