Commit d8f4de1f authored by Bertrand  NÉRON's avatar Bertrand NÉRON
Browse files

FIX the name of replicon is displayed in error message when a replicon is skipped

parent ba6f41fd
...@@ -180,13 +180,13 @@ def fill_db(server_uri, db_name, user, passwd, replicon_db, system_db, force_upd ...@@ -180,13 +180,13 @@ def fill_db(server_uri, db_name, user, passwd, replicon_db, system_db, force_upd
secreton_db = server.get_or_create_db(db_name) secreton_db = server.get_or_create_db(db_name)
system_codes = system_db.keys() system_codes = system_db.keys()
system_codes.sort() system_codes.sort()
print("number of documents:", len(system_codes), file=sys.stderr) print("number of system occurences:", len(system_codes), file=sys.stderr)
for syst_code in system_codes: for syst_code in system_codes:
system = system_db[syst_code] system = system_db[syst_code]
try: try:
replicon = replicon_db[system.replicon] replicon = replicon_db[system.replicon]
except KeyError: except KeyError:
print("ERROR Replicon {0} referenced in system annotation file is not present in replicon information file: replicon skipped") print("ERROR Replicon {0} referenced in system annotation file is not present in replicon information file: replicon skipped".format(system.replicon))
continue continue
secretion_system = SecretionSystem() secretion_system = SecretionSystem()
secretion_system._id = system.code secretion_system._id = system.code
......
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