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Sync: BioPortal v6.8.0 release - #18

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alexskr wants to merge 262 commits into

ontoportal:masterfrom

ncbo:master

Closed

Sync: BioPortal v6.8.0 release #18
alexskr wants to merge 262 commits into
ontoportal:masterfrom
ncbo:master

This pull request is big! We're only showing the most recent 250 commits

Commits on Oct 28, 2025
- Gemfile.lock update
  alexskr
  committed
  3fc97b1
Commits on Oct 31, 2025
- Refactor: use idiomatic Minitest assertions in ontology submissions tests
  alexskr
  committed
  bdca274
- Refactor test_access_control_helper to use class instance variables
  alexskr
  committed
  becf5d4
Commits on Nov 4, 2025
Commits on Nov 5, 2025
- Reset enable_slices in after_suite
  alexskr
  committed
  1ffbf63
- cleanup: remove dead code
  alexskr
  committed
  fa6f603
- test: use idiomatic Minitest assertions
  alexskr
  committed
  cef113f
- test: remove binding.pry
  alexskr
  committed
  7c774b0
- cleanup: remove leftover commented-out code
  alexskr
  committed
  08754e1
- added code to address random failures during unit test runs
  mdorf
  committed
  9a905c1
- Merge branch 'refactor/tests-stability-and-minitest-style' of github.com:ncbo/ontologies_api into refactor/tests-stability-and-minitest-style
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  committed
  a639b37
- Gemfile.lock update
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  b395c48
Commits on Nov 6, 2025
- test: remove suite globals in OntologySubmissions tests; add reusable user helpers
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  committed
  ba9e9d9
- tests: remove custom user creation/deletion, rely on default factory user
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  1036e0e
Commits on Nov 7, 2025
Commits on Nov 12, 2025
- Merge branch 'master' into develop
  alexskr
  committed
  c48c0cd
- Merge pull request #200 from ncbo/develop
  alexskr
  authored
  929a705
- reset branch specifier to master
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  committed
  4cabfcd
Commits on Dec 16, 2025
- addressed a minor vulnerability with ontology processing logs
  mdorf
  committed
  e3e983d
- reverted Gemfile.lock
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  committed
  0306738
Commits on Dec 17, 2025
- CI: Refactor deployment workflow (#201)
  alexskr
  authored
  52f4bbf
- Merge pull request #202 from ncbo/develop
  alexskr
  authored
  a1b5656
Commits on Jan 23, 2026
- initial commit, work-in-progress: sinatra 4.2.1 compatibiity
  mdorf
  committed
  5da0737
- initial commit, work-in-progress: sinatra 4.2.1 compatibiity
  mdorf
  committed
  c8919ec
- progress commit; sinatra 4.2.1 upgrade
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  committed
  9937e86
Commits on Jan 27, 2026
- Gemfile.lock update
  alexskr
  committed
  3753047
- Gemfile.lock update
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  committed
  dae3e85
Commits on Jan 28, 2026
- added solr admin endpoints
  mdorf
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  e91f1b2
- synchronized test ontology files with AgroPortal
  mdorf
  committed
  a15ccfd
- Gemfile.lock update
  mdorf
  committed
  9649a3a
- added code to disable security for test after_all calls
  mdorf
  committed
  a162678
- added a safeguard to disable security if test that uses it fails
  mdorf
  committed
  8638245
- updated test_rack_attack to Rackup
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  committed
  8768093
- search_helper improved language handling; metadata search options
  mdorf
  committed
  fad1d19
- Gemfile.lock udpate
  mdorf
  committed
  f711f82
- added endpoints for ontologies and content searches
  mdorf
  committed
  daf7063
- added ability to filter and paginate submission endpoint
  mdorf
  committed
  96c7e1d
- refactored test_submissions_includes tests
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  committed
  355e868
Commits on Jan 29, 2026
- added test_mappings_slices test to test_slices_helper
  mdorf
  committed
  7eaf9cd
- ruby 3.2 compatibility updates
  mdorf
  committed
  4a9ffbd
- re-added cube but will remove it again
  mdorf
  committed
  5671104
- removed cube integration as it's not being used
  mdorf
  committed
  65d1c3f
- removed the newrelic integration for now; it needs to be re-integrated
  mdorf
  committed
  cc92729
- fixed oboId and notation searches
  mdorf
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  697af25
- fixed the unit test test_language_attribute_filter
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  committed
  7ce9188
- resoved an issue with setting filenames in create_ontology
  mdorf
  committed
  e6971cb
Commits on Jan 30, 2026
Commits on Feb 1, 2026
- Gemfile.lock update
  mdorf
  committed
  546e92a
Commits on Feb 2, 2026
- updated test_default_multilingual unit test to correctly test for french prefLabels
  mdorf
  committed
  08b0ed0
Commits on Feb 3, 2026
- Gemfile.lock update
  mdorf
  committed
  72e2f1e
- fixed a failing unit test, test_default_multilingual
  mdorf
  committed
  3f720c3
- removed minitest-fail-fast gem, as minitest 6 already includes --fail-fast flag
  mdorf
  committed
  a9508b9
- Gemfile.lock update
  mdorf
  committed
  092df33
- Gemfile.lock update
  mdorf
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  6d58a85
- Gemfile.lock update
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  88a8aa1
Commits on Feb 5, 2026
- Gemfile.lock update
  mdorf
  committed
  bea5b8f
- fixed the warning: detected duplicate key creator in JSON object. This will raise an error in json 3.0
  mdorf
  committed
  ea570ed
- re-enabled the test test_search_models_controller/test_search_data. It appears to run consistently now
  mdorf
  committed
  0ae6948
- fixed a missing require
  mdorf
  committed
  ab55e41
- fixed docker-compose vars
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  committed
  71e1367
Commits on Feb 6, 2026
- added ability to return unmapped attributes for properties
  mdorf
  committed
  7b81f9a
- fixed the unit test test_show_all_collection to allow for two optional collections: term_search and test_solr
  mdorf
  committed
  721ea06
Commits on Feb 8, 2026
- added resource dereference controller and tests
  mdorf
  committed
  3044788
Commits on Feb 11, 2026
- moved redis_goo and redis_http to application_helper
  mdorf
  committed
  651cd58
- Gemfile.lock update
  mdorf
  committed
  b217034
- added user OAuth authentication capability
  mdorf
  committed
  f96728a
Commits on Feb 25, 2026
- use ruby 3.2.9
  alexskr
  committed
  ca1d1a8
- prune platforms
  alexskr
  committed
  175b077
- re-enable capistrano/rbenv
  alexskr
  committed
  748eb4c
Commits on Feb 26, 2026
- Gemfile.lock update
  mdorf
  committed
  5e9cd8d
- removed the use of shotgun server. Now use: bundle exec rackup -E development -p 9393
  mdorf
  committed
  decafc6
- Gemfile.lock update
  mdorf
  committed
  334131a
Commits on Feb 27, 2026
- fixed routes for Sinatra 4, which changed from objects to arrays
  mdorf
  committed
  223cae3
- added home controller tests to validate the routes
  mdorf
  committed
  2209513
Commits on Feb 28, 2026
- update ncbo_cron gem
  alexskr
  committed
  0b36528
- remove .second for compatiblty reasons
  alexskr
  committed
  7b122a3
- Gemfile.lock update
  alexskr
  committed
  9a95846
Commits on Mar 3, 2026
- fixed the @context not showing in home API service call
  mdorf
  committed
  1f8c695
- Gemfile.lock update
  mdorf
  committed
  d6d17cf
- Gemfile.lock update
  mdorf
  committed
  480a6bf
Commits on Mar 4, 2026
- Gemfile.lock update
  alexskr
  committed
  3b9db9b
- Gemfile.lock update
  alexskr
  committed
  829513d
- Gemfile.lock update
  alexskr
  committed
  60ae1ff
Commits on Mar 5, 2026
- re-added the use of shotgun, pointed to the updated version from syphax-bouazzouni/shotgun
  mdorf
  committed
  041553b
Commits on Mar 6, 2026
- Gemfile.lock
  mdorf
  committed
  cbf73be
- Gemfile.lock update
  mdorf
  committed
  2a04c02
Commits on Mar 7, 2026
- integrate ontoportal testkit
  alexskr
  committed
  b987bbd
- update test config file
  alexskr
  committed
  e55492c
- remove TESTOPTS env var
  alexskr
  committed
  6521ffe
Commits on Mar 9, 2026
- Merge branch 'chore/ontoportal-lirmm-goo-compat' into infra/ontoportal-testkit-integration
  alexskr
  committed
  12cdeec
- Merge pull request #204 from ncbo/infra/ontoportal-testkit-integration
  alexskr
  authored
  a7f3a9d
- Gemfile.lock update
  alexskr
  committed
  5e702a5
- Gemfile.lock update
  alexskr
  committed
  93aa0c2
- converted acronyms filter from Boolean to Term syntax to prevent 'too many boolean clauses' error
  mdorf
  committed
  388d1bd
- Gemfile.lock update
  mdorf
  committed
  440de76
Commits on Mar 10, 2026
- Gemfile.lock update
  alexskr
  committed
  09dab09
- Gemfile.lock update
  mdorf
  committed
  00a3dce
- replaced another search boolean query with a term query
  mdorf
  committed
  6cbcea5
- Merge branch 'chore/ontoportal-lirmm-goo-compat' of github.com:ncbo/ontologies_api into chore/ontoportal-lirmm-goo-compat
  mdorf
  committed
  eba9bd1
Commits on Mar 19, 2026
- Gemfile.lock update
  mdorf
  committed
  52b9437
Commits on Mar 23, 2026
- Reset branch specified to develop
  jvendetti
  committed
  eabaf34
Commits on Mar 24, 2026
- Ignore Claude Code local state
  jvendetti
  committed
  236416c
- Update Gemfile.lock
  jvendetti
  committed
  5a41504
- Gemfile.lock update
  alexskr
  committed
  f36af73
Commits on Mar 25, 2026
- change branch specifier for goo
  alexskr
  committed
  8bbce6f
Commits on Apr 1, 2026
- Merge branch 'develop' into chore/ontoportal-lirmm-goo-compat
  mdorf
  authored
  3ab8b56
- removed legacy Solr core names and updated to the new collection names
  mdorf
  committed
  47b935a
- Merge branch 'chore/ontoportal-lirmm-goo-compat' into develop
  mdorf
  committed
  f01fa05
- Gemfile.lock update
  mdorf
  committed
  d14a2b5
- Gemfile and Gemfile.lock updates
  mdorf
  committed
  2299c7d
- Gemfile and Gemfile.lock updates
  mdorf
  committed
  58b9413
- Merge branch 'develop' into feature/solrcloud-alias-indexing-codex
  mdorf
  authored
  90664c3
Commits on Apr 15, 2026
- Enforce slice-based access control on individual ontology endpoints
  alexskr
  committed
  cf6e61f
Commits on Apr 21, 2026
- Add run_metrics to test setup for classes and recommender tests
  alexskr
  committed
  46f8f08
- update ontoportal testkit
  alexskr
  committed
  2dd991a
- Gemfile.lock update
  alexskr
  committed
  f83aeac
- ontoportal testkit update
  alexskr
  committed
  7ca4a76
- Merge branch 'develop' into feature/enforce-slice-ontology-access
  alexskr
  committed
  aecc56a
- Gemfile.lock update
  mdorf
  committed
  22c7b9e
- Merge branch 'master' into develop
  mdorf
  authored
  d2d054d
- Gemfile.lock update
  mdorf
  committed
  ad51191
- Develop -> Master merge, release v7.0.0
  mdorf
  committed
  8f12d54
- Gemfile & Gemfile.lock update
  mdorf
  committed
  9441f41
Commits on Apr 22, 2026
- Use id_from_unique_attribute for slice ontology ID lookup
  alexskr
  committed
  3ff50f7
- remove unnesesary platform constrains from Gemfile
  alexskr
  committed
  46b2372
- re-enable newrelic
  alexskr
  committed
  31bb035
- re-enable newrelic
  alexskr
  committed
  5504f65
- re-enable newrelic
  alexskr
  committed
  58cc1f9
- re-enable newrelic
  alexskr
  committed
  6ec8414
- Merge branch 'master' into develop
  alexskr
  committed
  1ac7d2f
- re-enable newrelic integration (#211)
  alexskr
  authored
  2f17144
- Gemfile.lock update
  alexskr
  committed
  29acae6
- remove agent based newrelic deployment recording
  alexskr
  committed
  b7e1036
- Merge branch 'develop'
  alexskr
  committed
  88d8b6c
- remove agent based newrelic deployment recording
  alexskr
  committed
  b68115c
- Merge pull request #209 from ncbo/feature/enforce-slice-ontology-access
  alexskr
  authored
  0c78ca2
Commits on Apr 23, 2026
- fix /documentation NameError by extracting home helpers to HomeHelper
  alexskr
  committed
  b85ee2b
- drop dead `cardinality` column from HomeHelper#metadata_all
  alexskr
  committed
  6303343
- swap pandoc-ruby for kramdown to render :markdown in documentation view
  alexskr
  committed
  99d0df1
- add regression tests for GET /metadata/:class
  alexskr
  committed
  5ca5f8d
- resolve nested model classes in HomeHelper#metadata
  alexskr
  committed
  c37e214
- reword /metadata/:class 404 in user-facing vocabulary
  alexskr
  committed
  d2e5b64
- broaden /metadata/:class tests; narrow 404 test to bogus-only names
  alexskr
  committed
  2b105ef
- Merge pull request #213 from ncbo/fix/documentation-route-namespace-issue-212
  alexskr
  authored
  ce24c18
- reset branch specifier to develop
  alexskr
  committed
  d82044c
- Merge pull request #215 from ncbo/develop
  alexskr
  authored
  73f4fea
- reset branch specifier to master
  alexskr
  committed
  b960887
Commits on Apr 28, 2026
- use fix/users-endpoint-perf-with-security oLD
  alexskr
  committed
  26f5508
- Gemfile update
  alexskr
  committed
  5ab66a1
- Gemfile update
  alexskr
  committed
  951b6c0
- Gemfile update
  alexskr
  committed
  14e5e23
- always paginate GET /users; default order_by username
  mdorf
  committed
  dc54aca
- Gemfile.lock update
  mdorf
  committed
  f05f568
- fix /search and /property_search 400 when acronym filter is empty
  mdorf
  committed
  0875917
Commits on May 1, 2026
- Merge pull request #216 from ncbo/fix/slow-users-endpoint
  alexskr
  authored
  8828e8c
Commits on May 2, 2026
- Merge branch 'master' into develop
  alexskr
  committed
  75c5a84
- Merge pull request #218 from ncbo/develop
  alexskr
  authored
  a36a23c
Commits on May 4, 2026
- Gemfile.lock update
  mdorf
  committed
  4102a5b
- fix trailing-slash 301 redirects downgrading https to http (issue #217)
  mdorf
  committed
  af9751b
- Merge branch 'develop' into fix/trailing-slash-redirect
  mdorf
  authored
  e2999da
Commits on May 5, 2026
- Gemfile.lock update
  alexskr
  committed
  c2590ad
- Merge pull request #219 from ncbo/fix/trailing-slash-redirect
  alexskr
  authored
  2d9775c
- Merge pull request #220 from ncbo/develop
  alexskr
  authored
  edd3e23
Commits on May 8, 2026
- Gemfile & Gemfile.lock update
  mdorf
  committed
  d6209db
Commits on May 9, 2026
Commits on May 11, 2026
- Merge pull request #223 from ncbo/fix/search-too-many-boolean-nomethoderror
  mdorf
  authored
  fe7417f
- Merge pull request #224 from ncbo/develop
  alexskr
  authored
  ba62abe
- reset branch specifier to master
  alexskr
  committed
  1aa0851
- Gemfile.lock update
  mdorf
  committed
  7df8a66
Commits on May 13, 2026
- Expand user search fields
  jvendetti
  committed
  93635a3
Commits on May 14, 2026
Commits on May 15, 2026
- Support all user search fields shortcut
  jvendetti
  committed
  0e2c21b
Commits on May 19, 2026
- Update Solr alias dependency revisions
  mdorf
  committed
  d4e7165
- Skip minitest reporters in RubyMine
  jvendetti
  committed
  8906ab2
- Fix some RuboCop warnings
  jvendetti
  committed
  a2b2284
- Ignore Serena project metadata
  jvendetti
  committed
  fed67fa
- Update API Solr alias dependency revisions
  mdorf
  committed
  77e1ac0
- Update API read-only alias dependency revisions
  mdorf
  committed
  e6321df
- Refactor user search field parsing
  jvendetti
  committed
  1088ecd
- Merge pull request #226 from ncbo/feature/expand-user-search/225
  jvendetti
  authored
  5aa9d49
- Merge branch 'develop' into feature/solrcloud-alias-indexing-codex
  mdorf
  authored
  d243b1e
- Merge pull request #207 from ncbo/feature/solrcloud-alias-indexing-codex
  mdorf
  authored
  0c5d519
- Gemfile & Gemfile.lock update
  mdorf
  committed
  95124b0
Commits on May 21, 2026
- Merge branch 'master' into develop
  mdorf
  authored
  3fc1032
Commits on May 22, 2026
- Gemfile & Gemfile.lock update
  mdorf
  committed
  1884b1d
- Develop -> Master merge, release v7.3.0
  mdorf
  authored
  101d0cb
- Gemfile & Gemfile.lock update
  mdorf
  committed
  814a527
Commits on May 27, 2026
- Gemfile.lock update
  mdorf
  committed
  7dad030
- Gemfile.lock update
  mdorf
  committed
  3754fff
- Merge branch 'master' into develop
  mdorf
  authored
  302c88b
- Gemfile & Gemfile.lock update
  mdorf
  committed
  d18ccba
- Develop -> Master merge, release v7.3.1
  mdorf
  authored
  9320a09
- Gemfile & Gemfile.lock update
  mdorf
  committed
  214795f
Commits on May 28, 2026
- Update Gemfile.lock
  jvendetti
  committed
  d6b28f9
Commits on Jun 1, 2026
- Add ontology-rank boost to term-search Solr query
  mdorf
  committed
  2a5c809
- Remove post-hoc Ruby sort from term search
  mdorf
  committed
  59ad6e8
- Remove unused ontology_rank attachment and fetch
  mdorf
  committed
  f02884d
Commits on Jun 2, 2026
- Gemfile.lock update
  mdorf
  committed
  3de4ed2
- Add ranking regression test for case-insensitive exact match
  mdorf
  committed
  65aa4a7
- Split ranking regression test into schema and boost concerns
  mdorf
  committed
  61a1a59
- Gemfile.lock update
  mdorf
  committed
  272d649
- Merge remote-tracking branch 'origin/develop' into fix/incorrect-search-result-ranking
  mdorf
  committed
  100df47
Commits on Jun 9, 2026
- Merge pull request #232 from ncbo/fix/incorrect-search-result-ranking
  mdorf
  authored
  29564e0
- Gemfile & Gemfile.lock update
  mdorf
  committed
  e9ed915
- Update search schema test to expect string_ci_exact type
  mdorf
  committed
  b1f0fe7
Commits on Jun 10, 2026
- Gemfile.lock update
  mdorf
  committed
  646be19
- Gemfile.lock update
  mdorf
  committed
  95e7314
- Gemfile.lock update
  mdorf
  committed
  ee3042c
Commits on Jun 17, 2026
- Fix empty annotator class population
  mdorf
  committed
  5bd851c
- Merge pull request #235 from ncbo/fix/solr-query-bad-request
  mdorf
  authored
  53cd57c
- Gemfile.lock update
  mdorf
  committed
  b6350f2
- Fix production access log output
  mdorf
  committed
  8e59039
- Merge pull request #236 from ncbo/fix/log-file-output
  mdorf
  authored
  50595c0
Commits on Jun 18, 2026
- merging with develop
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  committed
  64b8579
- Gemfile.lock update
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  committed
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Commits on Jun 22, 2026
- Gemfile.lock update
  alexskr
  committed
  b02cbcb
Commits on Jun 23, 2026
- Move trailing-slash redirect to Rack middleware
  alexskr
  committed
  6604cac
Commits on Jun 24, 2026
- Extract admin_only! helper for repeated admin authorization gate
  alexskr
  committed
  0850b6b
Commits on Jun 25, 2026
- Gemfile.lock update
  alexskr
  committed
  5e244c1
- Gemfile.lock update
  mdorf
  committed
  46dcce4
Commits on Jun 26, 2026
- Add admin_only! authorization gate test
  alexskr
  committed
  2845297
- Add backend-free unit tests for trailing-slash middleware
  alexskr
  committed
  de5f8b3
- Set Cache-Control: no-store on trailing-slash redirect
  alexskr
  committed
  570fbd7
- Isolate process-wide settings in tests via with_settings + snapshot nets
  alexskr
  committed
  ffadcd8
- Restore test settings before after_suite to fix cross-suite leak
  alexskr
  committed
  001b03c
Commits on Jul 2, 2026
Commits on Jul 14, 2026
- Gemfile.lock update
  mdorf
  committed
  ff14f24
- Gemfile.lock update
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  committed
  39d00c2
Commits on Jul 15, 2026
- Merge develop into master
  mdorf
  committed
  bd94801
Commits on Jul 20, 2026
- Batch missing metrics lookup
  mdorf
  committed
  229251f
- Add metrics missing query benchmark
  mdorf
  committed
  abf7c0d
- Add metrics missing latency benchmark
  mdorf
  committed
  854f78a
- Merge pull request #241 from ncbo/perf/metrics-missing-batching
  mdorf
  authored
  44114e4
- Update development dependency lockfile
  mdorf
  committed
  32d7a83
Commits on Jul 21, 2026
- Merge remote-tracking branch 'origin/develop'
  mdorf
  committed
  52537f2
- Update Gemfile.lock for production
  mdorf
  committed
  d5a0625

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