Merge Develop to Master, release v5.28.0

.github/workflows/deploy.yml

@@ -60,13 +60,13 @@ jobs:
         USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
         echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: ruby/setup-ruby@v1
       with:
-        ruby-version: 2.7.6 # Not needed with a .ruby-version file
+        ruby-version: 2.7.8 # Not needed with a .ruby-version file
         bundler-cache: true # runs 'bundle install' and caches installed gems automatically
     - name: get-deployment-config
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings
         token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
@@ -79,7 +79,7 @@ jobs:
         mkdir -p ~/.ssh
         ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts
       shell: bash
-    - uses: miloserdow/capistrano-deploy@master
+    - uses: miloserdow/capistrano-deploy@v3
       with:
         target: ${{ env.TARGET }} # which environment to deploy
         deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project

.github/workflows/docker-image.yml

@@ -10,28 +10,28 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           images: bioportal/ontologies_api
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64,linux/arm64

.github/workflows/ruby-unit-tests.yml

@@ -12,7 +12,7 @@ jobs:
         backend: ['api', 'api-agraph'] # api runs tests with 4store backend and api-agraph runs with AllegroGraph backend
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Build docker-compose
       run: docker-compose --profile 4store build #profile flag is set in order to build all containers in this step
     - name: Run unit tests
@@ -22,8 +22,9 @@ jobs:
         ci_env=`bash <(curl -s https://codecov.io/env)`
         docker-compose run $ci_env -e CI --rm ${{ matrix.backend }} bundle exec rake test TESTOPTS='-v'
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         flags: unittests
         verbose: true
         fail_ci_if_error: false # optional (default = false)

Gemfile.lock

@@ -26,7 +26,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: b01a9046c4c110f00e832e8c16073a74558fdba5
+  revision: 46bd8e7eb7cfde6d173bdf55808a8e28d6700f1e
   branch: master
   specs:
     ncbo_cron (0.0.1)
@@ -53,7 +53,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: ee0013f0ee23876076bff9d9258b46371ec3b248
+  revision: 0423a4559b9cf6f176a521a7c78471938c8f754e
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -127,7 +127,7 @@ GEM
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     dante (0.2.0)
@@ -153,16 +153,16 @@ GEM
       grpc (~> 1.59)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
-    google-analytics-data (0.4.0)
-      google-analytics-data-v1beta (>= 0.7, < 2.a)
+    google-analytics-data (0.5.0)
+      google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.11.1)
+    google-analytics-data-v1beta (0.11.2)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-cloud-core (1.6.1)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-env (2.1.0)
+    google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.3.1)
     google-protobuf (3.25.2-aarch64-linux)
@@ -175,23 +175,23 @@ GEM
       grpc (~> 1.27)
     googleapis-common-protos-types (1.11.0)
       google-protobuf (~> 3.18)
-    googleauth (1.9.1)
+    googleauth (1.10.0)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.60.0-aarch64-linux)
+    grpc (1.61.0-aarch64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.60.0-arm64-darwin)
+    grpc (1.61.0-arm64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.60.0-x86_64-darwin)
+    grpc (1.61.0-x86_64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.60.0-x86_64-linux)
+    grpc (1.61.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
@@ -221,7 +221,7 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1205)
+    mime-types-data (3.2024.0206)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
@@ -230,7 +230,7 @@ GEM
     multi_json (1.15.0)
     mutex_m (0.2.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.9.1)
+    net-imap (0.4.10)
       date
       net-protocol
     net-pop (0.1.2)
@@ -245,14 +245,14 @@ GEM
       net-protocol
     net-ssh (7.2.1)
     netrc (0.11.0)
-    newrelic_rpm (9.7.0)
+    newrelic_rpm (9.7.1)
     oj (3.16.1)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
     parallel (1.24.0)
     parseconfig (1.1.2)
-    parser (3.3.0.3)
+    parser (3.3.0.5)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -284,7 +284,7 @@ GEM
     rdf (1.0.8)
       addressable (>= 2.2)
     redcarpet (3.6.0)
-    redis (5.0.8)
+    redis (5.1.0)
       redis-client (>= 0.17.0)
     redis-client (0.19.1)
       connection_pool
@@ -303,11 +303,11 @@ GEM
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.59.0)
+    rubocop (1.60.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.4)
+      parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
@@ -427,4 +427,4 @@ DEPENDENCIES
   unicorn-worker-killer
 
 BUNDLED WITH
-   2.4.22
+   2.4.22

controllers/users_controller.rb

@@ -13,7 +13,7 @@ class UsersController < ApplicationController
     end
 
     ##
-    # This endpoint will create a token and store it on the user
+    # This endpoint will create a token and store it on the use-
     # An email is generated with this token, which allows the user
     # to click and login to the UI. The token can then be provided to
     # the /reset_password endpoint to actually reset the password.
@@ -24,6 +24,7 @@ class UsersController < ApplicationController
       error 404, "User not found" unless user
       reset_token = token(36)
       user.resetToken = reset_token
+      user.resetTokenExpireTime = Time.now.to_i + 1.hours.to_i
       if user.valid?
         user.save(override_security: true)
         LinkedData::Utils::Notifications.reset_password(user, reset_token)
@@ -46,10 +47,15 @@ class UsersController < ApplicationController
       user = LinkedData::Models::User.where(email: email, username: username).include(User.goo_attrs_to_load(includes_param)).first
       error 404, "User not found" unless user
       if token.eql?(user.resetToken)
+        error 401, "Invalid password reset token" if user.resetTokenExpireTime.nil?
+        error 401, "The password reset token expired" if user.resetTokenExpireTime < Time.now.to_i
+        user.resetToken = nil
+        user.resetTokenExpireTime = nil
+        user.save(override_security: true) if user.valid?
         user.show_apikey = true
         reply user
       else
-        error 403, "Password reset not authorized with this token"
+        error 401, "Password reset not authorized with this token"
       end
     end
 

docker-compose.yml

@@ -65,9 +65,9 @@ services:
       GOO_BACKEND_NAME: ag
       GOO_PORT: 10035
       GOO_HOST: agraph-ut
-      GOO_PATH_QUERY: /repositories/bioportal_test
-      GOO_PATH_DATA: /repositories/bioportal_test/statements
-      GOO_PATH_UPDATE: /repositories/bioportal_test/statements
+      GOO_PATH_QUERY: /repositories/ontoportal_test
+      GOO_PATH_DATA: /repositories/ontoportal_test/statements
+      GOO_PATH_UPDATE: /repositories/ontoportal_test/statements
     profiles:
       - agraph
     depends_on:
@@ -114,7 +114,7 @@ services:
       retries: 5
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.0
+    image: franzinc/agraph:v8.0.1
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test
@@ -124,18 +124,19 @@ services:
     #  - 10035:10035
     command: >
        bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start
-       ; agtool repos create bioportal_test
+       ; agtool repos create ontoportal_test
        ; agtool users add anonymous
-       ; agtool users grant anonymous root:bioportal_test:rw
+       ; agtool users grant anonymous root:ontoportal_test:rw
        ; tail -f /agraph/data/agraph.log"
     healthcheck:
-      test: ["CMD-SHELL", "agtool storage-report bioportal_test || exit 1"]
-      start_period: 10s
-      interval: 60s
-      timeout: 5s
-      retries: 3
+      test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"]
+      start_period: 30s
+      interval: 20s
+      timeout: 10s
+      retries: 10
     profiles:
       - agraph
 
 volumes:
   bundle:
+

test/controllers/test_ontologies_controller.rb

@@ -287,6 +287,8 @@ def test_on_demand_ontology_pull
       post "/ontologies/#{acronym}/pull?apikey=#{blocked_user.apikey}"
       assert_equal(403, last_response.status, msg="An unauthorized user was able to execute the on-demand pull")
     ensure
+      del = User.find("blocked").first
+      del.delete if del
       stop_server
       LinkedData.settings.enable_security = false
     end

test/controllers/test_users_controller.rb

@@ -67,9 +67,58 @@ def test_create_new_user
 
     get "/users/#{@@username}"
     assert last_response.ok?
-    assert MultiJson.load(last_response.body)["username"].eql?(@@username)
+    assert MultiJson.load(last_response.body)["username"].eql?(@@username) 
+    assert_equal "test_user@example.org", MultiJson.load(last_response.body)["email"]
+  end
+
+  def test_reset_password
+    username = 'resetpswd'
+    user = {email: "#{username}@example.org", password: "resetme"}
+    put "/users/#{username}", MultiJson.dump(user), "CONTENT_TYPE" => "application/json"
+    assert last_response.status == 201
+    user = User.find(username).include(User.attributes).first
+    assert_nil user.resetToken
+    post "/users/create_reset_password_token", {username: username, email: "bademail@example.org"}
+    user = User.find(username).include(User.attributes).first
+    assert_nil user.resetToken
+    assert_equal 404, last_response.status
+    post "/users/reset_password", {username: 'badusername', email: "#{username}@example.org", token: 'badtoken'}
+    post "/users/create_reset_password_token", {username: username, email: "#{username}@example.org"}
+    assert_equal 204, last_response.status
+    user = User.find(username).include(User.attributes).first
+    refute_nil user.resetToken
+    post "/users/reset_password", {username: username, email: "#{username}@example.org", token: 'badtoken'}
+    assert_equal 401, last_response.status
+    post "/users/reset_password", {username: 'badusername', email: "#{username}@example.org", token: 'badtoken'}
+    assert_equal 404, last_response.status
+    post "/users/reset_password", {username: username, token: user.resetToken}
+    assert_equal 404, last_response.status
+    post "/users/reset_password", {email: "#{username}@example.org", token: user.resetToken}
+    assert_equal 404, last_response.status
+    post "/users/reset_password", {username: username, email: "badexampe@example.org", token: user.resetToken}
+    assert_equal 404, last_response.status
+    post "/users/reset_password", {username: username, email: "#{username}@example.org", token: user.resetToken}
+    assert_equal 200, last_response.status
+    assert_equal "#{username}@example.org", MultiJson.load(last_response.body)["email"]
+    user = User.find(username).include(User.attributes).first
+    assert_nil user.resetToken
   end
 
+  def test_reset_password_expired_token
+    username = 'resetexpired'
+    user = {email: "#{username}@example.org", password: "resetme"}
+    put "/users/#{username}", MultiJson.dump(user), "CONTENT_TYPE" => "application/json"
+    assert last_response.status == 201
+    post "/users/create_reset_password_token", {username: username, email: "#{username}@example.org"}
+    assert_equal 204, last_response.status
+    user = User.find(username).include(User.attributes).first
+    user.resetTokenExpireTime = Time.now.to_i - 2.hours.to_i
+    user.save
+    post "/users/reset_password", {username: username, email: "#{username}@example.org", token: user.resetToken}
+    assert_equal 401, last_response.status
+  end
+
+
   def test_create_new_invalid_user
     put "/users/totally_new_user"
     assert last_response.status == 422
@@ -120,7 +169,6 @@ def test_authentication
     assert user["username"].eql?(@@usernames.first)
   end
 
-
   private
 
   def _delete_user(username)