def test_gene_history_loader(self): """ Test the gene history loading. """ call_command("pipeline", "--steps", "load", sections="GENE_HISTORY", dir=TEST_DATA_DIR, ini=MY_INI_FILE) INI_CONFIG = IniParser().read_ini(MY_INI_FILE) idx = INI_CONFIG["GENE_HISTORY"]["index"] idx_type = INI_CONFIG["GENE_HISTORY"]["index_type"] elastic = Search(idx=idx, idx_type=idx_type) Search.index_refresh(idx) self.assertTrue(elastic.get_count()["count"] > 1, "Count documents in the index") map1_props = Gene.gene_history_mapping(idx, idx_type, test_mode=True).mapping_properties map2_props = elastic.get_mapping() if idx not in map2_props: logger.error("MAPPING ERROR: " + json.dumps(map2_props)) self._cmpMappings(map2_props[idx]["mappings"], map1_props, idx_type)
def gene_history_parse(cls, *args, **kwargs): ''' Parse gene_history file from NCBI. ''' download_file = cls._get_download_file(*args, **kwargs) Gene.gene_history_mapping(kwargs['section']['index'], kwargs['section']['index_type']) with gzip.open(download_file, 'rt') as gene_his_f: Gene.gene_history_parse(gene_his_f, kwargs['section']['index'], kwargs['section']['index_type'])