biothings/biothings.api issues and pull requests

#351 - Improve index error messaging

Pull Request - State: open - Opened by ctrl-schaff about 1 month ago

#350 - Add slack config for pytest.

Pull Request - State: open - Opened by everaldorodrigo about 2 months ago

#349 - BioThings v0.12.5

Pull Request - State: closed - Opened by ctrl-schaff 2 months ago

#348 - Merger storage generalization

Pull Request - State: closed - Opened by ctrl-schaff 3 months ago
Labels: bug, enhancement

#347 - Rise exceptions correctly.

Pull Request - State: closed - Opened by everaldorodrigo 3 months ago

#346 - Refactor ES exceptions

Pull Request - State: closed - Opened by everaldorodrigo 3 months ago

#345 - Build Config Err Fix

Pull Request - State: closed - Opened by DylanWelzel 3 months ago
Labels: bug

#344 - Add id checking to IgnoreDuplicatedStorage ...

Pull Request - State: closed - Opened by ctrl-schaff 3 months ago
Labels: bug, enhancement

#343 - Fix Slack notifier test.

Pull Request - State: closed - Opened by everaldorodrigo 4 months ago

#342 - Upgrade tornado to 6.4.1

Pull Request - State: closed - Opened by everaldorodrigo 4 months ago

#341 - Fix metadata mapping and remove duplicated code.

Pull Request - State: closed - Opened by everaldorodrigo 4 months ago

#340 - Correct the pyproject.toml black configuration ...

Pull Request - State: closed - Opened by ctrl-schaff 4 months ago - 1 comment
Labels: bug

#339 - Replace deprecated imp module with importlib

Pull Request - State: closed - Opened by DylanWelzel 4 months ago

#338 - Add CLI mongodb support

Pull Request - State: closed - Opened by ctrl-schaff 4 months ago
Labels: enhancement

#337 - Implement notifiers using asyncio

Pull Request - State: closed - Opened by everaldorodrigo 4 months ago - 1 comment
Labels: enhancement

#336 - Api customization

Pull Request - State: closed - Opened by jal347 4 months ago

#335 - Add more idiomatic sqlite multiple document insert

Pull Request - State: closed - Opened by ctrl-schaff 5 months ago
Labels: enhancement

#334 - Metadata fields bug fix

Pull Request - State: closed - Opened by everaldorodrigo 5 months ago
Labels: bug

#333 - Improve metadata field index search

Pull Request - State: closed - Opened by ctrl-schaff 5 months ago
Labels: enhancement

#332 - DockerContainerDumper volume feature

Pull Request - State: closed - Opened by jal347 5 months ago

#331 - metadata query logical enhancements and bugfixes

Pull Request - State: closed - Opened by ctrl-schaff 5 months ago
Labels: bug, enhancement

#330 - Add metadata query field validation

Pull Request - State: closed - Opened by ctrl-schaff 5 months ago
Labels: enhancement

#329 - Add advanced plugin support for the command line tooling

Pull Request - State: closed - Opened by ctrl-schaff 5 months ago - 2 comments
Labels: enhancement

#328 - Extend MergerStorage Class to Support Both MongoDB and SQLite

Issue - State: closed - Opened by DylanWelzel 6 months ago
Labels: bug, enhancement

#327 - Handle sqlite duplicate _id

Pull Request - State: closed - Opened by DylanWelzel 6 months ago - 1 comment

#326 - This to prepare the biothings.api to 0.12.4 release

Pull Request - State: closed - Opened by everaldorodrigo 6 months ago

#325 - jmespath: removing higher-level objects based on lower-level matches

Issue - State: open - Opened by colleenXu 6 months ago

#324 - jmespath: 500 error

Issue - State: open - Opened by colleenXu 6 months ago - 1 comment
Labels: bug

#323 - Problem with jmespath: unexpected behavior with single items (not arrays)

Issue - State: open - Opened by colleenXu 6 months ago - 3 comments
Labels: bug

#322 - ES8 Migration Fixes for BioThings SDK Tests

Pull Request - State: closed - Opened by DylanWelzel 6 months ago

#321 - updated positional arguments to keyword arguments for elasticsearch upgrade

Pull Request - State: closed - Opened by DylanWelzel 7 months ago

#320 - 0.12.x

Pull Request - State: closed - Opened by everaldorodrigo 7 months ago

#319 - Revert studio tutorial

Pull Request - State: closed - Opened by everaldorodrigo 8 months ago

#318 - Fix cli tutorial rerouting

Pull Request - State: closed - Opened by everaldorodrigo 8 months ago

#317 - Add cli docs

Pull Request - State: closed - Opened by everaldorodrigo 8 months ago

#316 - Add the dataplugin template subdirectory to the MANIFEST ...

Pull Request - State: closed - Opened by ctrl-schaff 9 months ago - 6 comments
Labels: bug

#315 - fix utils.diff.diff_collections helper function to run diffs in parallel

Issue - State: open - Opened by newgene 9 months ago
Labels: enhancement

#314 - Correct the construction argument shadowing

Pull Request - State: closed - Opened by ctrl-schaff 9 months ago - 1 comment
Labels: bug

#313 - Add a "Data Plugins" tutorial chapter in in BioThings docs

Issue - State: closed - Opened by newgene 9 months ago
Labels: enhancement

#312 - Updated list comprehension to ensure _meta and biothing_type presence.

Pull Request - State: closed - Opened by DylanWelzel 9 months ago

#311 - added extra info for tutorial

Pull Request - State: closed - Opened by jal347 9 months ago

#310 - Tutorial update

Pull Request - State: closed - Opened by jal347 9 months ago

#309 - Revert "Tutorial update"

Pull Request - State: closed - Opened by jal347 9 months ago

#308 - Revert 307 tutorial update

Pull Request - State: closed - Opened by jal347 9 months ago

#307 - Tutorial update

Pull Request - State: closed - Opened by jal347 9 months ago

#306 - Support CURIE IDs in annotation endpoint (both GET and POST)

Issue - State: closed - Opened by newgene 9 months ago - 1 comment
Labels: enhancement

#305 - fix `autoscope` feature for annotation endpoint

Issue - State: closed - Opened by newgene 9 months ago - 1 comment
Labels: bug

#304 - Add sentry support to get request body data.

Pull Request - State: closed - Opened by everaldorodrigo 11 months ago - 1 comment

#303 - add an optional final report to dict_sweep helper function

Issue - State: open - Opened by newgene 12 months ago
Labels: enhancement

#302 - Implementation of new merge_source

Pull Request - State: closed - Opened by jal347 12 months ago

#301 - Fix critical security issues.

Pull Request - State: closed - Opened by everaldorodrigo almost 1 year ago

#300 - Orjson implementation of `dotfield` module

Pull Request - State: closed - Opened by erikyao about 1 year ago

#299 - Upgrade tornado to 6.4.0

Pull Request - State: closed - Opened by everaldorodrigo about 1 year ago

#298 - Upgrade tornado to patch security issues

Issue - State: closed - Opened by everaldorodrigo about 1 year ago - 1 comment

#297 - Orjson Implementation of `dotfield` module

Pull Request - State: closed - Opened by erikyao about 1 year ago - 2 comments

#296 - support filter query parameter

Issue - State: open - Opened by newgene about 1 year ago - 3 comments

#295 - Fix networkx import

Pull Request - State: closed - Opened by ericz1803 about 1 year ago - 1 comment

#294 - Undefined `IndexMissingException`

Issue - State: closed - Opened by erikyao about 1 year ago

#293 - Allow adding in custom volume or any other docker runtime parameters in DockerContainerDumper.

Issue - State: closed - Opened by jal347 about 1 year ago - 1 comment
Labels: enhancement

#292 - Fix dict default vals to work with dicts.

Pull Request - State: closed - Opened by everaldorodrigo about 1 year ago

#291 - Break Circular Dependency

Pull Request - State: closed - Opened by everaldorodrigo about 1 year ago

#290 - Set plugin name to the folder name for Advanced plugins.

Pull Request - State: closed - Opened by everaldorodrigo about 1 year ago

#289 - `get_code_for_mod_name` cannot load generic uploaders

Issue - State: closed - Opened by erikyao over 1 year ago - 3 comments

#288 - turn off some debugging logs in `doc_feeder`

Pull Request - State: closed - Opened by erikyao over 1 year ago

#287 - revise logging statements

Pull Request - State: closed - Opened by erikyao over 1 year ago

#286 - Fix to Issue#282

Pull Request - State: closed - Opened by erikyao over 1 year ago

#285 - Fix dict default vals.

Pull Request - State: closed - Opened by everaldorodrigo over 1 year ago

#284 - Allow to add version metadata check rules before triggering a release

Issue - State: closed - Opened by newgene over 1 year ago - 1 comment
Labels: enhancement

#283 - Allow changing the es index (#280)

Pull Request - State: closed - Opened by everaldorodrigo over 1 year ago

#282 - `CursorNotFound` Error in `doc_feeder`

Issue - State: closed - Opened by erikyao over 1 year ago - 3 comments

#281 - `biothings/utils/dataload.py` code cleaning/refactoring

Issue - State: closed - Opened by erikyao over 1 year ago - 3 comments

#280 - Allow changing the ES index

Issue - State: closed - Opened by everaldorodrigo over 1 year ago

#279 - Add async and sync support to metadata handler

Pull Request - State: closed - Opened by everaldorodrigo over 1 year ago

#278 - change extras method of MetadataSourceHandler to be async

Issue - State: closed - Opened by newgene over 1 year ago - 3 comments
Labels: enhancement

#277 - Allow manually mark a data source downloaded at the dump step

Issue - State: closed - Opened by newgene over 1 year ago - 1 comment
Labels: enhancement

#276 - Add S3 snapshot repository retention policy

Issue - State: open - Opened by newgene over 1 year ago
Labels: enhancement

#275 - Verify existing snapshot repository with the SNAPSHOT_CONFIG

Issue - State: closed - Opened by newgene over 1 year ago - 1 comment
Labels: enhancement

#274 - `boolean_convert` function converts `None` to `False`

Issue - State: closed - Opened by erikyao over 1 year ago - 1 comment

#273 - print out the current test url in BiothingsWebTest

Issue - State: closed - Opened by newgene over 1 year ago
Labels: enhancement

#272 - biothing_type value should be a single value when it's a single-value list

Issue - State: closed - Opened by newgene over 1 year ago - 2 comments
Labels: bug

#271 - Autobuild is not correctly triggered when last build is a failed one

Issue - State: closed - Opened by newgene over 1 year ago - 1 comment
Labels: bug

#270 - Switch to use poetry for packaging and dependency management

Issue - State: open - Opened by newgene over 1 year ago - 1 comment
Labels: enhancement

#269 - Create an Elasticsearch reindex helper function

Issue - State: open - Opened by newgene almost 2 years ago
Labels: enhancement

#268 - `ColdHotDiffer.diff_cols()` failed to invoke its super method

Issue - State: closed - Opened by erikyao almost 2 years ago - 1 comment