Changelog

This project adheres to Semantic Versioning and Keep a Changelog format.

[0.14.13] - 2026-07-13

Fixed:

• Cache get_stats() with a TTL to avoid running uncached COUNT queries on the bed table on every request to hot API paths (stats, neighbours, list, search)
• Eliminated an N+1 query in get_neighbours() by fetching all neighbour metadata in a single batched query (with annotations eager-loaded) instead of one query per neighbour; stale Qdrant points are now skipped rather than raising
• Eliminated an N+1 in BedAgentBedSet.get_ids_list(): it was refetching each bedset by id and lazy-loading its full bedfile membership just to build the list page. Now builds results directly from the paginated query; bed_ids is left unpopulated on list results (use get(identifier) for a single bedset's member ids)
• get_detailed_stats() no longer reuses a Session after its with block has closed (was forcing 3 extra connection checkouts for _stats_comments/_stats_geo_status/_get_geo_stats); all queries now share one session/transaction
• Replaced the bed_files_info() call inside get_detailed_stats() with a targeted 3-column query, avoiding a full-table FileInfo Pydantic construction (with per-row try/except) for every bed record just to extract number_of_regions/mean_region_width/file_size for histogram binning
• BedAgentBedFile.get_ids_list() (backs /bed/list) had no order_by() on its paginated query, so row order across pages was undefined -- rows could be duplicated or skipped between requests. Now orders by Bed.id.
• get_detailed_stats() crashed with a pydantic ValidationError whenever bed_compliance, data_format, genome_alias, species_name, assay, or cell_line had NULL rows: the GROUP BY queries included the NULL group, producing a None dict key, which FileStats's dict[str, int] fields reject. All six queries now filter out NULLs before grouping.

Added:

• Added a denormalized bedfile_count column to bedsets, exposed as BedSetMetadata.bedfile_count. Set once at bedset creation time (membership is write-once; add_bedfile/delete_bedfile are unimplemented), so reads never need to touch bedfile_bedset_relation to know a bedset's size. Requires a DB migration -- see scripts/migrations/2026_07_31_add_bedset_bedfile_count.sql

[0.15.0] - 2026-08-17

Added:

• Alembic migration support, including alembic.ini, migration script templates, and configuration files in bbconf/alembic/, with clear instructions in the README.md for generating and applying migrations.
• TTL-based cache (with locking) for the get_stats() method in bbconf/bbagent.py to avoid repeated expensive COUNT queries on hot API paths.
• jsonb columns for genomic distribution data storage in bedfiles and bedsets
• missing imports and properties for snapshot support in bbconf/bbagent.py

Updated:

• Updated binning functions to handle empty input lists gracefully, preventing errors when there is no data.
• Refactored get_detailed_stats() to gather numeric statistics in a single optimized query, filter out null values, and avoid loading unnecessary objects, increasing efficiency and accuracy.
• Minor workflow YAML formatting fix.
• Updated database indexes, making data query faster
• Updated bedhost endpoints, making them more efficient
• Updated the pull request template to require confirmation of completed migration steps when schema changes are made.

[0.14.12] - 2026-04-22

Changed:

• Updated yacman version to 2.0.0

[0.14.11] - 2026-04-15

Fixed:

• External id search

[0.14.10] - 2026-04-05

Fixed:

• version info bug

[0.14.9] - 2026-02-26

Changed:

• Modernized docstrings
• Type annotation for python 3.10+
• Updated requirements
• Updated package installation way to use pyproject.toml and hatchling

[0.14.8] - 2026-02-17

Changed:

• Updated versions of dependencies

[0.14.7] - 2026-02-16

Changed:

• Updated requirements

[0.14.6] - 2026-02-06

Fixed:

• Fixed qdrant upload exception catching

[0.14.5] - 2026-02-05

Changed:

• Updated reindexing script

[0.14.4] - 2026-02-04

Changed:

• Updated reindexing of bed files to use only verified genome digests

[0.14.3] - 2026-01-31

Added:

• Cell line to detailed bedbase statistics

Fixed:

• Saving of big file size (changed to bigint db column type)

[0.14.2] - 2026-01-21

Added:

• Added method that fetches available reference genomes

[0.14.1] - 2025-12-22

Fixed:

• Fixed hybrid search reindexing
• Updated limits in reindexing

[0.14.0] - 2025-12-18

Fixed:

• Insertion of tokenized files

Changed:

• Updated qdrant and encoder model initialization. (One connection for qdrant and one initialized object per model)

Added:

• Hybrid semantic search: dense + sparse search

Added:

• Added hybrid semantic search.(dense + sparse search)

[0.13.0] - 2025-11-24

Added:

• Conversion of bedfile to umap from predefined model

[0.12.0] - 2025-09-11

Added:

• New qdrant semantic search
• Added more plots to bedbase summary page
• New reference genome compatibility that supports new refgenie
• Genomes table, with ability of automatic updates from refgenie
• Added filter in search (Assay and genome)

Changed:

• Improved reindexing methods

Fixed:

• Issues in bedfile update method

[0.11.4] - 2025-06-01

Fixed:

• SQL search

[0.11.3] - 2025-05-27

Fixed:

• Usage tracker
• Order of comprehensive stats

Added:

• Platform usage stats method
• Concise option in stats method

[0.11.2] - 2025-06-22

Added:

• Statistics about bed files grouped by organism

[0.11.1] - 2025-05-22

Fixed:

• Bedbuncher bug

[0.11.0] - 2025-04-21

Added:

• Added usage tracking and statistics
• Added platform comprehensive statistics
• Updated database to a new database schema
• Added new items for bed compliance
• Added head of bed file as a new column in bed table
• Added file digest column to the file table
• Changed global sample and project source to be an array instead of string

[0.10.4] - 2025-01-21

Fixed:

• Changes boto3 #78

[0.10.3] - 2025-01-16

Added:

• Added config analyzer
• Added new methods get_missing_stats and get_missing_files to retrieve lists of bed files that are missing statistics and files, respectively.

Fixed:

• Fixed bugs in updating bed files

[0.10.2] - 2025-01-09

Changed:

• Updated version of zarr

[0.10.1] - 2025-01-07

Changed:

• Updated geo_gsm_status and geo_gse_status tables to include additional information.

[0.10.0] - 2025-01-03

Added:

• Added a new method get_neighbours in bbconf/modules/bedfiles.py to retrieve the nearest neighbors of a bed file from Qdrant.
• Added a new method sql_search in bbconf/modules/bedfiles.py for performing SQL exact searches on bed files.
• Added a new method get_track_hub_file in bbconf/modules/bedsets.py to generate track hub files for bedsets.
• Added processed for uploading bed files and bedsets
• Added update bedfile method

Changed:

• Updated exception handling in the create method of bbconf/modules/bedsets.py to provide more specific error messages.

[0.9.0] - 2024-11-07

Changed

• Fixed bug with uploading tss dist plot

Added

• Added annotations to bedsets (author, source)
• get_genome_list method to bedfiles, that lists all available genomes
• Added method that lists all missing plots for bedfiles (get_missing_plots)

[0.8.0] - 2024-10-23

Added:

• New text2vec search (bivec search)
• Added get_pep to bedset methods

[0.7.1] - 2024-10-15

Added:

• Added table with standardized bed annotation
• Added table with bed reference genome prediction values.

Changed:

• Updated requirements

[0.7.0] - 2024-09-20

Added

• Table and methods for reference genome validator
• Table with standard metadata schema
• Bed file opening improvements

[0.6.1] - 2024-08-21

Added

• DB tables for GEO uploader status

[0.6.0] - 2024-05-01

Added

• Added tokenized files and universes.
• Added bed embedding get endpoint to the API #50
• Fixed test speed #48
• Added license for the bed files #51
• Added payloads to qdrant
• Fixed search, and query results info
• Many other small bug fixes

[0.5.1] - 2024-04-09

Changed

• updated qdrant uploader
• bedset bedfile list query improvement
• other minor fixes in uploading

[0.5.0] - 2024-04-08

Changed

• Rebuild bbconf
• Introduced new DB schema
• Added bbagent that will be used to interact with the database
• Updated config schema
• Added new functionality to the bbagent
• New tests

[0.4.2] - 2024-03-12

Change

• Updated logger
• Updated requirements
• Added upload_status column to the bedfile table

[0.4.1] - 2024-01-01

Fix

• Requirements

[0.4.0] - 2023-12-18

Change

• bbconf to use pipestat v0.6.0 and SQLModel
• Fixed tests

Added

• qdrant search, insert and update functionality
• functions that return results in the DRS format for both bed and bedhost. DRS

[0.3.0] - 2022-08-18

Change

• update select_bedfiles_for_distance
• update database table schema

[0.2.1] - 2021-11-11

Fix

• attempt to fix database connection error

[0.2.0] - 2021-10-25

This release introduces backwards incompatible changes

Changed

• switched to object-relational mapping approach (ORM) for database interface

[0.1.1] - 2021-04-15

Added

• added new fields in the bedfiles and bedsets schema

[0.1.0] - 2021-02-22

This release introduces backwards incompatible changes

Changed

• BedBaseConf backend (database) to PostgreSQL
• complete BedBaseConf class redesign

[0.0.2] - 2020-05-28

Added

• index deleting methods:
  • delete_bedsets_index
  • delete_bedfiles_index
• multiple new keys constants

Changed

• make search_bedfiles and search_bedsets methods return all hits by default instead of just 10. Parametrize it.
• added more arguments to insert_bedfiles_data and insert_bedsets_data method interfaces: doc_id and force_update
• Elasticsearch documents are inserted into the indices more securily, insert_* methods prevent documents duplication

[0.0.1] - 2020-02-05

Added

• initial project release