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nlpie / biomedicus

BioMedICUS: A biomedical and clinical NLP engine.
https://nlpie.github.io/biomedicus/
Apache License 2.0
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Bump org.rocksdb:rocksdbjni from 9.6.1 to 9.7.3 in /java #428

Open dependabot[bot] opened 1 month ago

dependabot[bot] commented 1 month ago

Bumps org.rocksdb:rocksdbjni from 9.6.1 to 9.7.3.

Release notes

Sourced from org.rocksdb:rocksdbjni's releases.

RocksDB 9.7.3

9.7.3 (10/16/2024)

Behavior Changes

  • OPTIONS file to be loaded by remote worker is now preserved so that it does not get purged by the primary host. A similar technique as how we are preserving new SST files from getting purged is used for this. min_options_file_numbers_ is tracked like pending_outputs_ is tracked.

9.7.2 (10/08/2024)

Bug Fixes

  • Fix a bug for surfacing write unix time: Iterator::GetProperty("rocksdb.iterator.write-time") for non-L0 files.

9.7.1 (09/26/2024)

Bug Fixes

  • Several DB option settings could be lost through GetOptionsFromString(), possibly elsewhere as well. Affected options, now fixed:background_close_inactive_wals, write_dbid_to_manifest, write_identity_file, prefix_seek_opt_in_only
  • Fix under counting of allocated memory in the compressed secondary cache due to looking at the compressed block size rather than the actual memory allocated, which could be larger due to internal fragmentation.
  • Skip insertion of compressed blocks in the secondary cache if the lowest_used_cache_tier DB option is kVolatileTier.

9.7.0 (09/20/2024)

New Features

  • Make Cache a customizable class that can be instantiated by the object registry.
  • Add new option prefix_seek_opt_in_only that makes iterators generally safer when you might set a prefix_extractor. When prefix_seek_opt_in_only=true, which is expected to be the future default, prefix seek is only used when prefix_same_as_start or auto_prefix_mode are set. Also, prefix_same_as_start and auto_prefix_mode now allow prefix filtering even with total_order_seek=true.
  • Add a new table property "rocksdb.key.largest.seqno" which records the largest sequence number of all keys in file. It is verified to be zero during SST file ingestion.

Behavior Changes

  • Changed the semantics of the BlobDB configuration option blob_garbage_collection_force_threshold to define a threshold for the overall garbage ratio of all blob files currently eligible for garbage collection (according to blob_garbage_collection_age_cutoff). This can provide better control over space amplification at the cost of slightly higher write amplification.
  • Set write_dbid_to_manifest=true by default. This means DB ID will now be preserved through backups, checkpoints, etc. by default. Also add write_identity_file option which can be set to false for anticipated future behavior.
  • In FIFO compaction, compactions for changing file temperature (configured by option file_temperature_age_thresholds) will compact one file at a time, instead of merging multiple eligible file together (#13018).
  • Support ingesting db generated files using hard link, i.e. IngestExternalFileOptions::move_files/link_files and IngestExternalFileOptions::allow_db_generated_files.
  • Add a new file ingestion option IngestExternalFileOptions::link_files to hard link input files and preserve original files links after ingestion.
  • DB::Close now untracks files in SstFileManager, making avaialble any space used by them. Prior to this change they would be orphaned until the DB is re-opened.

Bug Fixes

  • Fix a bug in CompactRange() where result files may not be compacted in any future compaction. This can only happen when users configure CompactRangeOptions::change_level to true and the change level step of manual compaction fails (#13009).
  • Fix handling of dynamic change of prefix_extractor with memtable prefix filter. Previously, prefix seek could mix different prefix interpretations between memtable and SST files. Now the latest prefix_extractor at the time of iterator creation or refresh is respected.
  • Fix a bug with manual_wal_flush and auto error recovery from WAL failure that may cause CFs to be inconsistent (#12995). The fix will set potential WAL write failure as fatal error when manual_wal_flush is true, and disables auto error recovery from these errors.
Changelog

Sourced from org.rocksdb:rocksdbjni's changelog.

9.7.3 (10/16/2024)

Behavior Changes

  • OPTIONS file to be loaded by remote worker is now preserved so that it does not get purged by the primary host. A similar technique as how we are preserving new SST files from getting purged is used for this. min_options_file_numbers_ is tracked like pending_outputs_ is tracked.

9.7.2 (10/08/2024)

Bug Fixes

  • Fix a bug for surfacing write unix time: Iterator::GetProperty("rocksdb.iterator.write-time") for non-L0 files.

9.7.1 (09/26/2024)

Bug Fixes

  • Several DB option settings could be lost through GetOptionsFromString(), possibly elsewhere as well. Affected options, now fixed:background_close_inactive_wals, write_dbid_to_manifest, write_identity_file, prefix_seek_opt_in_only
  • Fix under counting of allocated memory in the compressed secondary cache due to looking at the compressed block size rather than the actual memory allocated, which could be larger due to internal fragmentation.
  • Skip insertion of compressed blocks in the secondary cache if the lowest_used_cache_tier DB option is kVolatileTier.

9.7.0 (09/20/2024)

New Features

  • Make Cache a customizable class that can be instantiated by the object registry.
  • Add new option prefix_seek_opt_in_only that makes iterators generally safer when you might set a prefix_extractor. When prefix_seek_opt_in_only=true, which is expected to be the future default, prefix seek is only used when prefix_same_as_start or auto_prefix_mode are set. Also, prefix_same_as_start and auto_prefix_mode now allow prefix filtering even with total_order_seek=true.
  • Add a new table property "rocksdb.key.largest.seqno" which records the largest sequence number of all keys in file. It is verified to be zero during SST file ingestion.

Behavior Changes

  • Changed the semantics of the BlobDB configuration option blob_garbage_collection_force_threshold to define a threshold for the overall garbage ratio of all blob files currently eligible for garbage collection (according to blob_garbage_collection_age_cutoff). This can provide better control over space amplification at the cost of slightly higher write amplification.
  • Set write_dbid_to_manifest=true by default. This means DB ID will now be preserved through backups, checkpoints, etc. by default. Also add write_identity_file option which can be set to false for anticipated future behavior.
  • In FIFO compaction, compactions for changing file temperature (configured by option file_temperature_age_thresholds) will compact one file at a time, instead of merging multiple eligible file together (#13018).
  • Support ingesting db generated files using hard link, i.e. IngestExternalFileOptions::move_files/link_files and IngestExternalFileOptions::allow_db_generated_files.
  • Add a new file ingestion option IngestExternalFileOptions::link_files to hard link input files and preserve original files links after ingestion.
  • DB::Close now untracks files in SstFileManager, making avaialble any space used by them. Prior to this change they would be orphaned until the DB is re-opened.

Bug Fixes

  • Fix a bug in CompactRange() where result files may not be compacted in any future compaction. This can only happen when users configure CompactRangeOptions::change_level to true and the change level step of manual compaction fails (#13009).
  • Fix handling of dynamic change of prefix_extractor with memtable prefix filter. Previously, prefix seek could mix different prefix interpretations between memtable and SST files. Now the latest prefix_extractor at the time of iterator creation or refresh is respected.
  • Fix a bug with manual_wal_flush and auto error recovery from WAL failure that may cause CFs to be inconsistent (#12995). The fix will set potential WAL write failure as fatal error when manual_wal_flush is true, and disables auto error recovery from these errors.

9.6.0 (08/19/2024)

New Features

  • *Best efforts recovery supports recovering to incomplete Version with a clean seqno cut that presents a valid point in time view from the user's perspective, if versioning history doesn't include atomic flush.
  • New option BlockBasedTableOptions::decouple_partitioned_filters should improve efficiency in serving read queries because filter and index partitions can consistently target the configured metadata_block_size. This option is currently opt-in.
  • Introduce a new mutable CF option paranoid_memory_checks. It enables additional validation on data integrity during reads/scanning. Currently, skip list based memtable will validate key ordering during look up and scans.

Public API Changes

  • Add ticker stats to count file read retries due to checksum mismatch
  • Adds optional installation callback function for remote compaction

Behavior Changes

  • There may be less intra-L0 compaction triggered by total L0 size being too small. We now use compensated file size (tombstones are assigned some value size) when calculating L0 size and reduce the threshold for L0 size limit. This is to avoid accumulating too much data/tombstones in L0.

Bug Fixes

  • *Make DestroyDB supports slow deletion when it's configured in SstFileManager. The slow deletion is subject to the configured rate_bytes_per_sec, but not subject to the max_trash_db_ratio.
  • Fixed a bug where we set unprep_seqs_ even when WriteImpl() fails. This was caught by stress test write fault injection in WriteImpl(). This may have incorrectly caused iteration creation failure for unvalidated writes or returned wrong result for WriteUnpreparedTxn::GetUnpreparedSequenceNumbers().

... (truncated)

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