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v0.12.4 (2024/04/02)
Highlights:
- New and updated tutorials and documentation
- CURIE id support in the annotation endpoint
- 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
Misc improvements:
- Upgraded Tornado to 6.4.0
- Upgraded elasticsearch-py and elasticsearch-dsl to 8.x
v0.12.3 (2023/10/31)
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
v0.12.2 (2023/07/17)
Bugfixes:
- 7e9583ec Fix dict default vals to work with dicts. (#292)
- 77c577cc Break Circular Dependency (#291)
- 7044abba Set plugin name to the folder name for Advanced plugins. (#290)
v0.12.1 (2023/07/05)
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
v0.12.0 (2023/06/21)
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
biothings.web improvements
- Support Google Analytics 4 https://github.com/newgene/biothings.api/pull/16
- Added a new `jmespath` query parameter for response transformation https://github.com/biothings/biothings.api/commit/31898fac7cd86b5c05520622885a3c0852f2494c
- Added date_format query parameter validation https://github.com/newgene/biothings.api/pull/97
- Added min for numeric query parameter validation (max is already supported) https://github.com/newgene/biothings.api/pull/97
- Fixed tornado.autoreload issue to support task-based reload hook https://github.com/newgene/biothings.api/pull/95
- Prevent biothing_type field in metadata from returning a single-item list https://github.com/biothings/biothings.api/issues/272
- Fixed the response formatter for histogram aggregation results https://github.com/biothings/biothings.api/issues/267
- Fixed an issue when only ES_INDEX is provided, not ES_DOC_TYPE https://github.com/biothings/biothings.api/commit/5c6d6dc6057073fb040dd7ae5b11b1b9967bf4f4
- Retired the use of pyinotify in autoreloader https://github.com/biothings/biothings.api/issues/260
- Logging all hanlders at server start https://github.com/biothings/biothings.api/commit/e9b3f9e6f8761746eb1e6f476dd9500b8bf8fe0e
- Adjusted sentry traces_sample_rate setting for better tracking tracebacks https://github.com/biothings/biothings.api/commit/eec03385e79394d1d99a7ed8537966ce2e995645
biothings.hub improvements
- 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 multiple target Elasticsearch hosts in data releases https://github.com/biothings/biothings.api/issues/251
- Allow to set AUTOHUB_VALIDATOR_CLASS to customize release validation logic https://github.com/newgene/biothings.api/pull/105
- Allow to override AutoHubFeature.validate_release method to add metadata validation https://github.com/biothings/biothings.api/issues/284
- Allow to manually mark a data source dump as success, e.g. manual downloads https://github.com/newgene/biothings.api/pull/101
- Verify existing snapshot config matches SNAPSHOT_CONFIG setting and allow to recreate if needed https://github.com/biothings/biothings.api/issues/275
- Support addtional filters (e.g. status) for the build list https://github.com/newgene/biothings.api/pull/94
- Implemented hub's Auto_Archive feature using AUTO_ARCHIVE_CONFIG https://github.com/biothings/biothings.api/issues/261
- Improved data inspection rules for validating field names and values https://github.com/newgene/biothings.api/pull/87
- Added a new re_index helper function https://github.com/biothings/biothings.api/issues/269
- Added a new helper function to generate local SSL certificate (e.g. to run dev on https) https://github.com/newgene/biothings.api/pull/84
- Allow Uploader.load_data method to be called with either data-folder or data-file path https://github.com/newgene/biothings.api/pull/81
- Support manifest-only date plugin (with a pre-defined parser) https://github.com/biothings/biothings.api/issues/259
- Support biothing_type and display_name in data plugin's manifest file https://github.com/biothings/biothings.api/issues/254
- Fixed cursor timeout issue in utils.mongo's doc_feeder helper function https://github.com/biothings/biothings.api/issues/282
- Fixed hub logging file names and returned sorting order https://github.com/newgene/biothings.api/pull/88
- Fixed CVE-2007-4559 when using tarfile module https://github.com/newgene/biothings.api/pull/74
- Fixed Autobuild is not correctly triggered when last build failed https://github.com/biothings/biothings.api/issues/271
- Replaced yapf with black as code formatter when exporting data plugins https://github.com/biothings/biothings.api/commit/fce0864b70802326d52ccc2dc71fb6fa1e4c1292
Experimental features
- Automatically clean up Elasticsearch snapshots via AUTO_SNAPSHOT_CLEANUP_CONFIG https://github.com/biothings/biothings.api/issues/276
- Allow to delete an existing snapshot https://github.com/newgene/biothings.api/pull/103
Misc improvements
- Added a new biothings.utils.common.DummyConfig class to create a temp config module https://github.com/newgene/biothings.api/pull/79
- Fixed all code-styling issue using fourmat (flake8 + black + isort)
- Print out the current test url and biothings version in BiothingsWebTest https://github.com/biothings/biothings.api/issues/273
- Added API documentation for biothings.hub module https://github.com/biothings/biothings.api/issues/265
- The hub commands documentation is now sorted by command names https://github.com/newgene/biothings.api/pull/76
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
v0.11.0 (2022/09/14)
biothings.web improvements
- Added Authentication Mixin class for BioThings SDK Web
- Added GitHub and ORCID Mixin class for BioThings SDK Web
- Allow customize cache settings https://github.com/biothings/biothings.api/issues/206
- Support exclude for "fields" parameter https://github.com/biothings/biothings.api/issues/195
- Support post_filter query parameter https://github.com/biothings/biothings.api/issues/208
- Added "max_total" parameter to POST query https://github.com/biothings/biothings.api/issues/233
- Support "analyzer" parameter to POST query
- Upgrade to use sentry-sdk https://github.com/biothings/biothings.api/issues/204
Support Elasticsearch both 7 and 8
Support Python 3.9 and 3.10 and dropped Python 3.5 support
- Replaced use of yield in coroutine with preferred async/await
- Using ProcessPoolExecutor in set_default_executor https://github.com/biothings/biothings.api/issues/153
- Upgrade aiocron to 1.6 https://github.com/biothings/biothings.api/issues/180
- Upgrade to pymongo v4 https://github.com/biothings/biothings.api/issues/222
- Fixed an error when using python 3.9, 3.10: thread.isAlive was replaced by thread.is_alive: https://bugs.python.org/issue37804
Hub log improvements
- Grouped log files by builds https://github.com/newgene/biothings.api/pull/8
- Switch to use TimedRotatingFileHandler for hub log files https://github.com/biothings/biothings.api/issues/211
- Remove redundant and unused hub log file https://github.com/biothings/biothings.api/issues/210
Data plugin improvements
- Support multiple uploaders in data plugin https://github.com/biothings/biothings_docker/issues/8
- Allow YAML-based manifest file (manifest.yaml) in a data plugin https://github.com/biothings/biothings.api/issues/245
Hub improvements
- Implement full release installation without downtime https://github.com/biothings/biothings.api/issues/134
- Add dumper and uploader timestamps in source metadata https://github.com/biothings/biothings.api/issues/230
- Hub console improvements https://github.com/biothings/biothings.api/issues/216
- Create hub's default settings https://github.com/biothings/biothings.api/issues/217
- Refactor _parse_comments method logic https://github.com/biothings/biothings.api/issues/218
- indexer should check _id length, skip if too long and raise a warning https://github.com/biothings/biothings.api/issues/253
- Removed Nginx weak etag prefix and quotes 'W/"<etag>"` when used as src version https://github.com/biothings/biothings.api/pull/234
get_python_version in utils.version does not return the correct package list https://github.com/biothings/biothings.api/issues/224
Fixed "UserWarning: MongoClient opened before fork" in hub logs https://github.com/biothings/biothings.api/issues/247
v0.10.1 (not publically released)
Fixed multiple issues involving Elasticsearch 7 support on BioThings SDK Hub.
Fixed a few timezone display issues in BioThings SDK Hub.
Correctly handles the situation when POST requests resulted in too many matches.
BioThings SDK Hub Builders only wait on Uploaders of dependency sources
Updated documentation and other minor fixes.
v0.10.0 (2021/09/26)
Separate "connections", "services", "applications" and "launcher" layers.
Support MongoDB, SQLAlchemy-compatible SQLs and AWS OpenSearch query backend.
Support Flask, and FastAPI web framework and WSGI and ASGI gateway interfaces.
Generalize analytics reporting from traditional GA-Universal Analytics support.
v0.9.1 (2021/03/10)
Revise str -> list parsing for backward compatibility.
v0.9.0 (2021/02/21)
Add features to request argument parsing module.
Support YAML content-type parsing in request body.
Support batch query concurrency control.
Improve a few elasticsearch error responses.
Revise query builder customization hook.
v0.8.5 (2021/1/7)
Improve es sniff stability under high load.
v0.8.4 (2020/12/8)
Expose a utility function for convenience.
v0.8.3 (2020/12/8)
Separate data testing utility from app test.
v0.8.2 (2020/11/17)
Allow multiple hits in annotation endpoint.
Refine multi-type JSON argument processing.
v0.8.1 (2020/07/14)
Improve field type mismatch query behavior.
Improve requried argument parsing restraint logic.
Improve metadata generation stability.
v0.8.0 (2020/06/24)
Add active data metadata generation utility.
Add metadata routing directly after app prefix.
Restructure web settings module.
v0.7.3 (2020/06/05)
Support aggregation on date type fields.
Support additional json content type headers.
v0.7.2 (2020/05/20)
Add API root path trailing slash redirection.
v0.7.1 (2020/05/19)
Improve metadata host info display under dev mode.
v0.7.0 (2020/05/19)
Support application/json input.
Support elasticsearch 7.x in addition to 6.x.
Support load balancing to database.
Support multiple web configs.
Add web parameter options module.
Restructure web module.
v0.6.0 (2020/04/25):
Add functionalities to create and publish data release (full & incremental)
v0.5.0 (2019/12/02):
Support adding license url from datasource metadata.
Improve concurrent performance with async elasticsearch transport client.
v0.4.0 (2019/08/07):
Improve a few test cases and test utility organization.
v0.3.0 (2019/05/01):
Support Elasticsearch 6.x as the backend, Elasticsearch 2.x is no longer supported.
Require Python>=3.4.
Removed httplib2 dependencies.
Changed "msgpack=1" query parameter to "format=msgpack".
Support "format=yaml" return format.
Support "format=html" return format (useful for demo purpose).
Support always_list and allow_null query parameters.
Support optional "q=__any__" to return random docs.
Redesigned test helper.
Other accumulated improvements at https://github.com/biothings/biothings.api/commits/v0.3.0
v0.2.x
Not been released to PyPI.
v0.1.0 (2017/07/22):
initial release