diff options
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 22 |
1 files changed, 7 insertions, 15 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 647e58a2..544e2fd1 100644 --- a/wqflask/maintenance/gen_select_dataset.py +++ b/wqflask/maintenance/gen_select_dataset.py @@ -30,18 +30,10 @@ It needs to be run manually when database has been changed. Run it as # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import print_function, division - -#from flask import config -# -#cdict = {} -#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS') -#print("cdict is:", cdict) - import sys # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead -sys.path.insert(0,'./') +sys.path.insert(0, './') # NEW: import app to avoid a circular dependency on utility.tools from wqflask import app @@ -50,7 +42,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI import MySQLdb import simplejson as json -import urlparse +import urllib.parse #import sqlalchemy as sa @@ -66,7 +58,7 @@ from pprint import pformat as pf def parse_db_uri(): """Converts a database URI to the db name, host name, user name, and password""" - parsed_uri = urlparse.urlparse(SQL_URI) + parsed_uri = urllib.parse.urlparse(SQL_URI) db_conn_info = dict( db = parsed_uri.path[1:], @@ -108,7 +100,7 @@ def get_types(groups): """Build types list""" types = {} #print("Groups: ", pf(groups)) - for species, group_dict in groups.iteritems(): + for species, group_dict in list(groups.items()): types[species] = {} for group_name, _group_full_name in group_dict: # make group an alias to shorten the code @@ -195,9 +187,9 @@ def build_types(species, group): def get_datasets(types): """Build datasets list""" datasets = {} - for species, group_dict in types.iteritems(): + for species, group_dict in list(types.items()): datasets[species] = {} - for group, type_list in group_dict.iteritems(): + for group, type_list in list(group_dict.items()): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) @@ -319,4 +311,4 @@ def _test_it(): if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main()
\ No newline at end of file + main() |