Changelog for kbase/relation_engine

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.0.22] 2022-08-15

Changed

The NCBI taxa scientfic name lookup queries below were updated to make use of the new NCBI taxa loader species_or_below flag and note that the strain flag is deprecated. See https://github.com/kbase/relation_engine_importers/blob/d8f87fb74e984cae1c94985b82349b13bc7f277e/docs/NCBI_taxa_sciname_lookup_issues_22_07.md
- taxonomy_search_species_strain
- taxonomy_search_species_strain_no_sort
The NCBI and GTDB taxon collections were updated to include the new flag.

[0.0.21] 2022-06-13

Added

Dependabot

Changed

Update Github Actions to use new format
Upgrades:
- flask: 1.0.2 -> 2.1.2
- gunicorn: 19.9.0 -> 20.1.0
- requests: 2.20.0 -> 2.28.0
- pyyaml: 5.4 -> 6.0
Use default instead of gevent for gunicorn

[0.0.20] 2022-05-17

Changed

Use locale en_US instead of c.utf-8
Upgrade to image arangodb:3.9

[0.0.19] - 2022-05-02

Added

github actions to build develop, pr-x and released version (e.g. 1.2.3) Tags
instructions for how to release to production

Removed

Generic fulltext search and tests

[0.0.18] - 2022-03-02

Added

taxonomy_search_species_strain and taxonomy_search_species_strain_no_sort stored queries

[0.0.17] - 2022-01-25

Added

Ensure local specs match server specs

Changed

Remove explicit namespace from "icu_tokenize" analyzer

[0.0.16] - 2022-01-14

Added

Added github actions to build docker images on ghcr.io
Added generic fulltext search stored query

[0.0.12] - 2021-01-29

Added

In the API, show the source file path or URL when updating the specs

[0.0.11] - 2020-11-19

Changed

DJORNL edge spec (`spec/collections/djornl/djornl_edge.yaml``) updated to indicate whether or not the edge is directed.
DJORNL parser and test suite updated accordingly.

[0.0.10] - 2020-10-08

Changed

Clean up some of the configuration logic, and add the SPEC_REPO_URL env var instead of hard-coding
Bundle the spec tarball in the docker image so other programs can use the image for testing

[0.0.9] - 2020-10-05

Fixed

Fixed the function that concatenates parts of the query for the API

[0.0.8] - 2020-09-18

Fixed

Remove need for authentication when waiting for the ArangoDB dependency to start (this is a staging server restriction)

[0.0.7] - 2020-09-18

Fixed

Modified the docker deployment script so it can be used to release to the staging server

[0.0.6] - 2020-08-20

Added

relation_engine_server/api_versions/api_v1.py: add and/or document API endpoints:
- /api/v1/specs/stored_queries
- /api/v1/specs/data_sources
spec/datasets: new directory for dataset-specific schemas, e.g. DJORNL parser manifest, spec/datasets/djornl/manifest.schema.json
spec/test/test_manifest_schema.py: to test the manifest schema against example input
importers/djornl/parser.py: use manifest file to specify the files to be parsed and loaded into ArangoDB

Changed

relation_engine_server/utils/spec_loader.py: refactor to return a schema or the path to a schema file
importers/djornl/parser.py: refactor parsing code to be more flexible and parse multiple files
spec/collections/djornl/*, spec/stored_queries/djornl/*, spec/views/djornl/*, and spec/test/djornl: rename DB fields and headers in test files

Removed

spec/test/djornl: delete unneeded test files

[0.0.5]

Last release with RE components in two repositories, https://github.com/kbase/relation_engine_api and https://github.com/kbase/relation_engine_spec