def test_update_raw_config_from_kwargs_falsy_not_none(mock_init):
# if kwargs supplies a falsy value, it should not evaluate to null
# (ensures code is 'if value is not None' vs. 'if value')
config = GalaxyAppConfiguration(property1=0)
assert config._raw_config['property1'] == '0' # updated
assert type(config._raw_config['property1']) is str # and converted to str
def test_overwrite_reloadable_attribute(mock_init, monkeypatch):
# This is similar to test_update_property, but here we overwrite the attribute before reloading.
# This can happen if a config property is modified AFTER it has been loaded from schema or kwargs.
# For example: load `foo` (from schema or kwargs), but then, in a # subsequent step while initializing
# GalaxyAppConfiguration, do something like this: `foo = resove_path(foo, bar)`. Now the value of `foo`
# is not what was initially loaded, and if `foo` is reloadable, it will be reset to its default as soon
# as the config file is modified. To prevent this, we compare the values read from the modified file
# to the `_raw_config` dict. This test ensures this works correctly.
# edits to config file: R2 modified
monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {
R1: 1,
R2: 42
})
appconfig = GalaxyAppConfiguration()
assert getattr(appconfig, R1) == 1
assert getattr(appconfig, R2) == 2
# overwrite R1
setattr(appconfig, R1, 99)
assert getattr(appconfig, R1) == 99
# then reload
reload_config_options(appconfig)
assert getattr(appconfig, R1) == 99 # no change; should remain overwritten
assert getattr(appconfig, R2) == 42 # change: reloadable option modified
def test_resolves_with_empty_component(mock_config, monkeypatch):
# A path can be None (root path is never None; may be asigned elsewhere)
mock_schema = {
'path0': {
'type': 'str',
'default': 'value0',
},
'path1': {
'type': 'str',
'path_resolves_to': 'path0',
},
'path2': {
'type': 'str',
'default': 'value2',
'path_resolves_to': 'path1',
},
}
def mock_load_schema(self):
self.appschema = mock_schema
monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema',
mock_load_schema)
config = GalaxyAppConfiguration()
assert config.path0 == 'value0'
assert config.path1 == 'value0'
assert config.path2 == 'value0/value2'
def test_resolves_with_empty_component(monkeypatch):
# A path can be None (root path is never None; may be asigned elsewhere)
mock_schema = {
'path0': {
'type': 'str',
'default': 'value0',
},
'path1': {
'type': 'str',
'path_resolves_to': 'path0',
},
'path2': {
'type': 'str',
'default': 'value2',
'path_resolves_to': 'path1',
},
}
monkeypatch.setattr(AppSchema, '_read_schema',
lambda a, b: get_schema(mock_schema))
monkeypatch.setattr(GalaxyAppConfiguration, '_process_config',
lambda a, b: None)
monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir',
lambda a, b: None)
config = GalaxyAppConfiguration()
assert config.path0 == 'value0'
assert config.path1 == 'value0'
assert config.path2 == 'value0/value2'
def test_path_resolution_cycle(mock_config, monkeypatch):
# Must be a DAG, but this one has a cycle
mock_schema = {
'path0': {
'type': 'str',
'default': 'value0',
'path_resolves_to': 'path2',
},
'path1': {
'type': 'str',
'default': 'value1',
'path_resolves_to': 'path0',
},
'path2': {
'type': 'str',
'default': 'value2',
'path_resolves_to': 'path1',
},
}
def mock_load_schema(self):
self.appschema = mock_schema
monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema',
mock_load_schema)
with pytest.raises(ConfigurationError):
GalaxyAppConfiguration()
def test_load_default_values(mock_configuration_init):
appconfig = GalaxyAppConfiguration()
reloadable_config_options = get_reloadable_config_options()
assert len(reloadable_config_options) == 14
assert appconfig.message_box_content == reloadable_config_options[
'message_box_content']
assert appconfig.welcome_url == reloadable_config_options['welcome_url']
assert appconfig.tool_name_boost == reloadable_config_options[
'tool_name_boost']
assert appconfig.tool_section_boost == reloadable_config_options[
'tool_section_boost']
assert appconfig.tool_description_boost == reloadable_config_options[
'tool_description_boost']
assert appconfig.tool_label_boost == reloadable_config_options[
'tool_label_boost']
assert appconfig.tool_stub_boost == reloadable_config_options[
'tool_stub_boost']
assert appconfig.tool_help_boost == reloadable_config_options[
'tool_help_boost']
assert appconfig.tool_search_limit == reloadable_config_options[
'tool_search_limit']
assert appconfig.tool_enable_ngram_search == reloadable_config_options[
'tool_enable_ngram_search']
assert appconfig.tool_ngram_minsize == reloadable_config_options[
'tool_ngram_minsize']
assert appconfig.tool_ngram_maxsize == reloadable_config_options[
'tool_ngram_maxsize']
assert appconfig.admin_users == reloadable_config_options['admin_users']
assert appconfig.cleanup_job == reloadable_config_options['cleanup_job']
def test_kwargs_relative_path_old_prefix_empty_after_strip(mock_init):
# Expect: use value from kwargs, strip old prefix, then resolve
new_path1 = 'old-config'
config = GalaxyAppConfiguration(path1=new_path1)
assert config.path1 == 'my-config/' # stripped of old prefix, then resolved
assert config.path2 == 'my-data/my-data-files' # stripped of old prefix, then resolved
assert config.path3 == 'my-other-files' # no change
def test_kwargs_set_to_null(mock_init):
# Expected: allow overriding with null, then resolve
# This is not a common scenario, but it does happen: one example is
# `job_config` set to `None` when testing
config = GalaxyAppConfiguration(path1=None)
assert config.path1 == 'my-config' # resolved
assert config.path2 == 'my-data/my-data-files' # resolved
assert config.path3 == 'my-other-files' # no change
def test_mock_schema_is_loaded(mock_init):
# Check that mock is loaded as expected
config = GalaxyAppConfiguration()
assert len(config._raw_config) == 5
assert config._raw_config['my_config_dir'] == 'my-config'
assert config._raw_config['my_data_dir'] == 'my-data'
assert config._raw_config['path1'] == 'my-config-files'
assert config._raw_config['path2'] == 'my-data-files'
assert config._raw_config['path3'] == 'my-other-files'
def test_kwargs_ablsolute_path(mock_init):
# Expected: use value from kwargs, do NOT resolve
new_path1 = '/foo1/bar'
new_path2 = '/foo2/bar'
config = GalaxyAppConfiguration(path1=new_path1, path2=new_path2)
assert config.path1 == new_path1 # NOT resolved
assert config.path2 == new_path2 # NOT resolved
assert config.path3 == 'my-other-files' # no change
def test_kwargs_relative_path_old_prefix(mock_init):
# Expect: use value from kwargs, strip old prefix, then resolve
new_path1 = 'old-config/foo1/bar'
new_path2 = 'old-database/foo2/bar'
config = GalaxyAppConfiguration(path1=new_path1, path2=new_path2)
assert config.path1 == 'my-config/foo1/bar' # stripped of old prefix, resolved
assert config.path2 == 'my-data/foo2/bar' # stripped of old prefix, resolved
assert config.path3 == 'my-other-files' # no change
def test_kwargs_relative_path(mock_init):
# Expected: use value from kwargs, then resolve
new_path1 = 'foo1/bar'
new_path2 = 'foo2/bar'
config = GalaxyAppConfiguration(path1=new_path1, path2=new_path2)
assert config.path1 == 'my-config/' + new_path1 # resolved
assert config.path2 == 'my-data/' + new_path2 # resolved
assert config.path3 == 'my-other-files' # no change
def test_kwargs_relative_path_old_prefix_for_other_option(mock_init):
# Expect: use value from kwargs, do NOT strip old prefix, then resolve
# Reason: deprecated dirs are option-specific: we don't want to strip 'old-config'
# (deprecated for the config_dir option) if it's used for another option
new_path1 = 'old-database/foo1/bar'
new_path2 = 'old-config/foo2/bar'
config = GalaxyAppConfiguration(path1=new_path1, path2=new_path2)
assert config.path1 == 'my-config/' + new_path1 # resolved
assert config.path2 == 'my-data/' + new_path2 # resolved
assert config.path3 == 'my-other-files' # no change
def test_deprecated_prefixes_set_correctly(monkeypatch):
# Before we mock them, check that correct values are assigned
monkeypatch.setattr(AppSchema, '_read_schema',
lambda a, b: get_schema(MOCK_SCHEMA))
monkeypatch.setattr(GalaxyAppConfiguration, '_process_config',
lambda a, b: None)
monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir',
lambda a, b: None)
config = GalaxyAppConfiguration()
assert config.deprecated_dirs == {
'config_dir': 'config',
'data_dir': 'database'
}
def test_update_raw_config_from_kwargs(mock_init):
config = GalaxyAppConfiguration(property2=2, property3=2.0, another_key=66)
assert len(config._raw_config) == 6 # no change: another_key NOT added
assert config._raw_config['property1'] == 'a' # no change
assert config._raw_config['property2'] == 2 # updated
assert config._raw_config['property3'] == 2.0 # updated
assert config._raw_config['property4'] is True # no change
assert config._raw_config['property5'] is None # no change
assert config._raw_config['property6'] is None # no change
assert type(config._raw_config['property1']) is str
assert type(config._raw_config['property2']) is int
assert type(config._raw_config['property3']) is float
assert type(config._raw_config['property4']) is bool
def test_load_config_from_schema(mock_init):
config = GalaxyAppConfiguration()
assert len(config._raw_config) == 6
assert config._raw_config['property1'] == 'a'
assert config._raw_config['property2'] == 1
assert config._raw_config['property3'] == 1.0
assert config._raw_config['property4'] is True
assert config._raw_config['property5'] is None
assert config._raw_config['property6'] is None
assert type(config._raw_config['property1']) is str
assert type(config._raw_config['property2']) is int
assert type(config._raw_config['property3']) is float
assert type(config._raw_config['property4']) is bool
def test_update_raw_config_from_string_kwargs(mock_init):
# kwargs may be passed as strings: property data types should not be affected
config = GalaxyAppConfiguration(property1='b',
property2='2',
property3='2.0',
property4='false')
assert len(config._raw_config) == 6 # no change
assert config._raw_config['property1'] == 'b' # updated
assert config._raw_config['property2'] == 2 # updated
assert config._raw_config['property3'] == 2.0 # updated
assert config._raw_config['property4'] is False # updated
assert type(config._raw_config['property1']) is str
assert type(config._raw_config['property2']) is int
assert type(config._raw_config['property3']) is float
assert type(config._raw_config['property4']) is bool
def test_deprecated_prefixes_set_correctly(monkeypatch):
# Before we mock them, check that correct values are assigned
def mock_load_schema(self):
self.appschema = {}
def mock_process_config(self, kwargs):
pass
monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema',
mock_load_schema)
monkeypatch.setattr(GalaxyAppConfiguration, '_process_config',
mock_process_config)
config = GalaxyAppConfiguration()
expected_deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
assert config.deprecated_dirs == expected_deprecated_dirs
def test_update_raw_config_from_kwargs_with_none(mock_init):
# should be able to set to null regardless of property's datatype
config = GalaxyAppConfiguration(
property1=None,
property2=None,
property3=None,
property4=None,
property5=None,
property6=None,
)
assert config._raw_config['property1'] is None
assert config._raw_config['property2'] is None
assert config._raw_config['property3'] is None
assert config._raw_config['property4'] is None
assert config._raw_config['property5'] is None
assert config._raw_config['property6'] is None
def init_models_from_config(config: GalaxyAppConfiguration,
map_install_models=False,
object_store=None,
trace_logger=None):
model = init(
config.file_path,
config.database_connection,
config.database_engine_options,
map_install_models=map_install_models,
database_query_profiling_proxy=config.database_query_profiling_proxy,
object_store=object_store,
trace_logger=trace_logger,
use_pbkdf2=config.get_bool('use_pbkdf2', True),
slow_query_log_threshold=config.slow_query_log_threshold,
thread_local_log=config.thread_local_log,
log_query_counts=config.database_log_query_counts,
)
return model
def test_basecase(mock_config, monkeypatch):
# Check that a valid graph is loaded correctly (this graph has 2 components)
mock_schema = {
'component1_path0': {
'type': 'str',
'default': 'value0',
},
'component1_path1': {
'type': 'str',
'default': 'value1',
'path_resolves_to': 'component1_path0',
},
'component1_path2': {
'type': 'str',
'default': 'value2',
'path_resolves_to': 'component1_path1',
},
'component2_path0': {
'type': 'str',
'default': 'value3',
},
'component2_path1': {
'type': 'str',
'default': 'value4',
'path_resolves_to': 'component2_path0',
},
}
def mock_load_schema(self):
self.appschema = mock_schema
monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema',
mock_load_schema)
config = GalaxyAppConfiguration()
assert config.component1_path0 == 'value0'
assert config.component1_path1 == 'value0/value1'
assert config.component1_path2 == 'value0/value1/value2'
assert config.component2_path0 == 'value3'
assert config.component2_path1 == 'value3/value4'
def test_basecase(monkeypatch):
# Check that a valid graph is loaded correctly (this graph has 2 components)
mock_schema = {
'component1_path0': {
'type': 'str',
'default': 'value0',
},
'component1_path1': {
'type': 'str',
'default': 'value1',
'path_resolves_to': 'component1_path0',
},
'component1_path2': {
'type': 'str',
'default': 'value2',
'path_resolves_to': 'component1_path1',
},
'component2_path0': {
'type': 'str',
'default': 'value3',
},
'component2_path1': {
'type': 'str',
'default': 'value4',
'path_resolves_to': 'component2_path0',
},
}
monkeypatch.setattr(AppSchema, '_read_schema',
lambda a, b: get_schema(mock_schema))
monkeypatch.setattr(GalaxyAppConfiguration, '_process_config',
lambda a, b: None)
monkeypatch.setattr(GalaxyAppConfiguration, '_override_tempdir',
lambda a, b: None)
config = GalaxyAppConfiguration()
assert config.component1_path0 == 'value0'
assert config.component1_path1 == 'value0/value1'
assert config.component1_path2 == 'value0/value1/value2'
assert config.component2_path0 == 'value3'
assert config.component2_path1 == 'value3/value4'
def test_resolves_to_invalid_property(mock_config, monkeypatch):
# 'path_resolves_to' should point to an existing property in the schema
mock_schema = {
'path0': {
'type': 'str',
'default': 'value0',
},
'path1': {
'type': 'str',
'default': 'value1',
'path_resolves_to': 'invalid', # invalid
},
}
def mock_load_schema(self):
self.appschema = mock_schema
monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema',
mock_load_schema)
with pytest.raises(ConfigurationError):
GalaxyAppConfiguration()
def test_resolves_to_invalid_type(mock_config, monkeypatch):
# Paths should be strings
mock_schema = {
'path0': {
'type': 'int', # invalid
'default': 'value0',
},
'path1': {
'type': 'str',
'default': 'value1',
'path_resolves_to': 'path0',
},
}
def mock_load_schema(self):
self.appschema = mock_schema
monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema',
mock_load_schema)
with pytest.raises(ConfigurationError):
GalaxyAppConfiguration()
def test_cant_delete_property(mock_init, monkeypatch):
# A property should not be deleted: we don't know whether it was initially
# set to a default, loaded from a config file, env var, etc. Therefore, if a property
# is removed from the config file, it will not be modified or deleted.
# edits to config file: R2, N2 deleted
monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {
R1: 1,
N1: 3
})
appconfig = GalaxyAppConfiguration()
assert getattr(appconfig, R1) == 1
assert getattr(appconfig, R2) == 2
assert getattr(appconfig, N1) == 3
assert getattr(appconfig, N2) == 4
reload_config_options(appconfig)
assert getattr(appconfig, R1) == 1 # no change
assert getattr(appconfig, R2) == 2 # no change: option cannot be deleted
assert getattr(appconfig, N1) == 3 # no change
assert getattr(appconfig, N2) == 4 # no change: option cannot be deleted
def test_update_property(mock_init, monkeypatch):
# This also covers adding a property. When a config file does not set a property,
# that property is set to its default value. Thus, if we add a reloadable property
# to the config file, it's the same as modifying that property's value.
# edits to config file: R2, N1 modified
monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {
R1: 1,
R2: 42,
N1: 99
})
appconfig = GalaxyAppConfiguration()
assert getattr(appconfig, R1) == 1
assert getattr(appconfig, R2) == 2
assert getattr(appconfig, N1) == 3
reload_config_options(appconfig)
assert getattr(appconfig, R1) == 1 # no change
assert getattr(appconfig, R2) == 42 # change: reloadable option modified
assert getattr(appconfig,
N1) == 3 # no change: option modified but is non-relodable
def test_update_reloadable_property__message_box_content(
mock_configuration_init):
appconfig = GalaxyAppConfiguration()
appconfig.update_reloadable_property('welcome_url', 'foo')
appconfig.update_reloadable_property('message_box_content', 'bar')
appconfig.update_reloadable_property('tool_name_boost', 1)
appconfig.update_reloadable_property('tool_section_boost', 2)
appconfig.update_reloadable_property('tool_description_boost', 3)
appconfig.update_reloadable_property('tool_label_boost', 4)
appconfig.update_reloadable_property('tool_stub_boost', 5)
appconfig.update_reloadable_property('tool_help_boost', 6)
appconfig.update_reloadable_property('tool_search_limit', 7)
appconfig.update_reloadable_property('tool_enable_ngram_search', True)
appconfig.update_reloadable_property('tool_ngram_minsize', 8)
appconfig.update_reloadable_property('tool_ngram_maxsize', 9)
appconfig.update_reloadable_property(
'admin_users', '[email protected], [email protected]')
appconfig.update_reloadable_property('cleanup_job', 'never')
assert appconfig.welcome_url == 'foo'
assert appconfig.message_box_content == 'bar'
assert appconfig.tool_name_boost == 1
assert appconfig.tool_section_boost == 2
assert appconfig.tool_description_boost == 3
assert appconfig.tool_label_boost == 4
assert appconfig.tool_stub_boost == 5
assert appconfig.tool_help_boost == 6
assert appconfig.tool_search_limit == 7
assert appconfig.tool_enable_ngram_search is True
assert appconfig.tool_ngram_minsize == 8
assert appconfig.tool_ngram_maxsize == 9
assert appconfig.admin_users == '[email protected], [email protected]'
assert appconfig.admin_users_list == [
'*****@*****.**', '*****@*****.**'
]
assert appconfig.cleanup_job == 'never'
def test_no_kwargs(mock_init):
# Expected: use default from schema, then resolve
config = GalaxyAppConfiguration()
assert config.path1 == 'my-config/my-config-files' # resolved
assert config.path2 == 'my-data/my-data-files' # resolved
assert config.path3 == 'my-other-files' # no change
def test_load_value_from_kwargs(mock_configuration_init):
appconfig = GalaxyAppConfiguration(welcome_url='foo')
assert appconfig.welcome_url == 'foo'
