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
Canonicalize ontology ID construction in ontology_in_slice? to match how slice.ontology_id_set entries are generated by Goo, avoiding silent comparison failures if the acronym ever contains chars that CGI.escape would encode.
re-enable newrelic
Enforce slice-based access control on individual ontology endpoints
Under sinatra-contrib 4.2.1 + mustermann 3.0, the before-filter that
Sinatra::Namespace uses to mix its namespace module into each request
instance (`before { extend(@namespace = namespace) }`) compiles for
`namespace "/"` to a pattern that matches only `/` and not sub-paths
like `/documentation` or `/metadata/:class`. Methods defined with bare
`def` inside the namespace block were therefore unreachable from those
routes, producing:
NameError: undefined local variable or method `metadata_all'
for #<Sinatra::Application:...>
Move the home-controller helpers (metadata_all, metadata,
resource_collection_link, sample_objects, hypermedia_links,
routes_by_class, route_to_class_map, routes_list, parse_route,
safe_type_uri, and CLASS_MAP) out of `namespace "/"` into a proper
`Sinatra::Helpers::HomeHelper` module registered via the top-level
`helpers` DSL — the same shape every other helper in this repo uses.
Helpers now attach to Sinatra::Application at class-load time and no
longer depend on the namespace before-filter firing.
Add a regression test that exercises GET /documentation.
Fixes #212
The producer (`cls.cardinality(attribute)`) was removed from goo in the AgroPortal fork in agroportal/goo#52 (commit 2206084, merged 2024-01-31) and subsequently synced into ncbo/goo via ncbo/goo#176 on 2024-04-03. The consumer — the `views/documentation/*.haml` tables — has no reference to `values[:cardinality]` either. The key in the attributes_info hash was being populated only to be thrown away. Delete the key from both branches of the conditional. No view change needed; the earlier `rescue nil` guard added in 1fe44f8 becomes unnecessary and is removed with it.
`views/documentation/documentation.haml` contains four `:markdown` filter blocks that HAML delegates to Tilt. In the current bundle the only markdown-capable gem was `pandoc-ruby`, so Tilt selected its PandocTemplate, which shells out to an external `pandoc` binary. Our Docker image inherits from `ontoportal/testkit-base` and does not install that binary, so `/documentation` failed with `RuntimeError: sh: pandoc: command not found` in any environment without pandoc on the PATH. Replace `pandoc-ruby` with `kramdown`, a pure-Ruby renderer already known to Tilt (`tilt/kramdown.rb`). This removes the system-binary dependency entirely rather than matching agroportal's approach of installing pandoc in their Dockerfile. Performance is indistinguishable for four short blocks on a rarely-hit developer page; pure-Ruby avoids cross-architecture compile/install churn across containers. Verified post-install: `Tilt[:md] → Tilt::KramdownTemplate`.
The home-helper extraction also restores `GET /metadata/:class`, which had been broken for years (#37) and was broken again for a different reason under sinatra-contrib 4.2.1 (#212). Lock the fix in with two tests: - /metadata/Metrics — exercises the common case (singularize + top-level LinkedData::Models::Metric lookup). - /metadata/Reply — exercises HomeHelper#routes_by_class's sub-module search branch (LinkedData::Models::Notes::Reply).
`metadata(cls)` did a bare `LinkedData::Models.const_get(name)`, so requests like `GET /metadata/Reply` blew up with `NameError: uninitialized constant LinkedData::Models::Reply` — `Reply` lives under `LinkedData::Models::Notes`, not at the top level. `routes_by_class` already has sub-module search for the same reason; `metadata` was missing the mirror. Extract a small `resolve_model_class(name)` helper that tries the top-level lookup first and falls back to scanning `LinkedData::Models.constants` for the name, matching the behavior of `routes_by_class`. This restores `GET /metadata/Reply` and any other nested model class (e.g. `Users::Role`, `Users::NotificationType`). test_metadata_route_resolves_submodule_class now passes.
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
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Sync BioPortal v6.8.0 release