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script/delete_records: Add option to match fields with regex pattern #151

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script/delete_records: Add option to match fields with regex pattern #151

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9 changes: 9 additions & 0 deletions scripts/delete_records.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
parser.add_argument("-db", "--database", help="database to delete from")
parser.add_argument("-v", "--virus", default="flu", help="virus table to interact with")
parser.add_argument("--filter", nargs="*", default=[], help="Filters for records to delete, i.e. inclusion_date: 2021-02-12")
parser.add_argument("--match", nargs="*", default=[], help="Match for records to delete with regex pattern, e.g. accession:^EPIEPI")
parser.add_argument('--interval', nargs="*", default=[], help="Select date interval of values for fields, e.g. assay_date:2019-09-03,2023-10-25")
parser.add_argument("--preview", action="store_true", help="Preview records to be deleted without deleting from db.")

Expand All @@ -29,6 +30,14 @@

rethinkdb_command = r.table(args.virus).filter(delete_filters)

delete_matches = {}
for delete_match in args.match:
field, pattern = delete_match.split(":")
rethinkdb_command = rethinkdb_command.filter(lambda doc: doc[field].match(pattern))
delete_matches[field] = pattern

print(f"Delete matches: {delete_matches}")

delete_intervals = {}
for interval in args.interval:
field, values = interval.split(':')
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