def test_get_config_loc(): test_config_loc = get_config_loc() assert os.path.isfile(test_config_loc) assert type(json.loads(open(test_config_loc).read())) is dict
def export_config(output_file=None): if output_file is None: print(open(get_config_loc()).read()) else: copy2(get_config_loc(), output_file)
def import_config(config_loc): copy2(config_loc, get_config_loc())
def set_database_paths(kegg_db_loc=None, kofam_hmm_loc=None, kofam_ko_list_loc=None, uniref_db_loc=None, pfam_db_loc=None, pfam_hmm_dat=None, dbcan_db_loc=None, dbcan_fam_activities=None, viral_db_loc=None, peptidase_db_loc=None, vogdb_db_loc=None, vog_annotations=None, description_db_loc=None, genome_summary_form_loc=None, module_step_form_loc=None, etc_module_database_loc=None, function_heatmap_form_loc=None, amg_database_loc=None, start_time=None, config_loc=None, use_current_locs=True, update_description_db=False): if start_time is None: start_time = datetime.now() print('%s: Setting database paths' % str(datetime.now() - start_time)) if use_current_locs: db_dict = get_database_locs() else: db_dict = {} db_dict = check_exists_and_add_to_location_dict(kegg_db_loc, 'kegg', db_dict) db_dict = check_exists_and_add_to_location_dict(kofam_hmm_loc, 'kofam', db_dict) db_dict = check_exists_and_add_to_location_dict(kofam_ko_list_loc, 'kofam_ko_list', db_dict) db_dict = check_exists_and_add_to_location_dict(uniref_db_loc, 'uniref', db_dict) db_dict = check_exists_and_add_to_location_dict(pfam_db_loc, 'pfam', db_dict) db_dict = check_exists_and_add_to_location_dict(pfam_hmm_dat, 'pfam_hmm_dat', db_dict) db_dict = check_exists_and_add_to_location_dict(dbcan_db_loc, 'dbcan', db_dict) db_dict = check_exists_and_add_to_location_dict(dbcan_fam_activities, 'dbcan_fam_activities', db_dict) db_dict = check_exists_and_add_to_location_dict(viral_db_loc, 'viral', db_dict) db_dict = check_exists_and_add_to_location_dict(peptidase_db_loc, 'peptidase', db_dict) db_dict = check_exists_and_add_to_location_dict(vogdb_db_loc, 'vogdb', db_dict) db_dict = check_exists_and_add_to_location_dict(vog_annotations, 'vog_annotations', db_dict) db_dict = check_exists_and_add_to_location_dict(genome_summary_form_loc, 'genome_summary_form', db_dict) db_dict = check_exists_and_add_to_location_dict(module_step_form_loc, 'module_step_form', db_dict) db_dict = check_exists_and_add_to_location_dict(etc_module_database_loc, 'etc_module_database', db_dict) db_dict = check_exists_and_add_to_location_dict(function_heatmap_form_loc, 'function_heatmap_form', db_dict) db_dict = check_exists_and_add_to_location_dict(amg_database_loc, 'amg_database', db_dict) print('%s: Database locations added to CONFIG' % str(datetime.now() - start_time)) if update_description_db: if description_db_loc is None: description_db_loc = db_dict['description_db'] populate_description_db(description_db_loc, db_dict, start_time) print('%s: Database descriptions updated' % str(datetime.now() - start_time)) db_dict = check_exists_and_add_to_location_dict(description_db_loc, 'description_db', db_dict) # change data paths if config_loc is None: config_loc = get_config_loc() with open(config_loc, 'w') as f: f.write(json.dumps(db_dict)) print('%s: Database locations set' % str(datetime.now() - start_time))