Add SQLite based cache store #6255
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Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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It includes a sqlite integration |
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This pull request introduces a new SQLite-based caching mechanism for Nextflow, enabling an alternative to the default cache store. Key changes include adding a new
SQLiteCacheStoreclass, modifying the cache factory to support multiple cache providers, and adding test coverage for the new SQLite implementation.New SQLite-based caching mechanism:
SQLiteCacheStoreimplementation: Added a new classSQLiteCacheStorethat provides an SQLite-based implementation of theCacheStoreinterface. This includes methods for managing cache entries, creating tables, handling database connections, and ensuring concurrency safety. (modules/nextflow/src/main/groovy/nextflow/cache/sqlite/SQLiteCacheStore.groovy)Test coverage for
SQLiteCacheStore: Added comprehensive unit tests forSQLiteCacheStoreto validate its functionality, including handling cache entries, managing indexes, and ensuring consistency and concurrency. (modules/nextflow/src/test/groovy/nextflow/cache/sqlite/SQLiteCacheStoreTest.groovy)Cache factory enhancements:
Dynamic cache provider selection: Updated the
DefaultCacheFactoryto dynamically select the cache provider (sqliteor default) based on theNXF_CACHE_PROVIDERenvironment variable. Added logging to indicate the selected cache provider. (modules/nextflow/src/main/groovy/nextflow/cache/DefaultCacheFactory.groovy)Logging support: Added the
@Slf4jannotation toDefaultCacheFactoryto enable logging for debugging and operational insights. (modules/nextflow/src/main/groovy/nextflow/cache/DefaultCacheFactory.groovy)Dependency updates:
org.xerial:sqlite-jdbc:3.46.1.3to the project dependencies to support SQLite database operations. (modules/nextflow/build.gradle)