Feature/user admin endpoints - fix unit tests and stability after merging feature branch

Gemfile

@@ -81,4 +81,5 @@ group :test do
   gem 'simplecov-cobertura' # for codecov.io
   gem 'webmock', '~> 3.19.1'
   gem 'webrick'
-end
+  gem 'minitest-bisect'
+end

Gemfile.lock

@@ -27,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: c4f16085b3e34b1e38e30232988297016e1f0e39
+  revision: 111c7263d8a98b1e8f7c033cb0b7d9c6cc10cd01
   branch: develop
   specs:
     ncbo_cron (0.0.1)
@@ -142,15 +142,16 @@ GEM
       rexml
     cube-ruby (0.0.3)
     dante (0.2.0)
-    date (3.4.1)
+    date (3.5.0)
     docile (1.4.1)
     domain_name (0.6.20240107)
+    drb (2.2.3)
     ed25519 (1.4.0)
     faraday (2.14.0)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
-    faraday-follow_redirects (0.3.0)
+    faraday-follow_redirects (0.4.0)
       faraday (>= 1, < 3)
     faraday-net_http (3.4.1)
       net-http (>= 0.5.0)
@@ -167,7 +168,7 @@ GEM
     ffi (1.17.2-x86_64-darwin)
     ffi (1.17.2-x86_64-linux-gnu)
     ffi (1.17.2-x86_64-linux-musl)
-    gapic-common (1.0.1)
+    gapic-common (1.1.0)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
       google-cloud-env (~> 2.2)
@@ -179,7 +180,7 @@ GEM
       grpc (~> 1.66)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
-    google-analytics-data (0.7.1)
+    google-analytics-data (0.7.2)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
     google-analytics-data-v1beta (0.17.0)
@@ -205,39 +206,39 @@ GEM
       grpc (~> 1.41)
     googleapis-common-protos-types (1.20.0)
       google-protobuf (>= 3.18, < 5.a)
-    googleauth (1.14.0)
+    googleauth (1.15.1)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.2)
       google-logging-utils (~> 0.1)
-      jwt (>= 1.4, < 3.0)
+      jwt (>= 1.4, < 4.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.74.0)
+    grpc (1.76.0)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-aarch64-linux-gnu)
+    grpc (1.76.0-aarch64-linux-gnu)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-aarch64-linux-musl)
+    grpc (1.76.0-aarch64-linux-musl)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-arm64-darwin)
+    grpc (1.76.0-arm64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-x86-linux-gnu)
+    grpc (1.76.0-x86-linux-gnu)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-x86-linux-musl)
+    grpc (1.76.0-x86-linux-musl)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-x86_64-darwin)
+    grpc (1.76.0-x86_64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-x86_64-linux-gnu)
+    grpc (1.76.0-x86_64-linux-gnu)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.74.0-x86_64-linux-musl)
+    grpc (1.76.0-x86_64-linux-musl)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
@@ -253,7 +254,7 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.8.1)
-    jwt (2.10.2)
+    jwt (3.1.2)
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.5)
@@ -275,16 +276,22 @@ GEM
     mime-types-data (3.2025.0924)
     mini_mime (1.1.5)
     minitest (5.26.0)
+    minitest-bisect (1.7.0)
+      minitest-server (~> 1.0)
+      path_expander (~> 1.1)
     minitest-hooks (1.5.2)
       minitest (> 5.3)
+    minitest-server (1.0.8)
+      drb (~> 2.0)
+      minitest (~> 5.16)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.17.0)
-    net-ftp (0.3.8)
+    net-ftp (0.3.9)
       net-protocol
       time
-    net-http (0.6.0)
+    net-http (0.7.0)
       uri
     net-http-persistent (2.9.4)
     net-imap (0.5.12)
@@ -303,7 +310,7 @@ GEM
     net-ssh (7.3.0)
     netrc (0.11.0)
     newrelic_rpm (9.19.0)
-    oj (3.16.11)
+    oj (3.16.12)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
@@ -315,6 +322,7 @@ GEM
     parser (3.3.8.0)
       ast (~> 2.4.1)
       racc
+    path_expander (1.1.3)
     pony (1.13.1)
       mail (>= 2.0)
     prism (1.4.0)
@@ -382,13 +390,13 @@ GEM
       prism (~> 1.4)
     ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
-    rubyzip (3.2.1)
+    rubyzip (3.2.2)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
-    signet (0.20.0)
+    signet (0.21.0)
       addressable (~> 2.8)
       faraday (>= 0.17.5, < 3.a)
-      jwt (>= 1.5, < 3.0)
+      jwt (>= 1.5, < 4.0)
       multi_json (~> 1.10)
     simplecov (0.22.0)
       docile (~> 1.1)
@@ -425,7 +433,7 @@ GEM
     tilt (2.6.1)
     time (0.4.1)
       date
-    timeout (0.4.3)
+    timeout (0.4.4)
     tzinfo (1.2.11)
       thread_safe (~> 0.1)
     unicode-display_width (3.1.4)
@@ -437,7 +445,7 @@ GEM
     unicorn-worker-killer (0.4.5)
       get_process_mem (~> 0)
       unicorn (>= 4, < 7)
-    uri (1.0.4)
+    uri (1.1.1)
     uuid (2.3.9)
       macaddr (~> 1.0)
     webmock (3.19.1)
@@ -479,6 +487,7 @@ DEPENDENCIES
   haml (~> 5.2.2)
   json-schema (~> 2.0)
   minitest (~> 5.0)
+  minitest-bisect
   minitest-hooks (~> 1.5)
   minitest-stub_any_instance
   multi_json

controllers/ontology_submissions_controller.rb

@@ -144,7 +144,7 @@ class OntologySubmissionsController < ApplicationController
           # Re-fetch ontology to avoid stale submissions cache
           ont_refreshed = Ontology.find(params["acronym"]).include(submissions: :submissionId).first
           new_latest_sub = ont_refreshed.latest_submission(status: :any)
-          NcboCron::Models::OntologySubmissionParser.new.queue_submission(new_latest_sub, all: true) if new_latest_sub
+          NcboCron::Models::OntologySubmissionParser.new.queue_submission(new_latest_sub, all: true) if new_latest_sub && ENV['RACK_ENV'] != 'test'
         end
 
         payload = { deleted_ids: deleted_ids, deleted_count: deleted_ids.size, missing_ids: missing }

helpers/application_helper.rb

@@ -492,7 +492,8 @@ def process_long_operation(timeout, args = {}, &block)
         end
 
         # 4) Background work (toggle via fork: false in tests)
-        if args.fetch(:fork, true)
+        fork_process = ENV['RACK_ENV'] != 'test'
+        if fork_process
           pid = Process.fork { worker.call }
           Process.detach(pid)
         else

test/controllers/test_batch_controller.rb

@@ -49,7 +49,7 @@ def test_class_wrong_params
       }
     }
     post "/batch/", call_params
-    assert last_response.status = 422
+    assert_equal 422, last_response.status
   end
 
   def test_class_batch_multiple
@@ -109,7 +109,7 @@ def test_class_all_bro
     assert_equal classes.length, classes_response.length
     classes_response.each do |klass|
       assert_instance_of String, klass["prefLabel"]
-      assert klass["prefLabel"] == class_ids[klass["@id"]]
+      assert_equal klass["prefLabel"], class_ids[klass["@id"]]
     end
   end
 end