def setup(self):
self.defaults = {
'type': 'movie',
'person': {
'name': 'P.T. Anderson',
'job': 'Director'
}
}
self.config = Config(defaults=self.defaults)
def test_init():
# Test lazy loading (not pointing to a config file)
config = Config()
assert config.markup is json
# Test loading with some defaults
config = Config(defaults=dict(name='P.T. Anderson'))
assert config['name'] == 'P.T. Anderson'
# Test loading with an alternate markup engine
config = Config(markup=toml)
assert config.markup is toml
# Test loading with a non-existent config file
config = Config(LazyFile('tests/fixtures/nothing.json', 'w'))
assert config == {}
# Test loading with an existing config file
config = Config(LazyFile('tests/fixtures/something.json', 'w'))
assert config['title'] == 'Magnolia'
def root(context, config, database, verbose, log_file):
"""Clinical sequencing coverage analysis tool."""
# setup logging
loglevel = LEVELS.get(min(verbose, 2), 'WARNING')
init_log(logging.getLogger(), loglevel=loglevel, filename=log_file)
logger.info("version {0}".format(__version__))
# avoid setting global defaults in Click options, do it below when
# updating the config object
context.obj = Config(config, markup=markup)
context.obj['database'] = (database or context.obj.get(
'database', 'coverage.sqlite3'))
# update the context with new defaults from the config file
context.default_map = context.obj
