Add run_metrics to test setup for classes and recommender tests

  After removing the metrics.csv fallback from class_count in ncbo/ontologies_linked_data#277,
  tests that don't compute metrics now fail because class_count returns
  -1 without a Metric object in the triplestore.

Author: alexskr

Gemfile.lock

@@ -66,7 +66,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: a4bbd57fcaa78fa66a11b494384b1791b6e9a6d8
+  revision: 7932bf41d442f3a2c0d589e0c14fbf2e4917d08a
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -124,7 +124,7 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (8.1.2)
+    activesupport (8.1.3)
       base64
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.3.1)
@@ -137,19 +137,19 @@ GEM
       securerandom (>= 0.3)
       tzinfo (~> 2.0, >= 2.0.5)
       uri (>= 0.13.1)
-    addressable (2.8.9)
+    addressable (2.9.0)
       public_suffix (>= 2.0.2, < 8.0)
     airbrussh (1.6.1)
       sshkit (>= 1.6.1, != 1.7.0)
     ansi (1.5.0)
     ast (2.4.3)
     base64 (0.3.0)
     bcp47_spec (0.2.1)
-    bcrypt (3.1.21)
+    bcrypt (3.1.22)
     bcrypt_pbkdf (1.1.2)
     bcrypt_pbkdf (1.1.2-arm64-darwin)
     bcrypt_pbkdf (1.1.2-x86_64-darwin)
-    bigdecimal (4.0.1)
+    bigdecimal (4.1.2)
     builder (3.3.0)
     byebug (12.0.0)
     capistrano (3.20.0)
@@ -173,8 +173,9 @@ GEM
     date (3.5.1)
     docile (1.4.1)
     domain_name (0.6.20240107)
-    down (5.4.2)
+    down (5.5.0)
       addressable (~> 2.8)
+      base64 (~> 0.3)
     drb (2.2.3)
     ed25519 (1.4.0)
     et-orbi (1.4.0)
@@ -189,11 +190,11 @@ GEM
       net-http (~> 0.5)
     faraday-retry (2.4.0)
       faraday (~> 2.0)
-    ffi (1.17.3)
-    ffi (1.17.3-aarch64-linux-gnu)
-    ffi (1.17.3-arm64-darwin)
-    ffi (1.17.3-x86_64-darwin)
-    ffi (1.17.3-x86_64-linux-gnu)
+    ffi (1.17.4)
+    ffi (1.17.4-aarch64-linux-gnu)
+    ffi (1.17.4-arm64-darwin)
+    ffi (1.17.4-x86_64-darwin)
+    ffi (1.17.4-x86_64-linux-gnu)
     fugit (1.12.1)
       et-orbi (~> 1.4)
       raabro (~> 1.4)
@@ -263,12 +264,12 @@ GEM
     hashdiff (1.2.1)
     htmlentities (4.4.2)
     http-accept (1.7.0)
-    http-cookie (1.1.0)
+    http-cookie (1.1.6)
       domain_name (~> 0.5)
     i18n (1.14.8)
       concurrent-ruby (~> 1.0)
     io-console (0.8.2)
-    json (2.19.3)
+    json (2.19.4)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -284,7 +285,7 @@ GEM
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.5)
-    libxml-ruby (5.0.5)
+    libxml-ruby (6.0.0)
     link_header (0.0.8)
     lint_roller (1.1.0)
     logger (1.7.0)
@@ -302,9 +303,9 @@ GEM
     mime-types (3.7.0)
       logger
       mime-types-data (~> 3.2025, >= 3.2025.0507)
-    mime-types-data (3.2026.0317)
+    mime-types-data (3.2026.0414)
     mini_mime (1.1.5)
-    minitest (6.0.2)
+    minitest (6.0.5)
       drb (~> 2.0)
       prism (~> 1.5)
     minitest-hooks (1.5.3)
@@ -317,7 +318,7 @@ GEM
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
-    multi_json (1.19.1)
+    multi_json (1.20.1)
     mustermann (3.0.4)
       ruby2_keywords (~> 0.0.1)
     net-ftp (0.3.9)
@@ -342,7 +343,7 @@ GEM
       net-protocol
     net-ssh (7.3.0)
     netrc (0.11.0)
-    oj (3.16.15)
+    oj (3.17.0)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
@@ -365,7 +366,7 @@ GEM
     public_suffix (7.0.5)
     raabro (1.4.0)
     racc (1.8.1)
-    rack (3.2.5)
+    rack (3.2.6)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-attack (6.8.0)
@@ -583,18 +584,18 @@ DEPENDENCIES
   webrick
 
 CHECKSUMS
-  activesupport (8.1.2) sha256=88842578ccd0d40f658289b0e8c842acfe9af751afee2e0744a7873f50b6fdae
-  addressable (2.8.9) sha256=cc154fcbe689711808a43601dee7b980238ce54368d23e127421753e46895485
+  activesupport (8.1.3) sha256=21a5e0dfbd4c3ddd9e1317ec6a4d782fa226e7867dc70b0743acda81a1dca20e
+  addressable (2.9.0) sha256=7fdf6ac3660f7f4e867a0838be3f6cf722ace541dd97767fa42bc6cfa980c7af
   airbrussh (1.6.1) sha256=9a5fc95583cefe722054a016d26ff0338cf00072b031b829086dde2039d5836a
   ansi (1.5.0) sha256=5408253274e33d9d27d4a98c46d2998266fd51cba58a7eb9d08f50e57ed23592
   ast (2.4.3) sha256=954615157c1d6a382bc27d690d973195e79db7f55e9765ac7c481c60bdb4d383
   base64 (0.3.0) sha256=27337aeabad6ffae05c265c450490628ef3ebd4b67be58257393227588f5a97b
   bcp47_spec (0.2.1) sha256=3fd62edf96c126bd9624e4319ac74082a966081859d1ee0ef3c3041640a37810
-  bcrypt (3.1.21) sha256=5964613d750a42c7ee5dc61f7b9336fb6caca429ba4ac9f2011609946e4a2dcf
+  bcrypt (3.1.22) sha256=1f0072e88c2d705d94aff7f2c5cb02eb3f1ec4b8368671e19112527489f29032
   bcrypt_pbkdf (1.1.2) sha256=c2414c23ce66869b3eb9f643d6a3374d8322dfb5078125c82792304c10b94cf6
   bcrypt_pbkdf (1.1.2-arm64-darwin) sha256=afdd6feb6ed5a97b8e44caacb3f2d641b98af78e6a516d4a3520b69af5cf9fea
   bcrypt_pbkdf (1.1.2-x86_64-darwin) sha256=35f5639d0058e6c2cc2f856f9c0b14080543268d3047abe6bc81c513093caa0e
-  bigdecimal (4.0.1) sha256=8b07d3d065a9f921c80ceaea7c9d4ae596697295b584c296fe599dd0ad01c4a7
+  bigdecimal (4.1.2) sha256=53d217666027eab4280346fba98e7d5b66baaae1b9c3c1c0ffe89d48188a3fbd
   builder (3.3.0) sha256=497918d2f9dca528fdca4b88d84e4ef4387256d984b8154e9d5d3fe5a9c8835f
   byebug (12.0.0) sha256=d4a150d291cca40b66ec9ca31f754e93fed8aa266a17335f71bb0afa7fca1a1e
   capistrano (3.20.0) sha256=0113e58dda99add0342e56a244f664734c59f442c5ed734f5303b0b559b479c9
@@ -609,19 +610,19 @@ CHECKSUMS
   date (3.5.1) sha256=750d06384d7b9c15d562c76291407d89e368dda4d4fff957eb94962d325a0dc0
   docile (1.4.1) sha256=96159be799bfa73cdb721b840e9802126e4e03dfc26863db73647204c727f21e
   domain_name (0.6.20240107) sha256=5f693b2215708476517479bf2b3802e49068ad82167bcd2286f899536a17d933
-  down (5.4.2) sha256=516e5e01e7a96214a7e2cd155aac6f700593038ae6c857c0f4a05413b1c58acf
+  down (5.5.0) sha256=787e14fcfe7824b8cac676c608359e4083b2e4d6e1d3b1745b79f27bcf931585
   drb (2.2.3) sha256=0b00d6fdb50995fe4a45dea13663493c841112e4068656854646f418fda13373
   ed25519 (1.4.0) sha256=16e97f5198689a154247169f3453ef4cfd3f7a47481fde0ae33206cdfdcac506
   et-orbi (1.4.0) sha256=6c7e3c90779821f9e3b324c5e96fda9767f72995d6ae435b96678a4f3e2de8bc
   faraday (2.14.1) sha256=a43cceedc1e39d188f4d2cdd360a8aaa6a11da0c407052e426ba8d3fb42ef61c
   faraday-follow_redirects (0.5.0) sha256=5cde93c894b30943a5d2b93c2fe9284216a6b756f7af406a1e55f211d97d10ad
   faraday-net_http (3.4.2) sha256=f147758260d3526939bf57ecf911682f94926a3666502e24c69992765875906c
   faraday-retry (2.4.0) sha256=7b79c48fb7e56526faf247b12d94a680071ff40c9fda7cf1ec1549439ad11ebe
-  ffi (1.17.3) sha256=0e9f39f7bb3934f77ad6feab49662be77e87eedcdeb2a3f5c0234c2938563d4c
-  ffi (1.17.3-aarch64-linux-gnu) sha256=28ad573df26560f0aedd8a90c3371279a0b2bd0b4e834b16a2baa10bd7a97068
-  ffi (1.17.3-arm64-darwin) sha256=0c690555d4cee17a7f07c04d59df39b2fba74ec440b19da1f685c6579bb0717f
-  ffi (1.17.3-x86_64-darwin) sha256=1f211811eb5cfaa25998322cdd92ab104bfbd26d1c4c08471599c511f2c00bb5
-  ffi (1.17.3-x86_64-linux-gnu) sha256=3746b01f677aae7b16dc1acb7cb3cc17b3e35bdae7676a3f568153fb0e2c887f
+  ffi (1.17.4) sha256=bcd1642e06f0d16fc9e09ac6d49c3a7298b9789bcb58127302f934e437d60acf
+  ffi (1.17.4-aarch64-linux-gnu) sha256=b208f06f91ffd8f5e1193da3cae3d2ccfc27fc36fba577baf698d26d91c080df
+  ffi (1.17.4-arm64-darwin) sha256=19071aaf1419251b0a46852abf960e77330a3b334d13a4ab51d58b31a937001b
+  ffi (1.17.4-x86_64-darwin) sha256=aa70390523cf3235096cf64962b709b4cfbd5c082a2cb2ae714eb0fe2ccda496
+  ffi (1.17.4-x86_64-linux-gnu) sha256=9d3db14c2eae074b382fa9c083fe95aec6e0a1451da249eab096c34002bc752d
   fugit (1.12.1) sha256=5898f478ede9b415f0804e42b8f3fd53f814bd85eebffceebdbc34e1107aaf68
   gapic-common (1.1.0) sha256=3270ab3c5135012a4ab4d8848f945cf35014192f24504cdb40c66fc67f1beaa3
   get_process_mem (0.2.7) sha256=4afd3c3641dd6a817c09806c7d6d509d8a9984512ac38dea8b917426bbf77eba
@@ -649,17 +650,17 @@ CHECKSUMS
   hashdiff (1.2.1) sha256=9c079dbc513dfc8833ab59c0c2d8f230fa28499cc5efb4b8dd276cf931457cd1
   htmlentities (4.4.2) sha256=bbafbdf69f2eca9262be4efef7e43e6a1de54c95eb600f26984f71d2fe96c5c3
   http-accept (1.7.0) sha256=c626860682bfbb3b46462f8c39cd470fd7b0584f61b3cc9df5b2e9eb9972a126
-  http-cookie (1.1.0) sha256=38a5e60d1527eebc396831b8c4b9455440509881219273a6c99943d29eadbb19
+  http-cookie (1.1.6) sha256=ba4b82be64de61dc281243dac70e3c382c45142f20268ed9276a3670c93feaa9
   i18n (1.14.8) sha256=285778639134865c5e0f6269e0b818256017e8cde89993fdfcbfb64d088824a5
   io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc
-  json (2.19.3) sha256=289b0bb53052a1fa8c34ab33cc750b659ba14a5c45f3fcf4b18762dc67c78646
+  json (2.19.4) sha256=670a7d333fb3b18ca5b29cb255eb7bef099e40d88c02c80bd42a3f30fe5239ac
   json-canonicalization (0.4.0) sha256=73ea88b68f210d1a09c2116d4cd1ff5a39684c6a409f7ccac70d5b1a426a8bef
   json-ld (3.2.5) sha256=98b96f1831b0fe9c7d2568a7d43b64f6b8c3f5892d55ccf91640e32a99c273fc
   json-schema (6.2.0) sha256=e8bff46ed845a22c1ab2bd0d7eccf831c01fe23bb3920caa4c74db4306813666
   jwt (3.1.2) sha256=af6991f19a6bb4060d618d9add7a66f0eeb005ac0bc017cd01f63b42e122d535
   kgio (2.11.4) sha256=bda7a2146115998a5b07154e708e0ac02c38dcee7e793c33e2e14f600fdfffc6
   language_server-protocol (3.17.0.5) sha256=fd1e39a51a28bf3eec959379985a72e296e9f9acfce46f6a79d31ca8760803cc
-  libxml-ruby (5.0.5) sha256=f1bc07152982df555d70159a694ee2a53539de2cdad4b3c8a447fbb15e7e4e9a
+  libxml-ruby (6.0.0) sha256=a9d9458d018dee591d0995fdc1110cd67ec32b7be67d36fdb9e0b01a4ca9dac4
   link_header (0.0.8) sha256=15c65ce43b29f739b30d05e5f25c22c23797e89cf6f905dbb595fb4c70cb55f9
   lint_roller (1.1.0) sha256=2c0c845b632a7d172cb849cc90c1bce937a28c5c8ccccb50dfd46a485003cc87
   logger (1.7.0) sha256=196edec7cc44b66cfb40f9755ce11b392f21f7967696af15d274dde7edff0203
@@ -668,14 +669,14 @@ CHECKSUMS
   mcp (0.8.0) sha256=ae8bd146bb8e168852866fd26f805f52744f6326afb3211e073f78a95e0c34fb
   method_source (1.1.0) sha256=181301c9c45b731b4769bc81e8860e72f9161ad7d66dd99103c9ab84f560f5c5
   mime-types (3.7.0) sha256=dcebf61c246f08e15a4de34e386ebe8233791e868564a470c3fe77c00eed5e56
-  mime-types-data (3.2026.0317) sha256=77f078a4d8631d52b842ba77099734b06eddb7ad339d792e746d2272b67e511b
+  mime-types-data (3.2026.0414) sha256=461c4c655373a44bd6c5fe54bcf5b7776026ea96e808144b1ec465c4b99148cc
   mini_mime (1.1.5) sha256=8681b7e2e4215f2a159f9400b5816d85e9d8c6c6b491e96a12797e798f8bccef
-  minitest (6.0.2) sha256=db6e57956f6ecc6134683b4c87467d6dd792323c7f0eea7b93f66bd284adbc3d
+  minitest (6.0.5) sha256=f007d7246bf4feea549502842cd7c6aba8851cdc9c90ba06de9c476c0d01155c
   minitest-hooks (1.5.3) sha256=ef50dd3bf47e6d1646befc358c640c71ca41f5650f0036b4c69929a44d6f32c4
   minitest-reporters (1.7.1) sha256=5060413a0c95b8c32fe73e0606f3631c173a884d7900e50013e15094eb50562c
   minitest-stub_any_instance (1.0.3) sha256=d53ca295d173817f828789ac44ad3c2a4a0752166eea7a63c9ae026d9e7660e8
   mlanett-redis-lock (0.2.7) sha256=55fea6e6fb9d9241d921187dd93f0d4ccc116138f873e5d5ee729f4c5aa9aad3
-  multi_json (1.19.1) sha256=7aefeff8f2c854bf739931a238e4aea64592845e0c0395c8a7d2eea7fdd631b7
+  multi_json (1.20.1) sha256=2f3934e805cc45ef91b551a1f89d0e9191abd06a5e04a2ef09a6a036c452ca6d
   mustermann (3.0.4) sha256=85fadcb6b3c6493a8b511b42426f904b7f27b282835502233dd154daab13aa22
   ncbo_annotator (0.0.1)
   ncbo_cron (0.0.1)
@@ -691,7 +692,7 @@ CHECKSUMS
   net-smtp (0.5.1) sha256=ed96a0af63c524fceb4b29b0d352195c30d82dd916a42f03c62a3a70e5b70736
   net-ssh (7.3.0) sha256=172076c4b30ce56fb25a03961b0c4da14e1246426401b0f89cba1a3b54bf3ef0
   netrc (0.11.0) sha256=de1ce33da8c99ab1d97871726cba75151113f117146becbe45aa85cb3dabee3f
-  oj (3.16.15) sha256=4d3324cac3e8fef54c0fa250b2af26a16dadd9f9788a1d6b1b2098b793a1b2cd
+  oj (3.17.0) sha256=5684b2127fb70e650fae90df521b91336ff8e55e2e1011ed80eb0283beac5360
   omni_logger (0.1.4) sha256=b61596f7d96aa8426929e46c3500558d33e838e1afd7f4735244feb4d082bb3e
   ontologies_linked_data (0.0.1)
   ontoportal_testkit (0.1.0)
@@ -707,7 +708,7 @@ CHECKSUMS
   public_suffix (7.0.5) sha256=1a8bb08f1bbea19228d3bed6e5ed908d1cb4f7c2726d18bd9cadf60bc676f623
   raabro (1.4.0) sha256=d4fa9ff5172391edb92b242eed8be802d1934b1464061ae5e70d80962c5da882
   racc (1.8.1) sha256=4a7f6929691dbec8b5209a0b373bc2614882b55fc5d2e447a21aaa691303d62f
-  rack (3.2.5) sha256=4cbd0974c0b79f7a139b4812004a62e4c60b145cba76422e288ee670601ed6d3
+  rack (3.2.6) sha256=5ed78e1f73b2e25679bec7d45ee2d4483cc4146eb1be0264fc4d94cb5ef212c2
   rack-accept (0.4.5) sha256=66247b5449db64ebb93ae2ec4af4764b87d1ae8a7463c7c68893ac13fa8d4da2
   rack-attack (6.8.0) sha256=f2499fdebf85bcc05573a22dff57d24305ac14ec2e4156cd3c28d47cafeeecf2
   rack-cache (1.17.0) sha256=49592f3ef2173b0f5524df98bb801fb411e839869e7ce84ac428dc492bf0eb90

test/controllers/test_classes_controller.rb

@@ -8,7 +8,7 @@ def before_suite
                submissions_to_process: [1, 2],
                process_submission: true,
                random_submission_count: false,
-               process_options: {process_rdf: true, extract_metadata: false}
+               process_options: {process_rdf: true, extract_metadata: false, run_metrics: true}
     }
     return LinkedData::SampleData::Ontology.create_ontologies_and_submissions(options)
   end

test/controllers/test_recommender_controller.rb

@@ -14,7 +14,8 @@ def before_suite
       @@redis.del(mappings)
     end
     LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
-    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true)
+    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true,
+                                                                          process_options: {process_rdf: true, extract_metadata: false, run_metrics: true})
     annotator = Annotator::Models::NcboAnnotator.new
     annotator.init_redis_for_tests()
     annotator.create_term_cache_from_ontologies(@@ontologies, false)