BioThings v0.12.5 release

What's Changed

• Handle sqlite duplicate _id by @DylanWelzel in #327
• Add metadata query field validation by @ctrl-schaff in #330
• metadata query logical enhancements and bugfixes by @ctrl-schaff in #331
• DockerContainerDumper volume feature by @jal347 in #332
• Metadata fields bug fix by @everaldorodrigo in #334
• Improve metadata field index search by @ctrl-schaff in #333
• Add more idiomatic sqlite multiple document insert by @ctrl-schaff in #335
• Api customization by @jal347 in #336
• Add advanced plugin support for the command line tooling by @ctrl-schaff in #329
• Implement notifiers using asyncio by @everaldorodrigo in #337
• Fix metadata mapping and remove duplicated code. by @everaldorodrigo in #341
• Fix Slack notifier test. by @everaldorodrigo in #343
• Upgrade tornado to 6.4.1 by @everaldorodrigo in #342
• Correct the pyproject.toml black configuration ... by @ctrl-schaff in #340
• Replace deprecated imp module with importlib by @DylanWelzel in #339
• Build Config Err Fix by @DylanWelzel in #345
• Add CLI mongodb support by @ctrl-schaff in #338
• Add id checking to IgnoreDuplicatedStorage ... by @ctrl-schaff in #344
• Refactor ES exceptions by @everaldorodrigo in #346
• Rise exceptions correctly. by @everaldorodrigo in #347

Full Changelog: v0.12.4...v0.12.5

BioThings v0.12.4 release

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: v0.12.3...v0.12.4

BioThings v0.12.3 release

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 #301
  • Switched to use orjson in utils.dotfield module #300
  • Changed default release date format in DockerContainerDumper

Full Changelog: v0.12.2...v0.12.3

BioThings v0.12.2 release

What's Changed

• Set plugin name to the folder name for Advanced plugins. by @everaldorodrigo in #290
• Break Circular Dependency by @everaldorodrigo in #291
• Fix dict default vals to work with dicts. by @everaldorodrigo in #292

Full Changelog: v0.12.1...v0.12.2

BioThings v0.12.1 release

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

BioThings v0.12.0 release

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 newgene#56
- New Docker Dumper based data plugins newgene#83
- Support manifest-only date plugin (with a pre-defined parser) #259
- Support Python 3.11 and dropped Python 3.6 support

BioThings v0.11.1 release

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 newgene#65
  • Resolved a hub error when installing a full release #257
  • Fixed a quick_index error when a data source has multiple uploaders newgene#66

BioThings v0.11.0 release

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

v0.8.5

Improve es sniff stability