Merge branch 'feature/add-portal-config-endpoint' into test

ontoportal-lirmm · Sep 4, 2024 · c111f51 · c111f51
2 parents 2ffbd55 + fc6635f
commit c111f51
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Showing 5 changed files with 63 additions and 25 deletions.
diff --git a/Gemfile b/Gemfile
@@ -19,7 +19,7 @@ gem 'json-ld'
 
 
 # Rack middleware
-gem 'ffi'
+gem 'ffi', '~> 1.16.3'
 gem 'rack-accept', '~> 0.4'
 gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
 gem 'rack-cache', '~> 1.13.0'
@@ -51,7 +51,7 @@ gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branc
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'feature/add-portal-config-model'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -57,8 +57,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 9605eb44c4271c60bedda0520e85d8c3fa2513ac
-  branch: development
+  revision: d893c08a2c2f11c743fad520873b7f98b0805240
+  branch: feature/add-portal-config-model
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -108,12 +108,13 @@ GEM
       multi_json (~> 1.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
-    airbrussh (1.5.2)
+    airbrussh (1.5.3)
       sshkit (>= 1.6.1, != 1.7.0)
     backports (3.25.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
+    bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (1.4.2)
     builder (3.3.0)
     capistrano (3.19.1)
@@ -164,7 +165,7 @@ GEM
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
-    ffi (1.17.0)
+    ffi (1.16.3)
     gapic-common (0.21.1)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
@@ -178,7 +179,7 @@ GEM
     google-analytics-data (0.6.1)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.13.0)
+    google-analytics-data-v1beta (0.13.1)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
@@ -211,11 +212,11 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.65.2-x86_64-linux)
+    grpc (1.65.2-x86_64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.62.0-x86_64-linux)
-      google-protobuf (~> 3.25)
+    grpc (1.65.2-x86_64-linux)
+      google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
       temple (>= 0.8.0)
@@ -239,7 +240,7 @@ GEM
     kgio (2.11.4)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.0)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -250,7 +251,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0820)
+    mime-types-data (3.2024.0903)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
@@ -261,7 +262,7 @@ GEM
     mutex_m (0.2.0)
     net-http-persistent (4.0.2)
       connection_pool (~> 2.2)
-    net-imap (0.4.14)
+    net-imap (0.4.15)
       date
       net-protocol
     net-pop (0.1.2)
@@ -276,7 +277,7 @@ GEM
       net-protocol
     net-ssh (7.2.3)
     netrc (0.11.0)
-    newrelic_rpm (9.12.0)
+    newrelic_rpm (9.13.0)
     oj (3.16.1)
     omni_logger (0.1.4)
       logger
@@ -344,8 +345,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.3.6)
-      strscan
+    rexml (3.3.7)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -386,7 +386,6 @@ GEM
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
-    strscan (3.1.0)
     systemu (2.6.5)
     temple (0.10.3)
     tilt (2.4.0)
@@ -423,7 +422,7 @@ DEPENDENCIES
   cube-ruby
   ed25519 (>= 1.2, < 2.0)
   faraday (~> 1.9)
-  ffi
+  ffi (~> 1.16.3)
   goo!
   haml (~> 5.2.2)
   json-ld
@@ -467,4 +466,4 @@ DEPENDENCIES
   webmock (~> 3.19.1)
 
 BUNDLED WITH
-   2.4.22
+   2.3.23
diff --git a/config/environments/config.rb.sample b/config/environments/config.rb.sample
@@ -87,6 +87,37 @@ LinkedData.config do |config|
         link: 'https://www.googleapis.com/oauth2/v3/userinfo'
       }
     }
+        config.ui_name                       = 'Bioportal'
+        config.title                         = 'NCBO BioPortal'
+        config.description                   = "The world's most comprehensive repository of biomedical ontologies "
+        config.color                         = '#234979'
+        config.logo                          = ''
+        config.fundedBy                      = [
+            {
+              img_src: 'https://identity.stanford.edu/wp-content/uploads/sites/3/2020/07/block-s-right.png',
+              url: 'https://www.stanford.edu',
+
+            },
+            {
+              img_src: 'https://ontoportal.org/images/logo.png',
+              url: 'https://ontoportal.org/',
+            }
+        ]
+        config.federated_portals = {
+              'agroportal' => {
+                api: 'http://data.agroportal.lirmm.fr',
+                ui: 'http://agroportal.lirmm.fr',
+                apikey: '1cfae05f-9e67-486f-820b-b393dec5764b',
+                color: '#1e2251'
+              },
+              'bioportal' => {
+                      api: 'http://data.bioontology.org',
+                      ui: 'http://bioportal.bioontology.org',
+                      apikey: '4a5011ea-75fa-4be6-8e89-f45c8c84844e',
+                      color: '#234979'
+               },
+
+        }
 end
 
 Annotator.config do |config|

diff --git a/controllers/home_controller.rb b/controllers/home_controller.rb
@@ -4,7 +4,7 @@
 class HomeController < ApplicationController
 
   CLASS_MAP = {
-      Property: "LinkedData::Models::ObjectProperty"
+    Property: "LinkedData::Models::ObjectProperty"
   }
 
   namespace "/" do
@@ -28,14 +28,22 @@ class HomeController < ApplicationController
         next if route.length < 3 || route.split("/").length > 2
         route_no_slash = route.gsub("/", "")
         context[route_no_slash] = route_to_class_map[route].type_uri.to_s if route_to_class_map[route] && route_to_class_map[route].respond_to?(:type_uri)
-        routes_hash[route_no_slash] = LinkedData.settings.rest_url_prefix+route_no_slash
+        routes_hash[route_no_slash] = LinkedData.settings.rest_url_prefix + route_no_slash
       end
-      routes_hash["@context"] = context
-      reply ({links: routes_hash})
+
+      config = LinkedData::Models::PortalConfig.current_portal_config
+
+      federated_portals = config.federated_portals
+      federated_portals. transform_values! { |v| v.delete(:apikey) ; v }
+      config.init_federated_portals_settings(federated_portals)
+
+      config.class.link_to *routes_hash.map { |key, url| LinkedData::Hypermedia::Link.new(key, url, context[key]) }
+
+      reply config
     end
 
     get "documentation" do
-      @metadata_all = metadata_all.sort {|a,b| a[0].name <=> b[0].name}
+      @metadata_all = metadata_all.sort { |a, b| a[0].name <=> b[0].name }
       haml "documentation/documentation".to_sym, :layout => "documentation/layout".to_sym
     end
 

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -49,7 +49,7 @@ services:
       - "9393:9393"
     volumes:
       # bundle volume for hosting gems installed by bundle; it speeds up gem install in local development
-      - app_api:/srv/ontoportal/ontologies_api
+      - .:/srv/ontoportal/ontologies_api
       - repository:/srv/ontoportal/data/repository
 
   ncbo_cron: