Sync: BioPortal v6.8.0 release #18
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…gies_api into feature/user-admin-endpoints
Feature: Ontology Admin Endpoints for Logs and Submission Management
…ests Replace non-idiomatic assertions with Minitest equivalents: - assert(x == y) -> assert_equal - .eql?() -> assert_equal - assert !x.empty? -> assert_operator x.length, :>, 0 - submissions.all? -> submissions.each for better error messages Extract repeated contact validation into helper method to reduce duplication. Fix intermittent test failures by sorting array keys before comparison to handle non-deterministic ordering. refs #197
- Replace class variables (@@) with class instance variables using accessors - Add attr_accessor definitions for shared test state - Modernize assertions to Minitest style (assert_equal, assert_includes, assert_nil) - Improve code formatting and readability
…dition - Replace random .sample(3) with deterministic .first(3) - Use dynamic assertion for keep_ids count instead of hardcoded value - Capture process_id before use for clarity - Simplify polling loop condition to check only for 'done' or 'errors' - Clean up assertion message formatting for consistency
…n/deletion - Replace `assert 201, ...` with `assert_equal 201, ...` to properly compare response status. - Add GET checks after slice creation to confirm the new slice exists. - Remove redundant manual reset of LinkedData.settings.enable_security. - Update DELETE test to expect 204 (No Content) instead of 201. - Add GET checks after deletion to verify the slice was actually removed.
- Add explicit flunk when status_payload contains 'errors' to prevent false positives from incomplete or invalid responses - Ensure test fails immediately on backend error instead of silently skipping assertions
Restore LinkedData.settings.enable_slices to its original value after tests.
…com:ncbo/ontologies_api into refactor/tests-stability-and-minitest-style
… user helpers This change refactors `TestOntologySubmissionsController` to eliminate suite-level globals and class-variable state in favor of per-test setup and shared helpers: - Replace `before_suite` + `@@acronym`/`@@name`/`@@file_params` with per-test `setup` that generates a unique ontology acronym and creates an ontology administered by a shared test user. - Introduce a suite-local `USERNAME = "test_user"` and use `ensure_user(USERNAME)` to guarantee the user exists without races. - Normalize assertion style: - Use `assert_equal(expected, actual, message)` with parentheses - Remove `msg=` pseudo-named args - Add `.sort` where appropriate when comparing unordered keys - Replace direct references to `@@acronym`/`@@name` with instance vars (`@acronym`, `@name`). New helper methods (in the base test class) used by this suite: - `create_user(username, email:, password:)` — always creates a user - `ensure_user(username, email:, password:)` — idempotently finds or creates - `delete_user(username)` — removes a user if present Notes: - `delete_ontologies_and_submissions` now runs in `setup` to guarantee a clean slate per test. `after_all` also cleans up the shared user via `delete_user(USERNAME)`. If the extra cleanup proves redundant, we can drop `before_all`/`after_all` and keep only the per-test cleanup.
…st-style Refactor/tests stability and minitest style
The previous "No metadata for \`X\` — not a LinkedData model class" leaked the Ruby gem name and used "model class", terms API users don't encounter elsewhere. The BioPortal /documentation page uses "media type" for exactly these /metadata/:X URIs (they surface as JSON-LD @type / @context identifiers in responses, documented under "Media Types and Hypermedia Links"), so match that vocabulary and point the user at a concrete working example. Also route the response through the repo's `error` helper so the 404 comes back as the standard `{ errors: [...], status: 404 }` shape through LinkedData's content-negotiating serializer, matching every other error response in the codebase (no more one-off `halt 404, "string"`). Strengthen the regression test to assert the new phrasing appears in the body, not just the status code.
- Extend `test_metadata_route_renders_for_model_class` to loop over `Ontology`, `Metrics`, `Class` — covers plain top-level lookup (`Ontology`), singularization (`Metrics` → `Metric`), and a second plain case with a distinctive name (`Class`). All three hit the same `resolve_model_class` top-level branch, but `Ontology` was the one case we previously had no explicit coverage for. - Rename `test_metadata_route_returns_404_for_non_class_names` → `test_metadata_route_returns_404_for_bogus_names` and trim its list to `DefinitelyNotAModel`, `nonexistent_thing`, `xyzqux123` — guaranteed-nonexistent identifiers that will stay 404 regardless of future features. The previous list (`created`, `body`, `prefixIRI`, `name`, `omvacronym`) was misleading: those *are* attribute URIs the API emits in JSON-LD @context, currently 404'd as a stop-gap but tracked in ncbo/bioportal-project#388 for actual attribute-documentation rendering. Leaving them asserted as 404 would turn into a false regression signal when #388 lands.
…ssue-212 fix: /documentation NameError from sinatra-contrib 4.2.1 namespace bug
Develop -> Master merge, release v7.1.0
Drops the `if page?` guard so /users unconditionally returns a Page object. Adds a deterministic default sort (username asc) so paged responses are stable for clients walking nextPage links. Addresses production timeouts on /users?include=all. Pairs with ncbo/ontologies_linked_data#286 (idempotent User#admin?, drop inverse attrs from auth load) and the corresponding ontologies_api_ruby_client auto-paginate change. Tests updated for the paged response shape and cover ?pagesize and ?include=all combinations.
Commit 388d1bd ("converted acronyms filter from Boolean to Term syntax") replaced get_quoted_field_query_param at the start of filter_query construction in BOTH search_helper.rb (line 160) and properties_search_helper.rb (line 48). The new term-syntax function correctly early-returns "" for an empty acronyms list (an empty terms-query would itself be malformed), but the rest of filter_query construction in both helpers implicitly relied on the prior function's vacuous `submissionAcronym:""` placeholder always producing a non-empty starting clause. When acronyms filtered to empty (e.g. ontology_types restriction matches nothing, or the requesting user has no access to any of the requested ontologies), filter_query was "" and the subsequent `<< " AND <clause>"` appends produced a stray-AND fq that Solr rejected with 400 (surfaced as 500 by the API), breaking both /search and /property_search for any call whose acronyms resolved empty. Fix: when filter_query is empty after the acronyms step, use Solr's match-all literal `*:*`. AND'ing further clauses onto `*:*` narrows correctly, producing well-formed queries semantically equivalent to the constraints that follow. Also more correct than the pre-388d1bd behavior, which always silently added `submissionAcronym:""` (matching zero docs) when acronyms was empty — search-without-acronyms now actually returns matches. The third in-tree call site (search_helper.rb:181 — valueset_root_ids) is unaffected: it's already guarded by `unless valueset_root_ids.empty?` on the line above, so the function input is guaranteed non-empty. Adds regression tests for both endpoints exercising the empty-acronyms path via ontology_types=NONEXISTENT.
Fix: always paginate GET /users; /search 500 on empty acronym filter
Develop to Master merge, Release v7.2.0
Fix: trailing-slash 301 redirects downgrading https to http (#217)
Develop to Master merge, Release 7.2.1
…hen using Annotator
Develop to Master merge, Release 7.2.2
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Sync BioPortal v6.8.0 release