Biothings.api Versions Save

What's Changed

• Highlights:

  • New and updated tutorials and documentation (#313)
  • CURIE id support in the annotation endpoint (#306)
  • Added new jmespath_exclude_empty option

• biothings.web improvements:

  • Jmespath now handles list as parent_path field

• biothings.hub improvements:

  • Added Elasticsearch index selector

• biothings.cli improvements:

  • Fixed missing data plugin manifest template

• documentation improvements:

  • Added new tutorial for Biothings CLI
  • Added tutorial for creating docker based data plugin (#313)

• Misc improvements:

  • Upgraded Tornado to 6.4.0 (#299)
  • Upgraded elasticsearch-py and elasticsearch-dsl to 8.x (#262)

Full Changelog: https://github.com/biothings/biothings.api/compare/v0.12.3...v0.12.4

What's Changed

• Highlights:

  • Implemented the new filter parameter for the query handler (#296)

• biothings.web improvements:

  • Enabled post_filter parameter for POST queries (#208)
  • Improved jmespath transformation with better support root-level transformation

• biothings.hub improvements:

  • Allow passing and customizing merge_struct with the new inclusion and exclustion parameters
  • Allow customization in Builder's merge order with the new merge_order method
  • Fixed the deprecated import of networkx module
  • Fixed the security issue when calling check_output https://github.com/biothings/biothings.api/pull/301
  • Switched to use orjson in utils.dotfield module https://github.com/biothings/biothings.api/pull/300
  • Changed default release date format in DockerContainerDumper

Full Changelog: https://github.com/biothings/biothings.api/compare/v0.12.2...v0.12.3

What's Changed

• Set plugin name to the folder name for Advanced plugins. by @everaldorodrigo in https://github.com/biothings/biothings.api/pull/290
• Break Circular Dependency by @everaldorodrigo in https://github.com/biothings/biothings.api/pull/291
• Fix dict default vals to work with dicts. by @everaldorodrigo in https://github.com/biothings/biothings.api/pull/292

Full Changelog: https://github.com/biothings/biothings.api/compare/v0.12.1...v0.12.2

This is a bug-fix release with these CHANGES: (see also CHANGES.txt)

v0.12.1 (2022/07/05) Bugfixes: - biothings.cli: fixed "logger is not defined" error when typer is not installed - biothings.web: fixed an error when build_date is None during the metadata merging - biothings.web: fixed an edge case when attempting to read ES6 mapping with doc_type

A major release with many new features and bug fixes. See CHANGES.txt for details.

v0.12.0 (2022/06/21) Highlights: - New CLI feature for developing and testing data plugins https://github.com/newgene/biothings.api/pull/56 - New Docker Dumper based data plugins https://github.com/newgene/biothings.api/pull/83 - Support manifest-only date plugin (with a pre-defined parser) https://github.com/biothings/biothings.api/issues/259 - Support Python 3.11 and dropped Python 3.6 support

This is a bug-fix release with these CHANGES (see also CHANGES.txt):

v0.11.1 (2022/10/03)

• Hub improvements:
  • use pickle protocol 4 as the pickle.dump default
• Hub bug fixes:
  • Fixed a JSON serialization error during incremental release https://github.com/newgene/biothings.api/pull/65
  • Resolved a hub error when installing a full release https://github.com/biothings/biothings.api/issues/257
  • Fixed a quick_index error when a data source has multiple uploaders https://github.com/newgene/biothings.api/pull/66

A major release with many web and hub component enhancement and bug fixes. See CHANGES.txt for details.