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 = {