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Changelog

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

[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