1. 22 Oct, 2015 2 commits
  2. 20 Oct, 2015 2 commits
    • Vermaat's avatar
      Merge pull request #94 from mutalyzer/redis-links · b80ac8ec
      Vermaat authored
      Cache transcript protein links in Redis
      b80ac8ec
    • Vermaat's avatar
      Cache transcript protein links in Redis · 473c732c
      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
      473c732c
  3. 16 Oct, 2015 3 commits
    • Vermaat's avatar
      Clarify Redis client import in stats module · 47ce0ee3
      Vermaat authored
      47ce0ee3
    • Vermaat's avatar
      Merge pull request #93 from mutalyzer/reconfigure-redis · 4e4798c5
      Vermaat authored
      Create new Redis connection when REDIS_URI changes
      4e4798c5
    • Vermaat's avatar
      Create new Redis connection when REDIS_URI changes · f56cbbda
      Vermaat authored
      When the REDIS_URI configuration setting is changed, the Redis
      client should be reconfigured with a new connection pool, just
      like we do with the database.
      
      It appears redis-py manages the connection pool by itself and
      doesn't expose ways to explicitely destroy it or close all
      connections (this is done automatically when all connections
      loose scope).
      
      This fix ensures that the unit tests don't accidentally work on
      the Redis database configured in MUTALYZER_SETTINGS, which was
      quite an unfortunate bug.
      f56cbbda
  4. 14 Oct, 2015 3 commits
  5. 13 Oct, 2015 11 commits
  6. 10 Oct, 2015 7 commits
  7. 01 Oct, 2015 8 commits
  8. 30 Sep, 2015 4 commits