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Vermaat
authored
Caching of transcript protein links received from the NCBI Entrez service is a typical use case for Redis. This implements this cache in Redis and removes all use of our original database table. An Alembic migration copies all existing links from the database to Redis. The original `TranscriptProteinLink` database table is not dropped. This will be done in a future migration to ensure running processes don't error and to provide a rollback scenario. We also remove the expiration of links (originally defaulting to 30 days), since we don't expect them to ever change. Negative links (caching a 'not found' result from Entrez) *are* still expiring, but with a longer default of 30 days (was 5 days). The configuration setting for the latter was renamed, yielding the following changes in the default configuration settings. Removed default settings: # Expiration time for transcript<->protein links from the NCBI (in seconds). PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 30 # Expiration time for negative transcript<->protein links from the NCBI (in # seconds). NEGATIVE_PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 5 Added default setting: # Cache expiration time for negative transcript<->protein links from the NCBI # (in seconds). NEGATIVE_LINK_CACHE_EXPIRATION = 60 * 60 * 24 * 30
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