Merge to master: Release 2.3.3 - Multi provider auth

.dockerignore

@@ -9,3 +9,4 @@ tmp/*
 # Editor temp files
 *.swp
 *.swo
+test/solr

Gemfile

@@ -13,6 +13,7 @@ gem 'rake', '~> 10.0'
 gem 'sinatra', '~> 1.0'
 gem 'sinatra-advanced-routes'
 gem 'sinatra-contrib', '~> 1.0'
+gem 'request_store'
 
 # Rack middleware
 gem 'ffi'

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: f440ae855a217807fead1d20629a0f187997b973
+  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
   branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -11,7 +11,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: bd7154217438c3b9160e0e9b495c7c718b55fbf8
+  revision: 74ea47defc7f6260b045a6c6997bbe6a59c7bf62
   branch: master
   specs:
     goo (0.0.2)
@@ -53,7 +53,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: f44f7baa96eb3ee10dfab4a8aca154161ba7dd89
+  revision: 80a331d053ea04397a903452288c2186822c340c
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -108,7 +108,8 @@ GEM
     airbrussh (1.5.0)
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.24.1)
-    bcrypt (3.1.19)
+    base64 (0.2.0)
+    bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
@@ -130,11 +131,10 @@ GEM
       rexml
     cube-ruby (0.0.3)
     dante (0.2.0)
-    date (3.3.3)
+    date (3.3.4)
     declarative (0.0.20)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20231109)
     ed25519 (1.3.0)
     faraday (1.10.3)
       faraday-em_http (~> 1.0)
@@ -164,7 +164,7 @@ GEM
       ffi (~> 1.0)
     google-apis-analytics_v3 (0.13.0)
       google-apis-core (>= 0.11.0, < 2.a)
-    google-apis-core (0.11.1)
+    google-apis-core (0.11.2)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (>= 0.16.2, < 2.a)
       httpclient (>= 2.8.1, < 3.a)
@@ -189,14 +189,14 @@ GEM
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
+    json (2.7.1)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    json_pure (2.6.3)
+    json_pure (2.7.1)
     jwt (2.7.1)
     kgio (2.11.4)
-    libxml-ruby (4.1.1)
-    logger (1.5.3)
+    libxml-ruby (4.1.2)
+    logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -216,20 +216,21 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.1)
+    net-imap (0.4.7)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
-    net-protocol (0.2.1)
+    net-protocol (0.2.2)
       timeout
     net-scp (4.0.0)
       net-ssh (>= 2.6.5, < 8.0.0)
     net-smtp (0.4.0)
       net-protocol
     net-ssh (7.2.0)
     netrc (0.11.0)
-    newrelic_rpm (9.5.0)
+    newrelic_rpm (9.6.0)
+      base64
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
@@ -240,7 +241,7 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -275,6 +276,8 @@ GEM
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
       uber (< 0.2.0)
+    request_store (1.5.1)
+      rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -317,20 +320,17 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.21.5)
+    sshkit (1.21.6)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
     temple (0.10.3)
     tilt (2.3.0)
-    timeout (0.4.0)
+    timeout (0.4.1)
     trailblazer-option (0.1.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
@@ -346,6 +346,8 @@ GEM
     webrick (1.8.1)
 
 PLATFORMS
+  x86_64-darwin-21
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
@@ -389,6 +391,7 @@ DEPENDENCIES
   redis-activesupport
   redis-rack-cache (~> 2.0)
   redis-store (= 1.9.1)
+  request_store
   shotgun!
   simplecov
   simplecov-cobertura
@@ -401,4 +404,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.3.23
+   2.4.21

config/environments/test.rb

@@ -55,6 +55,24 @@
       "apikey" => "1cfae05f-9e67-486f-820b-b393dec5764b"
     }
   }
+  config.oauth_providers = {
+    github: {
+      check: :access_token,
+      link: 'https://api.github.com/user'
+    },
+    keycloak: {
+      check: :jwt_token,
+      cert: 'KEYCLOAK_SECRET_KEY'
+    },
+    orcid: {
+      check: :access_token,
+      link: 'https://pub.orcid.org/v3.0/me'
+    },
+    google: {
+      check: :access_token,
+      link: 'https://www.googleapis.com/oauth2/v3/userinfo'
+    }
+  }
 end
 
 Annotator.config do |config|

controllers/users_controller.rb

@@ -1,14 +1,17 @@
 class UsersController < ApplicationController
   namespace "/users" do
     post "/authenticate" do
-      user_id       = params["user"]
-      user_password = params["password"]
+
       # Modify params to show all user attributes
       params["display"] = User.attributes.join(",")
-      user = User.find(user_id).include(User.goo_attrs_to_load(includes_param) + [:passwordHash]).first
-      authenticated = user.authenticate(user_password) unless user.nil?
-      error 401, "Username/password combination invalid" unless authenticated
-      user.show_apikey = true
+
+      if params["access_token"]
+        user = oauth_authenticate(params)
+        user.bring(*User.goo_attrs_to_load(includes_param))
+      else
+        user = login_password_authenticate(params)
+      end
+      user.show_apikey = true unless user.nil?
       reply user
     end
 
@@ -20,17 +23,13 @@ class UsersController < ApplicationController
     post "/create_reset_password_token" do
       email    = params["email"]
       username = params["username"]
-      user = LinkedData::Models::User.where(email: email, username: username).include(LinkedData::Models::User.attributes).first
-      error 404, "User not found" unless user
-      reset_token = token(36)
-      user.resetToken = reset_token
+      user = send_reset_token(email, username)
+
       if user.valid?
-        user.save(override_security: true)
-        LinkedData::Utils::Notifications.reset_password(user, reset_token)
+        halt 204
       else
         error 422, user.errors
       end
-      halt 204
     end
 
     ##
@@ -42,11 +41,11 @@ class UsersController < ApplicationController
       email             = params["email"] || ""
       username          = params["username"] || ""
       token             = params["token"] || ""
+
       params["display"] = User.attributes.join(",") # used to serialize everything via the serializer
-      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)
-        user.show_apikey = true
+
+      user, token_accepted = reset_password(email, username, token)
+      if token_accepted
         reply user
       else
         error 403, "Password reset not authorized with this token"
@@ -98,27 +97,14 @@ class UsersController < ApplicationController
 
     private
 
-    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)] }
-      token
-    end
 
     def create_user
       params ||= @params
       user = User.find(params["username"]).first
       error 409, "User with username `#{params["username"]}` already exists" unless user.nil?
       user = instance_from_params(User, params)
       if user.valid?
-        user.save
-        # Send an email to the administrator to warn him about the newly created user
-        begin
-          if !LinkedData.settings.admin_emails.nil? && !LinkedData.settings.admin_emails.empty?
-            LinkedData::Utils::Notifications.new_user(user)
-          end
-        rescue Exception => e
-        end
+        user.save(send_notifications: false)
       else
         error 422, user.errors
       end

docker-compose.yml

@@ -75,10 +75,14 @@ services:
 
   redis-ut:
     image: redis
+    ports:
+      - 6379:6379
 
   4store-ut:
     image: bde2020/4store
     #volume: fourstore:/var/lib/4store
+    ports:
+      - 9000:9000
     command: >
       bash -c "4s-backend-setup --segments 4 ontoportal_kb
       && 4s-backend ontoportal_kb
@@ -88,10 +92,20 @@ services:
 
 
   solr-ut:
-    image: ontoportal/solr-ut:0.1
+    image: solr:8
+    volumes:
+      - ./test/solr/configsets:/configsets:ro
+    ports:
+      - "8983:8983"
+    command: >
+      bash -c "precreate-core term_search_core1 /configsets/term_search
+      && precreate-core prop_search_core1 /configsets/property_search
+      && solr-foreground"
 
   mgrep-ut:
     image: ontoportal/mgrep-ncbo:0.1
+    ports:
+      - "55556:55555"
 
   agraph-ut:
     image: franzinc/agraph:v7.3.0

helpers/search_helper.rb

@@ -345,6 +345,7 @@ def populate_classes_from_search(classes, ontology_acronyms=nil)
           doc[:submission] = old_class.submission
           doc[:properties] = MultiJson.load(doc.delete(:propertyRaw)) if include_param_contains?(:properties)
           instance = LinkedData::Models::Class.read_only(doc)
+          instance.prefLabel =  instance.prefLabel.first if instance.prefLabel.is_a?(Array)
           classes_hash[ont_uri_class_uri] = instance
         end
 

helpers/users_helper.rb

@@ -17,6 +17,55 @@ def filter_for_user_onts(obj)
 
         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
+        reset_token = token(36)
+        user.resetToken = reset_token
+
+        return user if user.valid?
+
+        user.save(override_security: true)
+        LinkedData::Utils::Notifications.reset_password(user, reset_token)
+        user
+      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)] }
+        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)).first
+
+        error 404, "User not found" unless user
+
+        user.show_apikey = true
+
+        [user, token.eql?(user.resetToken)]
+      end
+
+      def oauth_authenticate(params)
+        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?
+        user
+      end
+
+      def login_password_authenticate(params)
+        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
+
+        user
+      end
     end
   end
 end