Commit f949a1e6 authored by Bertrand  NÉRON's avatar Bertrand NÉRON

file containig system info could refer replicon which are not in replicon file

so skip these systems and log them
parent 2e8a3cdf
......@@ -179,13 +179,19 @@ def fill_db(server_uri, db_name, user, passwd, replicon_db, system_db, force_upd
secreton_db = server.get_or_create_db(db_name)
system_codes = system_db.keys()
system_codes.sort()
print("number of documents:", len(system_codes), file=sys.stderr)
for syst_code in system_codes:
system = system_db[syst_code]
replicon = replicon_db[system.replicon]
try:
replicon = replicon_db[system.replicon]
except KeyError:
print("ERROR Replicon {0} referenced in system annotation file is not present in replicon information file: replicon skipped")
continue
secretion_system = SecretionSystem()
secretion_system._id = system.code
secretion_system.code = system.code
secretion_system.predicted_system = system.predicted_system
secretion_system.system_status = system.system_status
secretion_system.replicon = {'name': replicon.name,
'ncbi_id': replicon.ncbi_id,
'taxid': replicon.taxid,
......
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