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changelog.md

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Changelog

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

[0.7.0] -- 2021-04-27

Added

  • remotes section in the refgenieserver config, which supersedes remote_url_base. It can be used to define multiple remote data providers.
  • new endpoints:
    • /remotes/dict to get remotes dictionary
    • /assets/dir_contents/{genome}/{asset} to get a JSON object (array of strings) listing all files in the asset directory
    • /assets/file_path/{genome}/{asset}/{seek_key} to get a remote path to the specified file
  • direct unarchived asset file downloads from asset splash page, both for seek_keys and other asset files

Changed

  • endpoints that return digests return plain text instead of JSON objects for easier parsing; #67

[0.6.1] -- 2021-03-18

Added

  • private endpoint serving genomes dict to openAPI schema; #105

[0.6.0] -- 2021-03-11

Added

  • API v3, which is a complete redesign and extension of the previous version
  • in refgenieserver archive, when a archive_checksum is missing for a previously archived asset it will be recalculated.
  • response models to API endpoints
  • API version tags in the openAPI specification
  • a legacy_archive_digest to the tag attributes

Changed

  • split the user interface into: index, genome and asset pages
  • grouped endpoints by API version in the swagger docs
  • the archives created with refgenieserver archive are now named after digests

[0.5.1] -- 2020-07-10

Changed

  • in refgenieserver archive:
    • implement safer way of asset archive creation
    • follow symlinks

[0.5.0] -- 2020-07-06

Added

  • support for external asset sources via remote_url_base key in the config

Changed

  • path specified in genome_archive_config is considered relative to the refgenie genome config file, unless absolute.
  • non-servable assets purging is now performed prior to serving rather than after each archive job completion
  • dropped Python 2 support

Removed

  • support for old genome_archive key; use genome_archive_folder and genome_archive_config from now on.

[0.4.4] -- 2020-03-17

Changed

  • refgenieserver archive requires all assets to be complete prior to archiving

[0.4.3] -- 2020-01-16

Added

  • a possibility to decouple genome archive directory and genome archive config file. refgenieserver archive uses new key (genome_archive_config) from refgenconf
  • a genome archive config file writability check

Changed

  • key genome_archive to genome_archive_folder. Backwards compatiblity is preserved (both are currently supported)

[0.4.2] -- 2020-01-08

Fixed

  • undefined variable referencing issue; #73

[0.4.1] -- 2019-12-13

Fixed

  • relationship info not being updated during specific asset archivization; #70

Changed

  • order of the assets adn tags in the table in the index page: sorted alphabetically instead of oldest to newest

[0.4.0] -- 2019-12-06

Added

  • asset splash pages presenting all the asset attributes and related API endpoint links. Available at: /asset/{genome}/{asset}/splash
  • archive digest API endpoint. Available at /asset/{genome}/{asset}/{tag}/archive_digest

Changed

  • recipes are served as JSON objects, not files
  • refgenieserver archive enhancements; related to config file locking

[0.3.4] -- 2019-11-06

Added

  • distribute the license file with the package
  • test script
  • API endpoints for serving asset build logs and asset build recipes. Available at /asset/{genome}/{asset}/log and /asset/{genome}/{asset}/recipe, respectively

Fixed

  • fastapi - starlette dependency issue

[0.3.3] -- 2019-10-24

Fixed

  • PyPi installation problem; #59

[0.3.2] -- 2019-10-23

Added

  • dynamic website URL rendering in the page banner

Fixed

  • TypeError in refgenieserver archive; #55
  • AttributeError which was raised when no subcommand was specified; #54

[0.3.1] -- 2019-10-21

Fixed

  • refgenconf not being installed

[0.3.0] -- 2019-10-21

Added

  • possibility to use $REFGENIE environment variable to provide config path in refgenieserver archive
  • new API endpoints:
    • /genome/{genome} -- returns a dictionary with genome attributes (contents, checksum, genome_description)
    • /genome/{genome}/genome_digest -- returns just the genome digest
    • /asset/{genome}/{asset}/{tag}/asset_digest -- returns just the asset digest
    • /asset/{genome}/{asset}/default_tag -- returns the default tag of an asset
  • tag query parameter to the endpoints: /asset/{genome}/{asset}/archive, /asset/{genome}/{asset} to retrieve the archive/metadata associated with tagged asset
  • API versioning support
  • API versions: v1 (accessible with a v1/ prefix and without any) and v2 (accessible with v2/ prefix)
  • pigz support. If the command is callable, it will be used for archiving
  • incomplete assets skipping in refgenieserver archive
  • config manipulation support in multi-process contexts, it's racefree, uses file locks
  • archive removal support (added -r option in refgenieserver archive)
  • asset registry path support in refgenieserver archive

Changed

  • command order from refgenieserver -c CONFIG -d archive/serve to refgenieserver archive/serve -c CONFIG -d
  • the genome tarballs are not produced
  • config v0.3 is required
  • -g and -a flags to asset registry path

Fixed

  • AttributeError in refgenieserver archive; #35
  • issue with asset attributes serving in API v1 after config format change

[0.2.0] -- 2019-07-11

Added

  • Add an option to archive a specific genome:asset(s) bundle
  • Update to use genome config version 0.2
  • Added genome descriptions to web interface
  • Some visual improvements to links and layout of web interface

[0.1.0] -- 2019-06-21

  • Initial project release