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Add explicit commit statements #86

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4 changes: 3 additions & 1 deletion taxadb/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ def create_db(args):
if div in ['full', 'prot']:
acc_dl_list.append(prot)
parser = Accession2TaxidParser(verbose=args.verbose, fast=args.fast)
with db.atomic():
with db.atomic() as txn:
for acc_file in acc_dl_list:
inserted_rows = 0
logger.info("Parsing %s" % str(acc_file))
Expand All @@ -149,13 +149,15 @@ def create_db(args):
logger.info('%s: %s added to database (%d rows inserted)'
% (Accession.get_table_name(),
acc_file, inserted_rows))
txn.commit()
if not Accession.has_index(name='accession_accession'):
logger.info('Creating index for %s'
% Accession.get_table_name())
try:
# db.add_index(Accession, ['accession'], unique=True)
idx = db.index(db.Accession, name='accession', unique=True)
db.add_index(idx)
txn.commit()
except PeeweeException as err:
raise Exception("Could not create Accession index: %s"
% str(err))
Expand Down