def test_changing_prefix_works():
pyconfig.etcd(prefix='pyconfig/other')
eq_(pyconfig.etcd().prefix, '/pyconfig/other/')
conf = pyconfig.etcd().load()
eq_(conf, {})
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test')
eq_(pyconfig.etcd().prefix, '/pyconfig_test/test/')
def test_watching():
# Enable watching
os.environ['PYCONFIG_ETCD_WATCH'] = 'true'
pyconfig.Config().clear()
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/watching')
pyconfig.reload()
# Wait for 20ms before writing to ensure the watcher thread is ready
time.sleep(0.020)
# Write a new value directly to etcd
pyconfig.etcd().client.write('pyconfig_test/watching/it.works',
pytool.json.as_json(True))
# Try to get the value... this is a bit sloppy but good luck doing
# something better
retry = 50
while retry:
retry -= 1
if pyconfig.get('it.works', None) is not None:
break
# Wait 20ms more for it to show up
time.sleep(0.020)
eq_(pyconfig.get('it.works', False), True)
def test_changing_prefix_works():
pyconfig.etcd(prefix='pyconfig/other')
eq_(pyconfig.etcd().prefix, '/pyconfig/other/')
conf = pyconfig.etcd().load()
eq_(conf, {})
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test')
eq_(pyconfig.etcd().prefix, '/pyconfig_test/test/')
def main():
"""Create a bdb entry."""
parser = argparse.ArgumentParser(
description="Create a BDB entry. The BDB entry (.bdb) or WHY NOT\
(.whynot) file, log and json files will be created in a separate\
directory using the given pdb_id and the directory structure:\
BDB_ROOT/ab/1abc/1abc.(bdb|whynot|log|json)")
parser.add_argument("-v",
"--verbose",
help="show verbose output",
action="store_true")
parser.add_argument("bdb_root_path",
help="Root directory of the bdb data.",
type=lambda x: is_valid_directory(parser, x))
parser.add_argument("pdb_file_path",
help="PDB file location.",
type=lambda x: is_valid_file(parser, x))
parser.add_argument("pdb_id",
help="PDB accession code.",
type=lambda x: is_valid_pdbid(parser, x))
args = parser.parse_args()
pyconfig.set("BDB_FILE_DIR_PATH",
get_bdb_entry_outdir(args.bdb_root_path, args.pdb_id))
init_logger(args.pdb_id, args.verbose)
# Check that the system has the required programs and libraries installed
check_deps()
if create_bdb_entry(pdb_file_path=args.pdb_file_path,
pdb_id=args.pdb_id,
verbose=args.verbose):
_log.debug("Finished bdb entry.")
def test_setting_change():
class Test(object):
setting = pyconfig.Setting('test_setting_change', 'value')
eq_(Test.setting, 'value')
eq_(Test().setting, 'value')
pyconfig.set('test_setting_change', 'value2')
eq_(Test.setting, 'value2')
eq_(Test().setting, 'value2')
def test_setting_change():
class Test(object):
setting = pyconfig.Setting('test_setting_change', 'value')
eq_(Test.setting, 'value')
eq_(Test().setting, 'value')
pyconfig.set('test_setting_change', 'value2')
eq_(Test.setting, 'value2')
eq_(Test().setting, 'value2')
def test_inheritance_works():
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test2')
conf = pyconfig.etcd().load()
eq_(conf.get('pyconfig.json'), {"a": "b"})
eq_(conf.get('pyconfig.string'), 'Value')
eq_(conf.get('pyconfig.boolean'), True)
eq_(conf.get('pyconfig.number'), 2)
eq_(conf.get('config.inherit'), '/pyconfig_test/test/')
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test')
def test_setting_no_default():
class Test(object):
setting_no_default = pyconfig.Setting('test_setting_no_default',
allow_default=False)
# lambda because assert_raises needs a callable
assert_raises(LookupError, lambda: Test.setting_no_default)
pyconfig.set('test_setting_no_default', 'new_value')
eq_(Test.setting_no_default, 'new_value')
def test_inheritance_works():
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test2')
conf = pyconfig.etcd().load()
eq_(conf.get('pyconfig.json'), {"a": "b"})
eq_(conf.get('pyconfig.string'), 'Value')
eq_(conf.get('pyconfig.boolean'), True)
eq_(conf.get('pyconfig.number'), 2)
eq_(conf.get('config.inherit'), '/pyconfig_test/test/')
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test')
def test_setting_no_default():
class Test(object):
setting_no_default = pyconfig.Setting('test_setting_no_default',
allow_default=False)
# lambda because assert_raises needs a callable
assert_raises(LookupError, lambda: Test.setting_no_default)
pyconfig.set('test_setting_no_default', 'new_value')
eq_(Test.setting_no_default, 'new_value')
def test_ensure_index_can_be_skipped():
class Test(Document):
config_database = database_name()
config_collection = 'test'
config_indexes = [Index('value')]
value = 'v'
with DBTest:
with mock.patch.object(Test, 'collection') as coll:
coll.find_one.__name__ = 'find_one'
pyconfig.set('humbledb.ensure_indexes', False)
Test.find_one()
pyconfig.set('humbledb.ensure_indexes', True)
eq_(coll.ensure_index.called, False)
def setup():
if not pyconfig.etcd().module:
raise SkipTest("etcd not installed")
if not pyconfig.etcd().configured:
raise SkipTest("etcd not configured")
pyconfig.set('pyconfig.etcd.prefix', '/pyconfig_test/test/')
client = pyconfig.etcd().client
client.set('pyconfig_test/test/pyconfig.number', pytool.json.as_json(1))
client.set('pyconfig_test/test/pyconfig.boolean', pytool.json.as_json(True))
client.set('pyconfig_test/test/pyconfig.string', pytool.json.as_json("Value"))
client.set('pyconfig_test/test/pyconfig.json', pytool.json.as_json({"a": "b"}))
client.set('pyconfig_test/test2/pyconfig.number', pytool.json.as_json(2))
client.set('pyconfig_test/test2/config.inherit',
pytool.json.as_json('/pyconfig_test/test/'))
def setup():
if not pyconfig.etcd().module:
raise SkipTest("etcd not installed")
if not pyconfig.etcd().configured:
raise SkipTest("etcd not configured")
pyconfig.set('pyconfig.etcd.prefix', '/pyconfig_test/test/')
client = pyconfig.etcd().client
client.set('pyconfig_test/test/pyconfig.number', pytool.json.as_json(1))
client.set('pyconfig_test/test/pyconfig.boolean',
pytool.json.as_json(True))
client.set('pyconfig_test/test/pyconfig.string',
pytool.json.as_json("Value"))
client.set('pyconfig_test/test/pyconfig.json',
pytool.json.as_json({"a": "b"}))
client.set('pyconfig_test/test2/pyconfig.number', pytool.json.as_json(2))
client.set('pyconfig_test/test2/config.inherit',
pytool.json.as_json('/pyconfig_test/test/'))
def test_import_all_beards_return_None(self):
pyconfig.set('config_file', os.path.abspath('config.yml.example'))
with open(pyconfig.get('config_file')) as config_file:
for k, v in yaml.load(config_file).items():
pyconfig.set(k, v)
beard_paths = pyconfig.get('beard_paths')
pyconfig.set('beard_paths',
[os.path.expanduser(x) for x in beard_paths])
stache_paths = pyconfig.get('stache_paths')
pyconfig.set('stache_paths',
[os.path.expanduser(x) for x in stache_paths])
for path in pyconfig.get('beard_paths'):
with PythonPathContext(path):
for beard in pyconfig.get('beards'):
try:
importlib.import_module(beard)
except ImportError:
pass
# Once the modules are imported (or not), reimporting will return only
# the module. If we get an ImportError here, then one of them has gone
# wrong
successfully_imported_modules = []
import_exceptions = []
for beard in pyconfig.get('beards'):
try:
mod = importlib.import_module(beard)
successfully_imported_modules.append(mod)
except ImportError as e:
import_exceptions.append(e)
if import_exceptions:
self.fail("We got problems: {}".format("\n".join(
str(e) for e in import_exceptions)))
def test_get_flag_return_cli_flags():
pyconfig.set('cli.flags.fly', True)
assert get_flag('fly') is True
"""Configure logging and user settings."""
import logging
# Configure logging
LOG = logging.getLogger(__name__)
FILE = logging.FileHandler('mongo-bdb.log', 'a')
LOG.addHandler(FILE)
FORMATTER = logging.Formatter('%(asctime)s | %(levelname)-7s | %(message)s ')
LOG.setLevel(logging.DEBUG)
FILE.setFormatter(FORMATTER)
LOG.debug('Initialized logger.')
import json
import pyconfig
with open('settings.json', 'r') as file_handle:
settings = json.load(file_handle)
for key, value in settings.iteritems():
pyconfig.set(key, value)
LOG.debug('Read settings.')
def test_case_sensitive():
pyconfig.set('pyconfig.case_sensitive', True)
pyconfig.set('CaseSensitive', True)
eq_(pyconfig.get('CaseSensitive'), True)
eq_(pyconfig.get('casesensitive'), None)
pyconfig.reload(clear=True)
def test_set_get_change():
pyconfig.set('set_get_change', 'testing')
eq_(pyconfig.get('set_get_change'), 'testing')
pyconfig.set('set_get_change', 'tested')
eq_(pyconfig.get('set_get_change'), 'tested')
def test_set_get_change():
pyconfig.set('set_get_change', 'testing')
eq_(pyconfig.get('set_get_change'), 'testing')
pyconfig.set('set_get_change', 'tested')
eq_(pyconfig.get('set_get_change'), 'tested')
def test_reload_work_with_inheritance():
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test2')
pyconfig.reload()
def test_case_sensitive():
pyconfig.set('pyconfig.case_sensitive', True)
pyconfig.set('CaseSensitive', True)
eq_(pyconfig.get('CaseSensitive'), True)
eq_(pyconfig.get('casesensitive'), None)
pyconfig.reload(clear=True)
def test_case_insensitivity():
pyconfig.set('SomeSetting', True)
eq_(pyconfig.get('SomeSetting'), True)
eq_(pyconfig.get('somesetting'), True)
def test_case_insensitivity():
pyconfig.set('SomeSetting', True)
eq_(pyconfig.get('SomeSetting'), True)
eq_(pyconfig.get('somesetting'), True)
def test_autoloading_etcd_config_works():
pyconfig.Config().clear()
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test2')
pyconfig.reload()
eq_(pyconfig.get('pyconfig.string'), 'Value')
eq_(pyconfig.get('pyconfig.number'), 2)
def test_reload_work_with_inheritance():
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test2')
pyconfig.reload()
def setup_beards(cls, key, db_url):
"""Perform setup necessary for all beards."""
pyconfig.set('key', key)
pyconfig.set('db_url', db_url)
cls.key = key
cls.db_url = db_url
def test_autoloading_etcd_config_works():
pyconfig.Config().clear()
pyconfig.set('pyconfig.etcd.prefix', 'pyconfig_test/test2')
pyconfig.reload()
eq_(pyconfig.get('pyconfig.string'), 'Value')
eq_(pyconfig.get('pyconfig.number'), 2)
# BDB: A databank of PDB entries with full isotropic B-factors.
# Copyright (C) 2014 Wouter G. Touw (<*****@*****.**>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License in the
# LICENSE file that should have been included as part of this package.
# If not, see <http://www.gnu.org/licenses/>.
import pyconfig
# Default path to the dir with BDB, log, json and WHY NOT files
pyconfig.set("BDB_FILE_DIR_PATH", ".")
# TLSANL log file names
pyconfig.set("TLSANL_LOG", "tlsanl.log")
pyconfig.set("TLSANL_ERR", "tlsanl.err")
def test_set_and_get():
pyconfig.set('set_and_get', 'tested')
eq_(pyconfig.get('set_and_get'), 'tested')
parser.add_argument('--start-server',
action='store_const',
const=True,
default=False)
parser.add_argument('--no-auto-pip',
action='store_const',
const=True,
default=False)
parser.add_argument('--auto-pip-upgrade',
action='store_const',
const=True,
default=False)
parsed = parser.parse_args()
pyconfig.set('config_file', os.path.abspath(parsed.config_file))
# Load the config file and put it into pyconfig
with open(pyconfig.get('config_file')) as config_file:
for k, v in yaml.load(config_file).items():
pyconfig.set(k, v)
beard_paths = pyconfig.get('beard_paths')
pyconfig.set('beard_paths', [os.path.expanduser(x) for x in beard_paths])
stache_paths = pyconfig.get('stache_paths')
pyconfig.set('stache_paths', [os.path.expanduser(x) for x in stache_paths])
pyconfig.set('loglevel', parsed.loglevel)
pyconfig.set('start_server', parsed.start_server)
pyconfig.set('no_auto_pip', parsed.no_auto_pip)
pyconfig.set('auto_pip_upgrade', parsed.auto_pip_upgrade)
def set_flag(flag: str, value: Any) -> None:
"""Store a CLI flag in the config as "cli.flags.FLAG"."""
pyconfig.set(f"cli.flags.{flag}", value)
async def bot_message_loop_and_aiothttp_session():
async with aiohttp.ClientSession() as session:
pyconfig.set('aiohttp_session', session)
await bot.message_loop()
def test_set_and_get():
pyconfig.set('set_and_get', 'tested')
eq_(pyconfig.get('set_and_get'), 'tested')
def do_set_flag(flag: str, value: Any) -> None:
"""Store config values in global singleton config."""
pyconfig.set(f"{flag}", value)
import argparse
import pyconfig
import logging
import yaml
parser = argparse.ArgumentParser()
parser.add_argument("--config", help="The config file to load", default="config.yaml", type=str)
args = parser.parse_args()
logging.basicConfig()
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
logger.info("loading config file")
with open (args.config, "r") as f:
config = yaml.load(f)
logger.info("setting up default values")
for key, value in config.items():
pyconfig.set(key, value)
import service
from rpyc.utils.server import ThreadedServer
t = ThreadedServer(service.FreedomService, hostname = config['host'], port = config['port'],
logger=logger, protocol_config = {"allow_public_attrs" : True})
t.start()
def do_set_multi_flag(data: List[Tuple]) -> None:
"""Multi - Store a CLI flag in the config as "FLAG"."""
for d in data:
pyconfig.set(f"{d[0]}", d[1])