Merge to master: release 3.0.1

Dockerfile

@@ -30,6 +30,7 @@ RUN apt-get update && \
          git \
          curl \
          libffi-dev \
+         pandoc \
      pkg-config && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
@@ -48,10 +49,6 @@ COPY . .
 RUN cp config/environments/config.rb.sample config/environments/development.rb && \
     cp config/environments/config.rb.sample config/environments/production.rb
 
-# Create non-root user
-RUN adduser --disabled-password --gecos "" appuser && \
-    chown -R appuser:appuser /srv/ontoportal
-
 # Expose port
 EXPOSE 9393
 

Gemfile

@@ -47,6 +47,7 @@ gem 'unicorn-worker-killer'
 # Templating
 gem 'haml', '~> 5.2.2'
 gem 'rack-contrib'
+gem 'pandoc-ruby'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'

Gemfile.lock

@@ -29,7 +29,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: c863617c47ee224905d845a4baa5558b674a7b91
+  revision: cc4cd9218db7181c4843772631b7f3a96c74a4aa
   branch: master
   specs:
     ncbo_cron (0.0.1)
@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 728ac871578d607d1c4e4e7a4f0800e8d263890f
+  revision: b321d73a28b4f60fc5969da7a071b3c19c1a84f3
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -274,7 +274,8 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.8)
       domain_name (~> 0.5)
-    httpclient (2.8.3)
+    httpclient (2.9.0)
+      mutex_m
     i18n (1.14.7)
       concurrent-ruby (~> 1.0)
     json (2.10.1)
@@ -308,7 +309,7 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2025.0204)
+    mime-types-data (3.2025.0220)
     mini_mime (1.1.5)
     minitest (5.25.4)
     minitest-fail-fast (0.1.0)
@@ -357,6 +358,7 @@ GEM
       logger
     os (1.1.4)
     ostruct (0.6.1)
+    pandoc-ruby (2.1.10)
     parallel (1.26.3)
     parseconfig (1.1.2)
     parser (3.3.7.1)
@@ -408,7 +410,7 @@ GEM
     rdf-xsd (3.3.0)
       rdf (~> 3.3)
       rexml (~> 3.2)
-    redis (5.3.0)
+    redis (5.4.0)
       redis-client (>= 0.22.0)
     redis-client (0.23.2)
       connection_pool
@@ -434,7 +436,7 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.72.1)
+    rubocop (1.72.2)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
@@ -545,6 +547,7 @@ DEPENDENCIES
   newrelic_rpm
   oj
   ontologies_linked_data!
+  pandoc-ruby
   parallel
   parseconfig
   rack

controllers/artefacts.rb

@@ -4,11 +4,9 @@ class ArtefactsController < ApplicationController
         # Get all Semantic Artefacts
         get do
             check_last_modified_collection(LinkedData::Models::SemanticArtefact)
-            options = {
-                also_include_views: params['also_include_views'] ||= false,
-                includes: LinkedData::Models::SemanticArtefact.goo_attrs_to_load([])
-            }
-            artefacts = LinkedData::Models::SemanticArtefact.all_artefacts(options)
+            attributes, page, pagesize, _, _ = settings_params(LinkedData::Models::SemanticArtefact)
+            pagesize = 20 if params["pagesize"].nil?
+            artefacts = LinkedData::Models::SemanticArtefact.all_artefacts(attributes, page, pagesize)
             reply artefacts
         end
 

controllers/home_controller.rb

@@ -31,15 +31,36 @@ class HomeController < ApplicationController
         routes_hash[route_no_slash] = LinkedData.settings.rest_url_prefix + route_no_slash
       end
 
-      config = LinkedData::Models::PortalConfig.current_portal_config
+      catalog_class = LinkedData::Models::SemanticArtefactCatalog
+      catalog = catalog_class.all.first || create_catalog
+      attributes_to_include =  includes_param[0] == :all ? catalog_class.attributes(:all) : catalog_class.goo_attrs_to_load(includes_param)
+      catalog.bring(*attributes_to_include)
+      if catalog.loaded_attributes.include?(:federated_portals)
+        catalog.federated_portals = catalog.federated_portals.map { |item| JSON.parse(item.gsub('=>', ':').gsub('\"', '"')) }
+        catalog.federated_portals.each { |item| item.delete('apikey') }
+      end
+      if catalog.loaded_attributes.include?(:fundedBy)
+        catalog.fundedBy = catalog.fundedBy.map { |item| JSON.parse(item.gsub('=>', ':').gsub('\"', '"')) } 
+      end
+      catalog.class.link_to *routes_hash.map { |key, url| LinkedData::Hypermedia::Link.new(key, url, context[key]) }
+
+      reply catalog
+    end
 
-      federated_portals = config.federated_portals
-      federated_portals.transform_values! { |v| v.delete(:apikey); v }
-      config.init_federated_portals_settings(federated_portals)
-      config.id = RDF::URI.new(LinkedData.settings.id_url_prefix)
-      config.class.link_to *routes_hash.map { |key, url| LinkedData::Hypermedia::Link.new(key, url, context[key]) }
+    patch do
+      catalog = LinkedData::Models::SemanticArtefactCatalog.where.first
+      error 422, "There is no catalog configs in the triple store" if catalog.nil?
+      populate_from_params(catalog, params)
+      if catalog.valid?
+        catalog.save
+        status 200
+      else
+        error 422, catalog.errors
+      end
+    end
 
-      reply config
+    get "doc/api" do
+      redirect "/documentation", 301
     end
 
     get "documentation" do
@@ -49,7 +70,20 @@ class HomeController < ApplicationController
 
     private
 
-
+    def create_catalog
+      catalog = nil
+      catalogs = LinkedData::Models::SemanticArtefactCatalog.all
+      if catalogs.nil? || catalogs.empty?
+          catalog = instance_from_params(LinkedData::Models::SemanticArtefactCatalog, {"test_attr_to_persist" => "test_to_persist"})
+          if catalog.valid?
+              catalog.save
+          else
+              error 422, catalog.errors
+          end
+      end
+      catalog
+  end
+
 
   end
 end

controllers/submission_metadata_controller.rb

@@ -13,4 +13,7 @@ class SubmissionMetadataController < ApplicationController
     reply klass_metadata(LinkedData::Models::Ontology, "ontology_metadata")
   end
 
+  get "/catalog_metadata" do
+    reply klass_metadata(LinkedData::Models::SemanticArtefactCatalog, "catalog_metadata")
+  end
 end