def __init__(self, dae_config):
super(PhenoDb, self).__init__()
assert dae_config
configs = GPFConfigParser.load_directory_configs(
dae_config.phenotype_data.dir, pheno_conf_schema
)
self.config = {
config.phenotype_data.name: config.phenotype_data
for config in configs
if config.phenotype_data and config.phenotype_data.enabled
}
self.pheno_cache = {}
def test_config_parser_load_directory(conf_schema_basic, fixtures_dir):
configs = GPFConfigParser.load_directory_configs(
os.path.join(fixtures_dir, "sample_conf_directory"), conf_schema_basic
)
print(configs)
assert len(configs) == 4
configs = sorted(configs, key=lambda x: x.id)
assert configs[0].id == "1"
assert configs[0].name == "conf1"
assert configs[1].id == "2"
assert configs[1].name == "conf2"
assert configs[2].id == "3"
assert configs[2].name == "conf3"
assert configs[3].id == "4"
assert configs[3].name == "conf4"
def _load_study_configs(self):
default_config_filename = None
if self.dae_config.default_study_config and \
self.dae_config.default_study_config.conf_file:
default_config_filename = \
self.dae_config.default_study_config.conf_file
study_configs = GPFConfigParser.load_directory_configs(
self.dae_config.studies_db.dir,
study_config_schema,
default_config_filename=default_config_filename,
)
genotype_study_configs = {}
for study_config in study_configs:
assert study_config.id is not None, study_config
if study_config.enabled is False:
continue
genotype_study_configs[study_config.id] = \
study_config
return genotype_study_configs
def _load_group_configs(self):
default_config_filename = None
if self.dae_config.default_study_config and \
self.dae_config.default_study_config.conf_file:
default_config_filename = \
self.dae_config.default_study_config.conf_file
group_configs = GPFConfigParser.load_directory_configs(
self.dae_config.datasets_db.dir,
study_config_schema,
default_config_filename=default_config_filename,
)
genotype_group_configs = {}
for group_config in group_configs:
assert group_config.id is not None, group_config
if group_config.enabled is False:
continue
genotype_group_configs[group_config.id] = \
group_config
return genotype_group_configs
def fake_pheno_config(fake_dae_conf):
return GPFConfigParser.load_directory_configs(
fake_dae_conf.phenotype_data.dir, pheno_conf_schema)