Develop -> Master merge, release v7.3.0

.gitignore

@@ -59,6 +59,9 @@ test/data/ontology_files/repo/**/*
 # Claude Code
 .claude/
 
+# Serena
+.serena/
+
 *.swp
 
 config/environments/console.rb

Gemfile

@@ -50,12 +50,12 @@ gem 'rack-contrib'
 gem 'kramdown'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'main'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'main'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
-gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'development'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'development'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
+gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop'
+gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
 
 group :development do
   gem 'shotgun', github: 'syphax-bouazzouni/shotgun', branch: 'master'

Gemfile.lock

@@ -8,8 +8,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: ee72f43daa37f02362da1b747f037c442cfbf112
-  branch: main
+  revision: 0187c6c0ba3871fa8b67055c1a1adfdea38b2189
+  branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: b216bdde2de471fc0f851556ffa2327333516e79
-  branch: master
+  revision: 5243ea8db4302ca756c66bf50233e88606830326
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -37,8 +37,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 18a6c183d5dd59b3adda58af90bab334fb911537
-  branch: master
+  revision: 91fb6b34e6f0bb827a6da721b083640b823d1083
+  branch: develop
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -55,8 +55,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: e63da099a5d69cf08d2c1c0d58b2f80bd5d41bb0
-  branch: master
+  revision: 722a70afe43daea2be96ba46850d6c917e9d4132
+  branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -66,8 +66,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 32023829506089164a27da1e6aa05b901a019079
-  branch: master
+  revision: d4492a5cf76d78e74b677cc3f05c97dcbd53ccb7
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -89,7 +89,7 @@ GIT
 GIT
   remote: https://github.com/ncbo/sparql-client.git
   revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5
-  branch: main
+  branch: development
   specs:
     sparql-client (3.2.2)
       net-http-persistent (~> 4.0, >= 4.0.2)

helpers/users_helper.rb

@@ -3,13 +3,16 @@
 module Sinatra
   module Helpers
     module UsersHelper
+      USER_SEARCH_FIELDS = %i[username email firstName lastName].freeze
+      DEFAULT_USER_SEARCH_FIELDS = %i[username].freeze
+      ALL_USER_SEARCH_FIELDS = 'all'.freeze
+
       def get_users
         attributes, page, size, order_by, _ = settings_params(LinkedData::Models::User)
         query = User.where.include(attributes)
 
         if params['search']
-          filter = Goo::Filter.new(:username).regex(params['search'])
-          query = query.filter(filter)
+          query = query.filter(user_search_filter(params['search']))
         end
 
         query = query.order_by(order_by || { username: :asc })
@@ -18,24 +21,67 @@ def get_users
         query.all
       end
 
+      def user_search_filter(term)
+        field, *remaining_fields = user_search_fields
+        filter = Goo::Filter.new(field).regex(term)
+        remaining_fields.each do |search_field|
+          filter = filter.or(Goo::Filter.new(search_field).regex(term))
+        end
+        filter
+      end
+
+      def user_search_fields
+        fields = requested_user_search_fields
+        return DEFAULT_USER_SEARCH_FIELDS if fields.empty?
+
+        validate_all_user_search_fields!(fields)
+        return USER_SEARCH_FIELDS if fields == [ALL_USER_SEARCH_FIELDS]
+
+        fields = fields.map(&:to_sym)
+        validate_known_user_search_fields!(fields)
+
+        fields
+      end
+
+      def requested_user_search_fields
+        params['search_fields'].to_s.split(',').map(&:strip).reject(&:empty?)
+      end
+
+      def validate_all_user_search_fields!(fields)
+        return unless fields.include?(ALL_USER_SEARCH_FIELDS) && fields != [ALL_USER_SEARCH_FIELDS]
+
+        error_message = "Unsupported search_fields: #{params['search_fields']}. "
+        error_message += 'Use all by itself or list individual fields'
+        error 400, error_message
+      end
+
+      def validate_known_user_search_fields!(fields)
+        unknown_fields = fields - USER_SEARCH_FIELDS
+        return if unknown_fields.empty?
+
+        unsupported_fields = unknown_fields.join(', ')
+        allowed_fields = USER_SEARCH_FIELDS.join(', ')
+        error 400, "Unsupported search_fields: #{unsupported_fields}. Allowed fields: #{allowed_fields}"
+      end
+
       def filter_for_user_onts(obj)
         return obj unless obj.is_a?(Enumerable)
-        return obj unless env["REMOTE_USER"]
-        return obj if env["REMOTE_USER"].customOntology.empty?
-        return obj if params["ignore_custom_ontologies"]
+        return obj unless env['REMOTE_USER']
+        return obj if env['REMOTE_USER'].customOntology.empty?
+        return obj if params['ignore_custom_ontologies']
 
-        user = env["REMOTE_USER"]
+        user = env['REMOTE_USER']
 
         if obj.first.is_a?(LinkedData::Models::Ontology)
-          obj = obj.select {|o| user.custom_ontology_id_set.include?(o.id.to_s)}
+          obj = obj.select { |o| user.custom_ontology_id_set.include?(o.id.to_s) }
         end
 
         obj
       end
 
       def send_reset_token(email, username)
         user = LinkedData::Models::User.where(email: email, username: username).include(LinkedData::Models::User.attributes).first
-        error 404, "User not found" unless user
+        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
@@ -46,22 +92,22 @@ def send_reset_token(email, username)
       end
 
       def token(len)
-        chars = ("a".."z").to_a + ("A".."Z").to_a + ("1".."9").to_a
-        token = ""
-        1.upto(len) { |i| token << chars[rand(chars.size-1)] }
+        chars = ('a'..'z').to_a + ('A'..'Z').to_a + ('1'..'9').to_a
+        token = ''
+        1.upto(len) { |i| token << chars[rand(chars.size - 1)] }
         token
       end
 
       def reset_password(email, username, token)
         user = LinkedData::Models::User.where(email: email, username: username).include(User.goo_attrs_to_load(includes_param) + [:resetToken, :passwordHash, :resetTokenExpireTime]).first
 
-        error 404, "User not found" unless user
+        error 404, 'User not found' unless user
 
         user.show_apikey = true
         token_accepted = token.eql?(user.resetToken)
         if token_accepted
-          error 401, "Invalid password reset token" if user.resetTokenExpireTime.nil?
-          error 401, "The password reset token expired" if user.resetTokenExpireTime < Time.now.to_i
+          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?
@@ -72,20 +118,20 @@ def reset_password(email, username, token)
       end
 
       def oauth_authenticate(params)
-        access_token  = params["access_token"]
-        provider  = params["token_provider"]
+        access_token = params['access_token']
+        provider = params['token_provider']
         user = LinkedData::Models::User.oauth_authenticate(access_token, provider)
-        error 401, "Access token invalid"if user.nil?
+        error 401, 'Access token invalid' if user.nil?
         user
       end
 
       def login_password_authenticate(params)
-        user_id       = params["user"]
-        user_password = params["password"]
+        user_id       = params['user']
+        user_password = params['password']
         user = User.find(user_id).include(User.goo_attrs_to_load(includes_param) + [:passwordHash]).first
         authenticated = false
         authenticated = user.authenticate(user_password) unless user.nil?
-        error 401, "Username/password combination invalid" unless authenticated
+        error 401, 'Username/password combination invalid' unless authenticated
 
         user
       end

test/controllers/test_search_models_controller.rb

@@ -18,8 +18,8 @@ def test_show_all_collection
     get '/admin/search/collections'
     assert last_response.ok?
     res = MultiJson.load(last_response.body)
-    required = %w[ontology_data ontology_metadata prop_search_core1 term_search_core1]
-    allowed_extra = %w[term_search test_solr]
+    required = %w[ontology_data ontology_metadata property_search_bootstrap term_search_bootstrap]
+    allowed_extra = %w[property_search term_search test_solr]
     collections = res["collections"]
     assert_empty required - collections
     assert_empty collections - (required + allowed_extra)

test/controllers/test_users_controller.rb

@@ -10,6 +10,17 @@ def before_suite
       User.new(username: username, email: "#{username}@example.org", password: "pass_word").save
     end
 
+    search_users = [
+      { username: 'username_marker_account', email: 'search@example.org', firstName: 'Username', lastName: 'Search' },
+      { username: 'email_account', email: 'mailmarker@example.org', firstName: 'Email', lastName: 'Search' },
+      { username: 'first_name_account', email: 'search@example.org', firstName: 'given_marker', lastName: 'Search' },
+      { username: 'last_name_account', email: 'search@example.org', firstName: 'Last', lastName: 'family_marker' }
+    ]
+
+    @@users.concat(search_users.map do |user_params|
+      User.new(user_params.merge(password: 'pass_word')).save
+    end)
+
     # Test data
     @@username = "test_user"
   end
@@ -60,6 +71,64 @@ def test_all_users_include_all_is_paged
     assert users_page["collection"].all? { |u| u.key?("created") }
   end
 
+  def test_search_users_by_username
+    users_page = search_users('username_marker')
+    usernames = users_page['collection'].map { |user| user['username'] }
+
+    assert_equal ['username_marker_account'], usernames
+    assert_equal 1, users_page['totalCount']
+    assert_equal 1, users_page['pageCount']
+  end
+
+  def test_search_users_defaults_to_username_only
+    users_page = search_users('mailmarker')
+
+    assert_equal [], users_page['collection']
+    assert_equal 0, users_page['totalCount']
+    assert_equal 0, users_page['pageCount']
+  end
+
+  def test_search_users_by_email
+    users_page = search_users('mailmarker', search_fields: 'all')
+    usernames = users_page['collection'].map { |user| user['username'] }
+
+    assert_equal ['email_account'], usernames
+    assert_equal 1, users_page['totalCount']
+    assert_equal 1, users_page['pageCount']
+  end
+
+  def test_search_users_by_first_name
+    users_page = search_users('given_marker', search_fields: 'all')
+    usernames = users_page['collection'].map { |user| user['username'] }
+
+    assert_equal ['first_name_account'], usernames
+    assert_equal 1, users_page['totalCount']
+    assert_equal 1, users_page['pageCount']
+  end
+
+  def test_search_users_by_last_name
+    users_page = search_users('family_marker', search_fields: 'all')
+    usernames = users_page['collection'].map { |user| user['username'] }
+
+    assert_equal ['last_name_account'], usernames
+    assert_equal 1, users_page['totalCount']
+    assert_equal 1, users_page['pageCount']
+  end
+
+  def test_search_users_no_match
+    users_page = search_users('not_a_search_match', search_fields: 'all')
+
+    assert_equal [], users_page['collection']
+    assert_equal 0, users_page['totalCount']
+    assert_equal 0, users_page['pageCount']
+  end
+
+  def test_search_users_rejects_all_with_other_fields
+    get '/users', search: 'mailmarker', search_fields: 'all,email'
+
+    assert_equal 400, last_response.status
+  end
+
   def test_single_user
     user = 'fred'
     get "/users/#{user}"
@@ -243,6 +312,15 @@ def _delete_user(username)
     LinkedData::Models::User.find(@@username).first&.delete
   end
 
+  def search_users(term, search_fields: nil)
+    query_params = { search: term, pagesize: 100 }
+    query_params[:search_fields] = search_fields if search_fields
+
+    get '/users', query_params
+    assert last_response.ok?
+    MultiJson.load(last_response.body)
+  end
+
   def _create_admin_user(apikey: nil)
     user = {email: "#{@@username}@example.org", password: "pass_the_word", role: ['ADMINISTRATOR']}
     _delete_user(@@username)

test/test_case.rb

@@ -29,7 +29,11 @@
 require 'oj'
 require 'json-schema'
 require 'minitest/reporters'
-Minitest::Reporters.use! [Minitest::Reporters::SpecReporter.new(:color => true), Minitest::Reporters::MeanTimeReporter.new]
+unless ENV['RM_INFO']
+  Minitest::Reporters.use! [
+    Minitest::Reporters::SpecReporter.new(color: true),
+    Minitest::Reporters::MeanTimeReporter.new]
+end
 MAX_TEST_REDIS_SIZE = 10_000
 
 # Check to make sure you want to run if not pointed at localhost