diff options
Diffstat (limited to 'wqflask/maintenance/gen_select_dataset.py')
| -rw-r--r-- | wqflask/maintenance/gen_select_dataset.py | 49 |
1 files changed, 24 insertions, 25 deletions
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py index 647e58a2..db65a11f 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 @@ -63,16 +55,17 @@ from pprint import pformat as pf #conn = Engine.connect() + 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:], - host = parsed_uri.hostname, - user = parsed_uri.username, - passwd = parsed_uri.password) + db=parsed_uri.path[1:], + host=parsed_uri.hostname, + user=parsed_uri.username, + passwd=parsed_uri.password) print(db_conn_info) return db_conn_info @@ -108,7 +101,7 @@ 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 @@ -127,21 +120,23 @@ def get_types(groups): else: if not phenotypes_exist(group_name) and not genotypes_exist(group_name): types[species].pop(group_name, None) - groups[species] = tuple(group for group in groups[species] if group[0] != group_name) - else: #ZS: This whole else statement might be unnecessary, need to check + groups[species] = tuple( + group for group in groups[species] if group[0] != group_name) + else: # ZS: This whole else statement might be unnecessary, need to check types_list = build_types(species, group_name) if len(types_list) > 0: types[species][group_name] = types_list else: types[species].pop(group_name, None) - groups[species] = tuple(group for group in groups[species] if group[0] != group_name) + groups[species] = tuple( + group for group in groups[species] if group[0] != group_name) return types def phenotypes_exist(group_name): #print("group_name:", group_name) Cursor.execute("""select Name from PublishFreeze - where PublishFreeze.Name = '%s'""" % (group_name+"Publish")) + where PublishFreeze.Name = '%s'""" % (group_name + "Publish")) results = Cursor.fetchone() #print("RESULTS:", results) @@ -151,10 +146,11 @@ def phenotypes_exist(group_name): else: return False + def genotypes_exist(group_name): #print("group_name:", group_name) Cursor.execute("""select Name from GenoFreeze - where GenoFreeze.Name = '%s'""" % (group_name+"Geno")) + where GenoFreeze.Name = '%s'""" % (group_name + "Geno")) results = Cursor.fetchone() #print("RESULTS:", results) @@ -164,6 +160,7 @@ def genotypes_exist(group_name): else: return False + def build_types(species, group): """Fetches tissues @@ -192,12 +189,13 @@ def build_types(species, group): return results + 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]) @@ -254,7 +252,7 @@ def build_datasets(species, group, type_name): dataset_text = "%s Genotypes" % group datasets.append((dataset_id, dataset_value, dataset_text)) - else: # for mRNA expression/ProbeSet + else: # for mRNA expression/ProbeSet Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and @@ -316,7 +314,8 @@ def _test_it(): datasets = build_datasets("Mouse", "BXD", "Hippocampus") #print("build_datasets:", pf(datasets)) + if __name__ == '__main__': Conn = MySQLdb.Connect(**parse_db_uri()) Cursor = Conn.cursor() - main()
\ No newline at end of file + main() |