Subject instance collision after database connection recovery #85
Description
Just saw a weird error when running a cleanup scrape of the HD repo:
2025-10-29 19:44:10 [JsonldSpider] INFO: Processing JSON-LD 1 of 1 (https://dvn-cloud.s3.us-east-1.amazonaws.com/10.7910/DVN/ZHF9WC/export_schema.org.cached?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIEJ3NV7UYCSRJC7A%2F20251029%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20251029T194407Z&X-Amz-Expires=7200&X-Amz-SignedHeaders=host&X-Amz-Signature=2bd0a4651973356964363d36dc0fc4e0c83c1377f2c60ab431d6f373a1a04dfd)
2025-10-29 19:44:12 [OPersist] WARNING: OBSOLETED = sha256:8a04038ede53c159b00d7c5b3d4ef0eabb93a22f66fea71f262a0a2d149d8494 in series https://doi.org/10.7910/DVN/ZHF9WC
2025-10-29 19:44:17 [OPersist] ERROR: (sqlite3.OperationalError) database is locked
(Background on this error at: https://sqlalche.me/e/14/e3q8)
2025-10-29 19:44:17 [OPersist] ERROR: Caught sqlalchemy.exc.OperationalError; attempting session restart...
2025-10-29 19:44:17 [OPersist] INFO: Entering session recovery loop
2025-10-29 19:44:17 [OPersist] INFO: Closing old database connection session
2025-10-29 19:44:17 [OPersist] INFO: Opening new database connection session
2025-10-29 19:44:17 [OPersist] INFO: Retrying persist with new session...
2025-10-29 19:44:17 [OPersist] WARNING: OBSOLETED = sha256:8a04038ede53c159b00d7c5b3d4ef0eabb93a22f66fea71f262a0a2d149d8494 in series https://doi.org/10.7910/DVN/ZHF9WC
2025-10-29 19:44:17 [OPersist] ERROR: Failed to store entry in database.
2025-10-29 19:44:17 [OPersist] ERROR: Can't attach instance <Subject at 0x7f44ab9391f0>; another instance with key (<class 'opersist.models.subject.Subject'>, ('http://orcid.org/0000-0002-9528-9470',), None) is already present in this session.
2025-10-29 19:44:17 [OPersist] ERROR: Could not store item under new session: sha256:e52a802af0198b23c21fd6e981216c16fd7fc0c2f58cd834938b9433e883cfd6
The error then recurs for each subsequent item:
2025-10-29 19:44:23 [JsonldSpider] INFO: Processing JSON-LD 1 of 1 (https://dvn-cloud.s3.us-east-1.amazonaws.com/10.7910/DVN/AQVFSD/export_schema.org.cached?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIEJ3NV7UYCSRJC7A%2F20251029%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20251029T194421Z&X-Amz-Expires=7200&X-Amz-SignedHeaders=host&X-Amz-Signature=53f17dba7957da24e4126dc7b5dae06499b4006c786e861966d0e5e2b1bd8627)
2025-10-29 19:44:23 [OPersist] ERROR: Failed to store entry in database.
2025-10-29 19:44:23 [OPersist] ERROR: Can't attach instance <Subject at 0x7f44ab9391f0>; another instance with key (<class 'opersist.models.subject.Subject'>, ('http://orcid.org/0000-0002-9528-9470',), None) is already present in this session.