Fix: auto-flatten paged /users responses; slim User attributes

Gemfile.lock

@@ -28,79 +28,83 @@ GEM
       securerandom (>= 0.3)
       tzinfo (~> 2.0, >= 2.0.5)
       uri (>= 0.13.1)
-    addressable (2.8.7)
-      public_suffix (>= 2.0.2, < 7.0)
+    addressable (2.9.0)
+      public_suffix (>= 2.0.2, < 8.0)
     ast (2.4.3)
     base64 (0.3.0)
     benchmark (0.5.0)
-    bigdecimal (3.3.1)
+    bigdecimal (4.1.2)
     coderay (1.1.3)
-    concurrent-ruby (1.3.5)
-    connection_pool (2.5.4)
+    concurrent-ruby (1.3.6)
+    connection_pool (3.0.2)
     docile (1.4.1)
     drb (2.2.3)
-    excon (1.3.1)
+    excon (1.4.2)
       logger
-    faraday (2.14.0)
+    faraday (2.14.1)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
     faraday-excon (2.4.0)
       excon (>= 1.0.0)
       faraday (>= 2.11.0, < 3)
-    faraday-follow_redirects (0.4.0)
+    faraday-follow_redirects (0.5.0)
       faraday (>= 1, < 3)
-    faraday-multipart (1.1.1)
+    faraday-multipart (1.2.0)
       multipart-post (~> 2.0)
     faraday-net_http (3.4.2)
       net-http (~> 0.5)
-    i18n (1.14.7)
+    i18n (1.14.8)
       concurrent-ruby (~> 1.0)
-    json (2.16.0)
+    io-console (0.8.2)
+    json (2.19.4)
     language_server-protocol (3.17.0.5)
     lint_roller (1.1.0)
     logger (1.7.0)
     lz4-ruby (0.3.3)
     method_source (1.1.0)
-    minitest (5.26.2)
-    minitest-hooks (1.5.2)
+    minitest (5.27.0)
+    minitest-hooks (1.5.3)
       minitest (> 5.3)
-    multi_json (1.17.0)
+    multi_json (1.20.1)
     multipart-post (2.4.1)
-    net-http (0.8.0)
+    net-http (0.9.1)
       uri (>= 0.11.1)
-    oj (3.16.12)
+    oj (3.17.0)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     ostruct (0.6.3)
-    parallel (1.27.0)
-    parser (3.3.10.0)
+    parallel (1.28.0)
+    parser (3.3.11.1)
       ast (~> 2.4.1)
       racc
-    prism (1.6.0)
-    pry (0.15.2)
+    prism (1.9.0)
+    pry (0.16.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (6.0.2)
+      reline (>= 0.6.0)
+    public_suffix (7.0.5)
     racc (1.8.1)
     rainbow (3.1.1)
-    rake (13.3.1)
-    regexp_parser (2.11.3)
+    rake (13.4.2)
+    regexp_parser (2.12.0)
+    reline (0.6.3)
+      io-console (~> 0.5)
     rexml (3.4.4)
-    rubocop (1.81.7)
+    rubocop (1.86.1)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
-      parallel (~> 1.10)
+      parallel (>= 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 2.9.3, < 3.0)
-      rubocop-ast (>= 1.47.1, < 2.0)
+      rubocop-ast (>= 1.49.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.48.0)
+    rubocop-ast (1.49.1)
       parser (>= 3.3.7.2)
-      prism (~> 1.4)
+      prism (~> 1.7)
     ruby-progressbar (1.13.0)
     securerandom (0.4.1)
     simplecov (0.22.0)
@@ -116,11 +120,11 @@ GEM
       concurrent-ruby (~> 1.0)
     unicode-display_width (3.2.0)
       unicode-emoji (~> 4.1)
-    unicode-emoji (4.1.0)
+    unicode-emoji (4.2.0)
     uri (1.1.1)
 
 PLATFORMS
-  arm64-darwin-24
+  arm64-darwin-23
   ruby
 
 DEPENDENCIES
@@ -134,5 +138,63 @@ DEPENDENCIES
   simplecov
   simplecov-cobertura
 
+CHECKSUMS
+  activesupport (8.0.3) sha256=a711ce5e30660b23232f26a38699469f8d859d47aa1f722e183fda6d7cc17823
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+  ast (2.4.3) sha256=954615157c1d6a382bc27d690d973195e79db7f55e9765ac7c481c60bdb4d383
+  base64 (0.3.0) sha256=27337aeabad6ffae05c265c450490628ef3ebd4b67be58257393227588f5a97b
+  benchmark (0.5.0) sha256=465df122341aedcb81a2a24b4d3bd19b6c67c1530713fd533f3ff034e419236c
+  bigdecimal (4.1.2) sha256=53d217666027eab4280346fba98e7d5b66baaae1b9c3c1c0ffe89d48188a3fbd
+  coderay (1.1.3) sha256=dc530018a4684512f8f38143cd2a096c9f02a1fc2459edcfe534787a7fc77d4b
+  concurrent-ruby (1.3.6) sha256=6b56837e1e7e5292f9864f34b69c5a2cbc75c0cf5338f1ce9903d10fa762d5ab
+  connection_pool (3.0.2) sha256=33fff5ba71a12d2aa26cb72b1db8bba2a1a01823559fb01d29eb74c286e62e0a
+  docile (1.4.1) sha256=96159be799bfa73cdb721b840e9802126e4e03dfc26863db73647204c727f21e
+  drb (2.2.3) sha256=0b00d6fdb50995fe4a45dea13663493c841112e4068656854646f418fda13373
+  excon (1.4.2) sha256=32d8d8eda619717d9b8043b4675e096fb5c2139b080e2ad3b267f88c545aaa35
+  faraday (2.14.1) sha256=a43cceedc1e39d188f4d2cdd360a8aaa6a11da0c407052e426ba8d3fb42ef61c
+  faraday-excon (2.4.0) sha256=2a07ff3583468468eb62325c6263d0b2dd39282a8de7dc35908d782de531c8f6
+  faraday-follow_redirects (0.5.0) sha256=5cde93c894b30943a5d2b93c2fe9284216a6b756f7af406a1e55f211d97d10ad
+  faraday-multipart (1.2.0) sha256=7d89a949693714176f612323ca13746a2ded204031a6ba528adee788694ef757
+  faraday-net_http (3.4.2) sha256=f147758260d3526939bf57ecf911682f94926a3666502e24c69992765875906c
+  i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5
+  io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc
+  json (2.19.4) sha256=670a7d333fb3b18ca5b29cb255eb7bef099e40d88c02c80bd42a3f30fe5239ac
+  language_server-protocol (3.17.0.5) sha256=fd1e39a51a28bf3eec959379985a72e296e9f9acfce46f6a79d31ca8760803cc
+  lint_roller (1.1.0) sha256=2c0c845b632a7d172cb849cc90c1bce937a28c5c8ccccb50dfd46a485003cc87
+  logger (1.7.0) sha256=196edec7cc44b66cfb40f9755ce11b392f21f7967696af15d274dde7edff0203
+  lz4-ruby (0.3.3) sha256=011be5ee230cfddc8308d4e2e0b05300c7bc755a887de799377ca6c5b6aede89
+  method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5
+  minitest (5.27.0) sha256=2d3b17f8a36fe7801c1adcffdbc38233b938eb0b4966e97a6739055a45fa77d5
+  minitest-hooks (1.5.3) sha256=ef50dd3bf47e6d1646befc358c640c71ca41f5650f0036b4c69929a44d6f32c4
+  multi_json (1.20.1) sha256=2f3934e805cc45ef91b551a1f89d0e9191abd06a5e04a2ef09a6a036c452ca6d
+  multipart-post (2.4.1) sha256=9872d03a8e552020ca096adadbf5e3cb1cd1cdd6acd3c161136b8a5737cdb4a8
+  net-http (0.9.1) sha256=25ba0b67c63e89df626ed8fac771d0ad24ad151a858af2cc8e6a716ca4336996
+  oj (3.17.0) sha256=5684b2127fb70e650fae90df521b91336ff8e55e2e1011ed80eb0283beac5360
+  ontologies_api_client (2.8.1)
+  ostruct (0.6.3) sha256=95a2ed4a4bd1d190784e666b47b2d3f078e4a9efda2fccf18f84ddc6538ed912
+  parallel (1.28.0) sha256=33e6de1484baf2524792d178b0913fc8eb94c628d6cfe45599ad4458c638c970
+  parser (3.3.11.1) sha256=d17ace7aabe3e72c3cc94043714be27cc6f852f104d81aa284c2281aecc65d54
+  prism (1.9.0) sha256=7b530c6a9f92c24300014919c9dcbc055bf4cdf51ec30aed099b06cd6674ef85
+  pry (0.16.0) sha256=d76c69065698ed1f85e717bd33d7942c38a50868f6b0673c636192b3d1b6054e
+  public_suffix (7.0.5) sha256=1a8bb08f1bbea19228d3bed6e5ed908d1cb4f7c2726d18bd9cadf60bc676f623
+  racc (1.8.1) sha256=4a7f6929691dbec8b5209a0b373bc2614882b55fc5d2e447a21aaa691303d62f
+  rainbow (3.1.1) sha256=039491aa3a89f42efa1d6dec2fc4e62ede96eb6acd95e52f1ad581182b79bc6a
+  rake (13.4.2) sha256=cb825b2bd5f1f8e91ca37bddb4b9aaf345551b4731da62949be002fa89283701
+  regexp_parser (2.12.0) sha256=35a916a1d63190ab5c9009457136ae5f3c0c7512d60291d0d1378ba18ce08ebb
+  reline (0.6.3) sha256=1198b04973565b36ec0f11542ab3f5cfeeec34823f4e54cebde90968092b1835
+  rexml (3.4.4) sha256=19e0a2c3425dfbf2d4fc1189747bdb2f849b6c5e74180401b15734bc97b5d142
+  rubocop (1.86.1) sha256=44415f3f01d01a21e01132248d2fd0867572475b566ca188a0a42133a08d4531
+  rubocop-ast (1.49.1) sha256=4412f3ee70f6fe4546cc489548e0f6fcf76cafcfa80fa03af67098ffed755035
+  ruby-progressbar (1.13.0) sha256=80fc9c47a9b640d6834e0dc7b3c94c9df37f08cb072b7761e4a71e22cff29b33
+  securerandom (0.4.1) sha256=cc5193d414a4341b6e225f0cb4446aceca8e50d5e1888743fac16987638ea0b1
+  simplecov (0.22.0) sha256=fe2622c7834ff23b98066bb0a854284b2729a569ac659f82621fc22ef36213a5
+  simplecov-cobertura (3.1.0) sha256=6d7f38aa32c965ca2174b2e5bd88cb17138eaf629518854976ac50e628925dc5
+  simplecov-html (0.13.2) sha256=bd0b8e54e7c2d7685927e8d6286466359b6f16b18cb0df47b508e8d73c777246
+  simplecov_json_formatter (0.1.4) sha256=529418fbe8de1713ac2b2d612aa3daa56d316975d307244399fa4838c601b428
+  tzinfo (2.0.6) sha256=8daf828cc77bcf7d63b0e3bdb6caa47e2272dcfaf4fbfe46f8c3a9df087a829b
+  unicode-display_width (3.2.0) sha256=0cdd96b5681a5949cdbc2c55e7b420facae74c4aaf9a9815eee1087cb1853c42
+  unicode-emoji (4.2.0) sha256=519e69150f75652e40bf736106cfbc8f0f73aa3fb6a65afe62fefa7f80b0f80f
+  uri (1.1.1) sha256=379fa58d27ffb1387eaada68c749d1426738bd0f654d812fcc07e7568f5c57c6
+
 BUNDLED WITH
-   2.7.2
+  4.0.7

lib/ontologies_api_client/collection.rb

@@ -10,6 +10,8 @@ def self.included(base)
       end
 
       module ClassMethods
+        PAGED_COLLECTION_SIZE = 5_000
+
         ##
         # Allows for arbitrary find_by methods. For example:
         #   Ontology.find_by_acronym("BRO")
@@ -54,7 +56,12 @@ def collection_path
         # Get all resources from the base collection for a resource
         def all(*args)
           params = args.shift || {}
-          entry_point(@media_type, params)
+          request_params = collection_request_params(params)
+          response = entry_point(@media_type, request_params)
+
+          return response if page_requested?(params) || !paged_collection?(response)
+
+          all_pages(response, request_params)
         end
 
         ##
@@ -114,6 +121,49 @@ def find_by(attrs, *args)
             bools.all?
           end
         end
+
+        private
+
+        def all_pages(first_page, params)
+          collection = Array(first_page.collection)
+          next_page = first_page.nextPage
+
+          while next_page
+            page = entry_point(@media_type, next_page_params(params, next_page))
+            collection.concat(Array(page.collection))
+            next_page = page.nextPage
+          end
+
+          collection
+        end
+
+        def collection_request_params(params)
+          return params if page_requested?(params) || page_size_requested?(params)
+
+          params.merge(pagesize: PAGED_COLLECTION_SIZE)
+        end
+
+        def next_page_params(params, page)
+          page_params = params.dup
+          page_params[page_params.key?("page") ? "page" : :page] = page
+          page_params[:pagesize] = PAGED_COLLECTION_SIZE unless page_size_requested?(page_params)
+          page_params
+        end
+
+        def page_requested?(params)
+          params.key?(:page) || params.key?("page")
+        end
+
+        def page_size_requested?(params)
+          params.key?(:pagesize) || params.key?("pagesize")
+        end
+
+        def paged_collection?(response)
+          response.respond_to?(:collection) &&
+            response.respond_to?(:pageCount) &&
+            response.respond_to?(:nextPage) &&
+            response.collection.is_a?(Array)
+        end
       end
     end
   end

lib/ontologies_api_client/models/user.rb

@@ -9,7 +9,12 @@ class User < LinkedData::Client::Base
         include LinkedData::Client::ReadWrite
 
         @media_type = "http://data.bioontology.org/metadata/User"
-        @include_attrs = "all"
+        @include_attrs = "username,email,role,firstName,lastName,created"
+
+        def self.all(*args)
+          params = args.shift || {}
+          super({ display_context: false, display_links: false }.merge(params), *args)
+        end
 
         def self.authenticate(user, password)
           auth_params = {user: user, password: password, include: "all"}