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Release v1.9.1 - #11

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alex-omophub merged 4 commits into
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Sep 7, 2026
Merged

Release v1.9.1#11
alex-omophub merged 4 commits into
mainfrom
develop

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@alex-omophub

@alex-omophub alex-omophub commented Sep 7, 2026

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Summary by cubic

Bumps the package to 1.9.1 and aligns search$similar(), search$autocomplete(), and mappings$map() with the current OMOPHub API. Similarity search now supports pagination, returns the response envelope's metadata, adds page, concept_class_ids, and exclude_self parameters, and the default algorithm changes from hybrid to semantic; autocomplete now uses page_size and domain_ids, keeping old arguments as deprecated aliases.

Migration

  • similar() now sends algorithm = "semantic" when omitted; pass algorithm = "hybrid" to keep the old behavior.
  • similar() results include a pagination element; page while pagination$has_next is TRUE, and search_metadata$totals_are_lower_bound signals lower-bound totals.
  • Autocomplete aliases domains and max_suggestions still work but warn when used alongside their replacements.

Bug Fixes

  • mappings$map() now sends include_invalid = FALSE explicitly, so invalid mappings are excluded as documented.
  • Autocomplete tests and docs now cover the complete suggestion response shape.

Written for commit 4520bff. Summary will update on new commits.

Review in cubic

alex-omophub added 2 commits September 7, 2026 15:41
- Updated `autocomplete` and `similar` methods in `SearchResource` to use `page_size` instead of deprecated `max_suggestions` and `domains` parameters, improving clarity and consistency.
- Added `preserve_pagination` option to `perform_post` to retain pagination information in responses.
- Enhanced documentation for parameters and updated examples to reflect changes in method signatures.
- Improved tests to validate the new parameter mappings and ensure backward compatibility with deprecated aliases.
- Introduced pagination support for similarity search and enhanced response metadata.
- Updated autocomplete functionality to utilize `domain_ids` and `page_size`, while maintaining compatibility with previous aliases.
- Fixed bugs related to the `include_invalid` parameter in mapping requests and improved documentation for autocomplete responses.
- Added `jsonlite` as a test-only dependency and regenerated package manuals to reflect current source.

@cubic-dev-ai cubic-dev-ai Bot left a comment

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All reported issues were addressed across 13 files

Reply with feedback, questions, or to request a fix.

Re-trigger cubic

Comment thread R/search.R Outdated
Comment thread R/search.R Outdated
Comment thread DESCRIPTION Outdated
Comment thread tests/testthat/test-request-pagination.R
- Reintroduced `page` and `concept_class_ids` parameters in the documentation for clarity.
- Enhanced validation in the `similar` method to ensure a single non-missing page value is provided.
- Updated tests to confirm the correct handling of pagination and maintain consistency with method signatures.
@codecov

codecov Bot commented Sep 7, 2026

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Codecov Report

❌ Patch coverage is 93.54839% with 2 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
R/search.R 90.90% 2 Missing ⚠️

📢 Thoughts on this report? Let us know!

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All reported issues were addressed across 4 files (changes from recent commits).

Reply with feedback, questions, or to request a fix.

Re-trigger cubic

Comment thread tests/testthat/test-search.R
- Changed package version from 1.19.1 to 1.9.1 in DESCRIPTION and NEWS.md files.
- Updated tests to reflect the new parameter order in the `similar` method, ensuring consistency with the latest changes.
@alex-omophub
alex-omophub merged commit ac93f7a into main Sep 7, 2026
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