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))