def test_unique_kegg_names():
kegg_list = Kegg.get_org_list()
from collections import Counter
l = []
d = csv.DictReader(kegg_list.split('\n'), delimiter='\t', fieldnames=('code', 'org', 'tax'))
for row in d:
code, org, tax = row['code'], row['org'], row['tax']
l.append(tax)
c = Counter(l)
max_val = max(c.values())
print "Max val:", max_val
while max_val > 1:
print "#", max_val, " count:", len([v for v in c.values() if v == max_val])
max_val -= 1
def initdb():
"""Creates the database."""
db.create_all()
logging.info('Getting kegg organism list...')
kegg_list = Kegg.get_org_list()
# use only get memory error otherwise
# print BiomodelMongo.objects.only('organism', 'name').all()
mongo_list = dict(
(b.organism, b.name)
for b in BiomodelMongo.objects.only('organism', 'name').all()
)
mongo_orgs = set(mongo_list.keys())
# to prevent insertion porting the same name
kegg_names = set()
logging.info('Insertion begins...')
d = csv.DictReader(kegg_list.split('\n'), delimiter='\t', fieldnames=('code', 'org', 'tax'))
for row in d:
code, org, tax = row['code'], row['org'], row['tax']
if org in mongo_orgs:
if tax not in kegg_names:
o = Organism(row['code'], row['org'], row['tax'])
o.save()
b = Biomodel(name=tax, kegg_org=org)
b.save()
# finally tax to the set
kegg_names.add(tax)
# insert user
u = User(username='******', email='*****@*****.**', password='******')
u.save()
logging.info('Done !')
