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
class TestConfig:
def setup(self):
self.defaults = {
'type': 'movie',
'person': {
'name': 'P.T. Anderson',
'job': 'Director'
}
}
self.config = Config(defaults=self.defaults)
def test_load(self):
# Test loading non-conflicting data
with io.open('tests/fixtures/something.json',
encoding='utf-8') as handle:
self.config.load(handle)
assert self.config['person']['name'] == 'P.T. Anderson'
assert self.config['title'] == 'Magnolia'
# Test loading conflicting data
with io.open('tests/fixtures/conflict.json',
encoding='utf-8') as handle:
self.config.load(handle)
assert self.config['name'] == 'Alfonso Cuarón'
# Test loading with a non-supported markup engine
self.config.markup = dict()
with pytest.raises(NotImplementedError):
with io.open('tests/fixtures/something.json',
encoding='utf-8') as handle:
self.config.load(handle)
# Test loading config with bad syntax
self.config.markup = json
with pytest.raises(ValueError):
with io.open('tests/fixtures/bad-syntax.json',
encoding='utf-8') as handle:
self.config.load(handle)
def test_resolve_key(self):
# Test simple case
section, key = self.config._resolve_key('person.name')
assert section == self.defaults['person']
assert key == 'name'
# Test with a different base
section, key = self.config._resolve_key('person.job',
base=self.config.user_data)
assert section == {} # 'user_data' is an empty ``dict`` in this case
assert key == 'job'
def test_set(self):
# Test setting a global setting
self.config.set('country', 'United States')
assert self.config['country'] == 'United States'
# Test setting a nested setting (in existing sub-group)
self.config.set('person.name', 'Quentin Tarantino')
assert self.config['person']['name'] == 'Quentin Tarantino'
# Test setting a nested setting (in a new sub-group)
self.config.set('bonus.joke', 'Knock, knock.')
assert self.config['bonus']['joke'] == 'Knock, knock.'
# Test multiple nested settings
value = 'Do not ask me'
self.config.set('what.is.this.useful.for', value)
assert self.config['what']['is']['this']['useful']['for'] == value
# Test set on a different scope (than ``self``)
self.config.set('nested.key', 'value', scope=self.config.user_data)
assert self.config.user_data['nested']['key'] == 'value'
def test_unset(self):
# Test removing a global setting
assert self.config['type'] == 'movie'
self.config.unset('type')
assert self.config.get('type') is None
# Test removing a nested setting
assert self.config['person']['name'] == 'P.T. Anderson'
self.config.unset('person.name')
assert self.config['person'].get('name') is None
# Test removing a whole sub-group of settings
assert self.config['person'] is not None
self.config.unset('person')
assert self.config.get('person') is None
# Test removing a setting in a different scope
scope = {'person': {'name': 'Tarantino'}}
self.config.unset('person.name', scope=scope)
assert scope['person'].get('name') is None
def setup(self):
self.defaults = {"type": "movie", "person": {"name": "P.T. Anderson", "job": "Director"}}
self.config = Config(defaults=self.defaults)
class TestConfig:
def setup(self):
self.defaults = {"type": "movie", "person": {"name": "P.T. Anderson", "job": "Director"}}
self.config = Config(defaults=self.defaults)
def test_load(self):
# Test loading non-conflicting data
path = "tests/fixtures/something.json"
with io.open(path, encoding="utf-8") as handle:
self.config.load(handle)
assert self.config["person"]["name"] == "P.T. Anderson"
assert self.config["title"] == "Magnolia"
# Test loading conflicting data
conflict_path = "tests/fixtures/conflict.json"
with io.open(conflict_path, encoding="utf-8") as handle:
self.config.load(handle)
assert self.config["name"] == u"Alfonso Cuarón"
# Test loading with a non-supported markup engine
self.config.markup = dict()
with pytest.raises(NotImplementedError):
with io.open(path, encoding="utf-8") as handle:
self.config.load(handle)
# Test loading config with bad syntax
self.config.markup = json
json_path = "tests/fixtures/bad-syntax.json"
with pytest.raises(ValueError):
with io.open(json_path, encoding="utf-8") as handle:
self.config.load(handle)
def test_resolve_key(self):
# Test simple case
section, key = self.config._resolve_key("person.name")
assert section == self.defaults["person"]
assert key == "name"
# Test with a different base
section, key = self.config._resolve_key("person.job", base=self.config.user_data)
assert section == {} # 'user_data' is an empty ``dict`` in this case
assert key == "job"
def test_set(self):
# Test setting a global setting
self.config.set("country", "United States")
assert self.config["country"] == "United States"
# Test setting a nested setting (in existing sub-group)
self.config.set("person.name", "Quentin Tarantino")
assert self.config["person"]["name"] == "Quentin Tarantino"
# Test setting a nested setting (in a new sub-group)
self.config.set("bonus.joke", "Knock, knock.")
assert self.config["bonus"]["joke"] == "Knock, knock."
# Test multiple nested settings
value = "Do not ask me"
self.config.set("what.is.this.useful.for", value)
assert self.config["what"]["is"]["this"]["useful"]["for"] == value
def setup(self):
self.defaults = {
'type': 'movie',
'person': {'name': 'P.T. Anderson', 'job': 'Director'}
}
self.config = Config(defaults=self.defaults)
class TestConfig:
def setup(self):
self.defaults = {
'type': 'movie',
'person': {'name': 'P.T. Anderson', 'job': 'Director'}
}
self.config = Config(defaults=self.defaults)
def test_load(self):
# Test loading non-conflicting data
with open('tests/fixtures/something.json', encoding='utf-8') as handle:
self.config.load(handle)
assert self.config['person']['name'] == 'P.T. Anderson'
assert self.config['title'] == 'Magnolia'
# Test loading conflicting data
with open('tests/fixtures/conflict.json', encoding='utf-8') as handle:
self.config.load(handle)
assert self.config['name'] == 'Alfonso Cuarón'
# Test loading with a non-supported markup engine
self.config.markup = dict()
with pytest.raises(NotImplementedError):
with open('tests/fixtures/something.json', encoding='utf-8') as handle:
self.config.load(handle)
# Test loading config with bad syntax
self.config.markup = json
with pytest.raises(ValueError):
with open('tests/fixtures/bad-syntax.json', encoding='utf-8') as handle:
self.config.load(handle)
def test_resolve_key(self):
# Test simple case
section, key = self.config._resolve_key('person.name')
assert section == self.defaults['person']
assert key == 'name'
# Test with a different base
section, key = self.config._resolve_key('person.job',
base=self.config.user_data)
assert section == {} # 'user_data' is an empty ``dict`` in this case
assert key == 'job'
def test_set(self):
# Test setting a global setting
self.config.set('country', 'United States')
assert self.config['country'] == 'United States'
# Test setting a nested setting (in existing sub-group)
self.config.set('person.name', 'Quentin Tarantino')
assert self.config['person']['name'] == 'Quentin Tarantino'
# Test setting a nested setting (in a new sub-group)
self.config.set('bonus.joke', 'Knock, knock.')
assert self.config['bonus']['joke'] == 'Knock, knock.'
# Test multiple nested settings
value = 'Do not ask me'
self.config.set('what.is.this.useful.for', value)
assert self.config['what']['is']['this']['useful']['for'] == value
# Test set on a different scope (than ``self``)
self.config.set('nested.key', 'value', scope=self.config.user_data)
assert self.config.user_data['nested']['key'] == 'value'
def test_unset(self):
# Test removing a global setting
assert self.config['type'] == 'movie'
self.config.unset('type')
assert self.config.get('type') is None
# Test removing a nested setting
assert self.config['person']['name'] == 'P.T. Anderson'
self.config.unset('person.name')
assert self.config['person'].get('name') is None
# Test removing a whole sub-group of settings
assert self.config['person'] is not None
self.config.unset('person')
assert self.config.get('person') is None
# Test removing a setting in a different scope
scope = {'person': {'name': 'Tarantino'}}
self.config.unset('person.name', scope=scope)
assert scope['person'].get('name') is None