def test_init_loqusextension_init_app_get_version(loqus_exe, loqus_version):
"""Test a init a loqus extension object with flask app with version and config"""
# GIVEN a loqusdb binary
# THEN initialising a loqusdb extension with init app
loqus_obj = LoqusDB(version=loqus_version)
assert loqus_obj.get_version() == loqus_version
def test_loqusdb_wrong_version(loqus_exe):
"""Test to instantiate a loqus extension whe version is to low"""
# GIVEN a loqusdb version < 2.5
loqus_extension = LoqusDB(loqusdb_binary=loqus_exe, version=1.0)
# WHEN instantiating an adapter
with pytest.raises(SyntaxError):
# THEN assert a syntax error is raised since version is wrong
loqus_extension.version_check()
def test_init_loqusextension_init_app_wrong_version(loqus_exe):
"""Test a init a loqus extension object with flask app"""
# GIVEN a loqusdb binary
configs = {"LOQUSDB_SETTINGS": {"binary_path": loqus_exe, "version": 1.0}}
# WHEN initialising a loqusdb extension with init app
app = Flask(__name__)
loqus_obj = LoqusDB()
with pytest.raises(EnvironmentError):
with app.app_context():
app.config = configs
loqus_obj.init_app(app)
def test_init_loqusextension_version(loqus_exe, loqus_version):
"""Test a init a loqus extension object with a specified version"""
# GIVEN a loqusdb binary and a version
# WHEN initialising a loqusdb extension
loqus_obj = LoqusDB(loqusdb_binary=loqus_exe, version=loqus_version)
# THEN assert that the binary is correct
assert loqus_obj.get_bin_path() == loqus_exe
# THEN assert that the version is correct
assert loqus_obj.version == loqus_version
# THEN assert that there is no config
assert loqus_obj.get_config_path() is None
def test_init_loqusextension(loqus_exe):
"""Test a init a loqus extension object"""
# GIVEN a loqusdb binary
# WHEN initialising a loqusdb extension
loqus_obj = LoqusDB(loqusdb_binary=loqus_exe)
# THEN assert that the binary is correct
assert loqus_obj.get_bin_path() == loqus_exe
# THEN assert that the version is 0
assert loqus_obj.version is None
# THEN assert that there is no config
assert loqus_obj.get_config_path() is None
def test_init_loqusextension_config(loqus_exe, loqus_config, loqus_version):
"""Test a init a loqus extension object with a specified version"""
# GIVEN a loqusdb binary, a version and a config
# WHEN initialising a loqusdb extension
loqus_obj = LoqusDB(loqusdb_binary=loqus_exe,
loqusdb_config=loqus_config,
version=loqus_version)
# THEN assert that the binary is correct
assert loqus_obj.get_bin_path() == loqus_exe
# THEN assert that the version is correct
assert loqus_obj.version == loqus_version
# THEN assert that there is no config
assert loqus_obj.loqusdb_settings == [{
"id": "default",
"binary_path": loqus_exe,
"config_path": None
}]
def test_set_coordinates_no_variant_type():
"""Test update coordinates when nothing to update"""
# GIVEN a variant with some coordinates
pos = 10
end = 10
length = 1
var = {
"_id": "1_10_A_C",
"pos": pos,
"end": end,
"length": length,
}
# WHEN setting the coordinates
LoqusDB.set_coordinates(var)
# THEN assert that nothing changed
assert var["pos"] == pos
assert var["end"] == end
assert var["length"] == length
def test_init_loqusextension_init_app_no_version(mocker, loqus_exe,
loqus_version):
"""Test a init a loqus extension object with flask app"""
# GIVEN a loqusdb binary
configs = {"LOQUSDB_SETTINGS": {"binary_path": loqus_exe}}
mocker.patch.object(subprocess, "check_output")
subprocess.check_output.return_value = b"loqusdb, version %f" % loqus_version
# WHEN initialising a loqusdb extension with init app
app = Flask(__name__)
loqus_obj = LoqusDB()
with app.app_context():
app.config = configs
loqus_obj.init_app(app)
# THEN assert that the binary is correct
assert loqus_obj.loqusdb_binary == loqus_exe
assert loqus_obj.version == loqus_version
# THEN assert that there is no config
assert loqus_obj.loqusdb_config is None
def test_set_coordinates_unknown_ins():
"""Test update coordinates when insertion length is unknown"""
# GIVEN a variant with some coordinates
pos = 10
end = 10
length = -1
var_type = "INS"
var = {
"_id": "1_10_INS",
"pos": pos,
"end": end,
"length": length,
"variant_type": var_type,
}
# WHEN setting the coordinates
LoqusDB.set_coordinates(var)
# THEN assert that end coordinate is updated
assert var["pos"] == pos
assert var["end"] == end
assert var["length"] == length
def test_init_loqusextension_init_app(loqus_exe, loqus_version):
"""Test a init a loqus extension object with flask app with version"""
# GIVEN a loqusdb binary
configs = {
"LOQUSDB_SETTINGS": {
"binary_path": loqus_exe,
"version": loqus_version
}
}
# WHEN initialising a loqusdb extension with init app
app = Flask(__name__)
loqus_obj = LoqusDB()
with app.app_context():
app.config = configs
loqus_obj.init_app(app)
# THEN assert that the binary is correct
assert loqus_obj.get_bin_path() == loqus_exe
# THEN assert that the version is correct
assert loqus_obj.version == loqus_version
# THEN assert that config.py has been read
assert loqus_obj.loqusdb_settings is not None
def test_init_loqusextension_init_app_get_version_CalledProcessError(
loqus_exe, loqus_config, mocker):
"""Test a init a loqus extension object with flask app with version and config"""
# GIVEN mocking subprocess to raise CalledProcessError
mocker.patch.object(subprocess,
"check_output",
side_effect=CalledProcessError(123, "case_count"))
configs = {
"LOQUSDB_SETTINGS": [{
"binary_path": loqus_exe,
"id": "default",
"config_path": loqus_config,
}]
}
app = Flask(__name__)
loqus_obj = LoqusDB()
with app.app_context():
app.config = configs
with pytest.raises(EnvironmentError):
# THEN during app init, version is set to -1 and EnvironmentError is raised
loqus_obj.init_app(app)
def test_init_loqusextension(loqus_exe):
"""Test a init a loqus extension object"""
# GIVEN a loqusdb binary
# WHEN initialising a loqusdb extension
loqus_obj = LoqusDB(loqusdb_binary=loqus_exe)
# THEN assert that the binary is correct
assert loqus_obj.loqusdb_binary == loqus_exe
# THEN assert that the base call is correct
assert loqus_obj.base_call == [loqus_exe]
# THEN assert that the version is 0
assert loqus_obj.version == 0
# THEN assert that there is no config
assert loqus_obj.loqusdb_config is None
def test_init_loqusextension_init_app_with_config(loqus_exe, loqus_config):
"""Test a init a loqus extension object with flask app with version and config"""
# GIVEN a loqusdb binary
version = 2.5
configs = {
"LOQUSDB_SETTINGS": {
"binary_path": loqus_exe,
"version": version,
"config_path": loqus_config,
}
}
# WHEN initialising a loqusdb extension with init app
app = Flask(__name__)
loqus_obj = LoqusDB()
with app.app_context():
app.config = configs
loqus_obj.init_app(app)
# THEN assert that the binary is correct
assert loqus_obj.loqusdb_binary == loqus_exe
# THEN assert that the version is correct
assert loqus_obj.version == version
# THEN assert that the config is correct
assert loqus_obj.loqusdb_config == loqus_config
def test_init_loqusextension_config(loqus_exe, loqus_config, loqus_version):
"""Test a init a loqus extension object with a specified version"""
# GIVEN a loqusdb binary, a version and a config
# WHEN initialising a loqusdb extension
loqus_obj = LoqusDB(loqusdb_binary=loqus_exe,
loqusdb_config=loqus_config,
version=loqus_version)
# THEN assert that the binary is correct
assert loqus_obj.loqusdb_binary == loqus_exe
# THEN assert that the base call is correct
assert loqus_obj.base_call == [loqus_exe, "--config", loqus_config]
# THEN assert that the version is correct
assert loqus_obj.version == loqus_version
# THEN assert that there is no config
assert loqus_obj.loqusdb_config == loqus_config
def test_init_loqusextension_init_app_with_config_multiple(
loqus_exe, loqus_config):
"""Test a init a loqus extension object with flask app with version and config"""
# GIVEN a loqusdb config as list
version = 2.5
configs = {
"LOQUSDB_SETTINGS": [{
"binary_path": loqus_exe,
"version": version,
"id": "default",
"config_path": loqus_config,
}]
}
# WHEN initialising a loqusdb extension with init app
app = Flask(__name__)
loqus_obj = LoqusDB()
with app.app_context():
app.config = configs
loqus_obj.init_app(app)
# THEN assert that the binary is correct -with id
assert loqus_obj.get_bin_path("default") == loqus_exe
# THEN assert that the binary is correct -without id
assert loqus_obj.get_bin_path(None) == loqus_exe
# THEN non-configured id raises
with pytest.raises(ConfigError):
assert loqus_obj.get_bin_path("not configured id")
# THEN assert that the config_path is correct -with id
assert loqus_obj.get_config_path("default") == loqus_config
# THEN assert that the config_path is correct -without id
assert loqus_obj.get_config_path(None) == loqus_config
# THEN non-configured id raises
with pytest.raises(ConfigError):
assert loqus_obj.get_config_path("not configured id")
# THEN assert that the version is correct -with id
assert loqus_obj.get_configured_version("default") == version
# THEN assert that the version is correct -without id
assert loqus_obj.get_configured_version(None) == version
# THEN non-configured id raises
with pytest.raises(ConfigError):
assert loqus_obj.get_configured_version("not configured id")
# THEN assert that the version is correct
assert loqus_obj.version == version
def fixture_loqus_extension(loqus_exe, loqus_config, loqus_version):
"""Return a loqusdb extension"""
loqus_obj = LoqusDB(loqusdb_binary=loqus_exe,
loqusdb_config=loqus_config,
version=loqus_version)
return loqus_obj