Sync: align ncbo/ontologies_api with the AgroPortal codebase#205
Draft
Sync: align ncbo/ontologies_api with the AgroPortal codebase#205
Conversation
… goo commit: 98bd870
…nsistency, per AgroPortal
…ax-bouazzouni/shotgun
…l-testkit-integration
Infra/ontoportal testkit integration
… many boolean clauses' error
…ntologies_api into chore/ontoportal-lirmm-goo-compat
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Overview
This PR aligns
ncbo/ontologies_apimore closely with the implementation maintained by the AgroPortal team.The changes are based on the AgroPortal ontologies_api repository (
developmentbranch) and selectively incorporate its functionality while preserving NCBO-specific behavior where required.Unlike the migrations performed for goo and sparql-client, this PR does not replace the existing codebase. Instead, it incrementally aligns the implementation while maintaining compatibility with the NCBO stack.
Prerequisites
This PR is part of a broader effort to align NCBO repositories with the AgroPortal codebase. It depends on the following related PRs:
These PRs introduce foundational changes and shared functionality that are required for the updates in
ontologies_api.Major changes
Search functionality
search_helper, including:These changes expand the flexibility and consistency of the API search layer.
NCBO-specific search behavior
oboIdandnotationsearch behaviorThese updates preserve expected BioPortal behavior while incorporating upstream improvements.
New API capabilities
API and controller updates
Runtime and framework compatibility
Test infrastructure
Additional fixes
Notable features
PR impact
Reviewers may want to focus on:
Changes to endpoints and query construction may affect results and filtering.
Reintroduced Solr-related behavior may impact existing expectations.
Dereferencing and OAuth introduce new functionality and flows.
Sinatra and Ruby upgrades affect request handling.
Testkit integration changes how tests are executed.
Summary
This PR aligns
ncbo/ontologies_apimore closely with the AgroPortal implementation while preserving NCBO-specific functionality. It expands search capabilities, introduces new API features, updates runtime compatibility, and integrates the repository into the shared OntoPortal testing infrastructure.