Merge branch 'develop'

Dockerfile

@@ -14,6 +14,10 @@ COPY Gemfile* /srv/ontoportal/ontologies_linked_data/
 
 WORKDIR /srv/ontoportal/ontologies_linked_data
 
+# set rubygem and bundler to the last version supported by ruby 2.7
+# remove version after ruby v3 upgrade
+RUN gem update --system '3.4.22'
+RUN gem install bundler -v 2.4.22
 RUN gem update --system
 RUN gem install bundler
 ENV BUNDLE_PATH=/srv/ontoportal/bundle

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 657149d6b33813253fa7440252f69c04e0631190
+  revision: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f
   branch: master
   specs:
     goo (0.0.2)
@@ -32,12 +32,13 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.5)
+    addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     ansi (1.5.0)
     ast (2.4.2)
     base64 (0.2.0)
-    bcrypt (3.1.19)
+    bcrypt (3.1.20)
+    bigdecimal (3.1.5)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.2)
@@ -46,14 +47,13 @@ GEM
     daemons (1.4.1)
     date (3.3.4)
     docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    domain_name (0.6.20240107)
     email_spec (2.2.2)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
       mail (~> 2.7)
     eventmachine (1.2.7)
-    faraday (2.7.11)
+    faraday (2.8.1)
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
@@ -66,12 +66,12 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.3)
-    json_pure (2.6.3)
+    json (2.7.1)
+    json_pure (2.7.1)
     language_server-protocol (3.17.0.3)
     launchy (2.5.2)
       addressable (~> 2.8)
-    libxml-ruby (4.1.2)
+    libxml-ruby (5.0.2)
     logger (1.6.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
@@ -81,9 +81,9 @@ GEM
       net-pop
       net-smtp
     method_source (1.0.0)
-    mime-types (3.5.1)
+    mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1003)
+    mime-types-data (3.2023.1205)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -93,21 +93,22 @@ GEM
       powerbar
     multi_json (1.15.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.4)
+    net-imap (0.4.9.1)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
     net-protocol (0.2.2)
       timeout
-    net-smtp (0.4.0)
+    net-smtp (0.4.0.1)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.1)
+    oj (3.16.3)
+      bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
-    parallel (1.23.0)
-    parser (3.2.2.4)
+    parallel (1.24.0)
+    parser (3.3.0.3)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -117,7 +118,7 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
+    public_suffix (5.0.4)
     racc (1.7.3)
     rack (2.2.8)
     rack-test (0.8.3)
@@ -128,9 +129,9 @@ GEM
       addressable (>= 2.2)
     redis (5.0.8)
       redis-client (>= 0.17.0)
-    redis-client (0.18.0)
+    redis-client (0.19.1)
       connection_pool
-    regexp_parser (2.8.2)
+    regexp_parser (2.9.0)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -140,15 +141,15 @@ GEM
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.57.2)
+    rubocop (1.59.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.2.2.4)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.1, < 2.0)
+      rubocop-ast (>= 1.30.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
     rubocop-ast (1.30.0)
@@ -173,17 +174,13 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.1)
     tzinfo (0.3.62)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
     unicode-display_width (2.5.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
   aarch64-linux
   arm64-darwin-22
-  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
@@ -215,4 +212,4 @@ DEPENDENCIES
   thin
 
 BUNDLED WITH
-   2.3.15
+   2.3.22

docker-compose.yml

@@ -117,8 +117,7 @@ services:
       retries: 5
 
   agraph-ut:
-    # image: franzinc/agraph:v7.3.1
-    image: ontoportal/agraph:v7.3.1-patch1 #in place untill agraph v7.4.0 is released
+    image: franzinc/agraph:v8.0.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test

lib/ontologies_linked_data/models/ontology_submission.rb

@@ -147,6 +147,11 @@ def valid?
         return valid_result && sc
       end
 
+      def remote_pulled?
+        self.bring(:pullLocation) if self.bring?(:pullLocation)
+        self.pullLocation != nil
+      end
+
       def sanity_check
         self.bring(:ontology) if self.bring?(:ontology)
         self.ontology.bring(:summaryOnly) if self.ontology.bring?(:summaryOnly)

lib/ontologies_linked_data/security/authorization.rb

@@ -78,6 +78,8 @@ def find_apikey(env, params)
           apikey = params["apikey"]
         elsif apikey.nil? && header_auth
           token = Rack::Utils.parse_query(header_auth.split(" ")[1])
+          return unless token["token"]
+
           # Strip spaces from start and end of string
           apikey = token["token"].gsub(/\"/, "")
           # If the user apikey is passed, use that instead

test/rack/test_request_authorization.rb

@@ -60,31 +60,32 @@ def _delete_user
 
   def test_authorize
     get "/ontologies"
-    assert last_response.status == 401
+    assert_equal 401, last_response.status
+    get "/ontologies", {}, {"Authorization" => "bogus auth header"}
+    assert_equal 401, last_response.status
     get "/ontologies", {}, {"Authorization" => 'apikey token="'+@apikey+''+'"'}
-    assert last_response.status == 200
+    assert_equal 200, last_response.status
     apikey = MultiJson.load(last_response.body)
     assert @apikey.eql?(apikey)
     get "/ontologies", {}, {"Authorization" => "apikey token=#{@apikey}"}
-    assert last_response.status == 200
+    assert_equal 200, last_response.status
     apikey = MultiJson.load(last_response.body)
-    assert @apikey.eql?(apikey)
+    assert_equal @apikey, apikey
     get "/ontologies?apikey=#{@apikey}"
-    assert last_response.status == 200
+    assert_equal 200, last_response.status
     apikey = MultiJson.load(last_response.body)
-    assert @apikey.eql?(apikey)
+    assert_equal @apikey, apikey
     get "/ontologies", {}, {"Authorization" => 'apikey token="'+@apikey+'&userapikey='+@userapikey+'"'}
-    assert last_response.status == 200
+    assert_equal 200, last_response.status
     apikey = MultiJson.load(last_response.body)
-    assert @userapikey.eql?(apikey)
+    assert_equal @userapikey, apikey
     get "/ontologies", {}, {"Authorization" => "apikey token=#{@apikey}&userapikey=#{@userapikey}"}
-    assert last_response.status == 200
+    assert_equal 200, last_response.status
     apikey = MultiJson.load(last_response.body)
-    assert @userapikey.eql?(apikey)
+    assert_equal @userapikey, apikey
     get "/ontologies?apikey=#{@apikey}&userapikey=#{@userapikey}"
-    assert last_response.status == 200
+    assert_equal 200, last_response.status
     apikey = MultiJson.load(last_response.body)
-    assert @userapikey.eql?(apikey)
+    assert_equal @userapikey, apikey
   end
-
 end