Merge branch 'development' into stage

.github/workflows/docker-image.yml

@@ -3,6 +3,7 @@ name: Docker branch Images build
 on:
   push:
     branches:
+      - master
       - development
       - stage
       - test

Dockerfile

@@ -7,6 +7,7 @@ RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
   openjdk-11-jre-headless \
   raptor2-utils \
   wait-for-it \
+  libraptor2-dev \
   && rm -rf /var/lib/apt/lists/*
 
 RUN mkdir -p /srv/ontoportal/ontologies_api
@@ -24,4 +25,4 @@ COPY . /srv/ontoportal/ontologies_api
 RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
 
 EXPOSE 9393
-CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]
+CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]

Gemfile

@@ -17,6 +17,7 @@ gem 'request_store'
 gem 'parallel'
 gem 'json-ld'
 
+
 # Rack middleware
 gem 'ffi'
 gem 'rack-accept', '~> 0.4'

Gemfile.lock

@@ -11,7 +11,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 3f8b1f0b62c4334306f9ed5cb7b17a1b645e7db3
+  revision: 0e554fce49713ce4d5a742a06c2fb59a547caf47
   branch: development
   specs:
     goo (0.0.2)
@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 337dce98ec27627d14a440ff2a6ed09483cdac12
+  revision: 026c9c46baf6c0d638568528c2adcb7bcb1c2796
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -117,7 +117,7 @@ GEM
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
-    capistrano (3.18.0)
+    capistrano (3.18.1)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -183,7 +183,7 @@ GEM
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.15.0)
       google-apis-core (>= 0.14.0, < 2.a)
-    google-apis-core (0.14.0)
+    google-apis-core (0.14.1)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (~> 1.9)
       httpclient (>= 2.8.1, < 3.a)
@@ -197,12 +197,13 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
+    google-protobuf (3.25.3-x86_64-darwin)
     google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.5.0)
       google-protobuf (~> 3.18)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
-    googleapis-common-protos-types (1.13.0)
+    googleapis-common-protos-types (1.14.0)
       google-protobuf (~> 3.18)
     googleauth (1.11.0)
       faraday (>= 1.0, < 3.a)
@@ -211,6 +212,9 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
+    grpc (1.62.0-x86_64-darwin)
+      google-protobuf (~> 3.25)
+      googleapis-common-protos-types (~> 1.0)
     grpc (1.62.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
@@ -225,17 +229,17 @@ GEM
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.7.1)
+    json (2.7.2)
     json-ld (3.0.2)
       multi_json (~> 1.12)
       rdf (>= 2.2.8, < 4.0)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    json_pure (2.7.1)
+    json_pure (2.7.2)
     jwt (2.8.1)
       base64
     kgio (2.11.4)
-    libxml-ruby (5.0.2)
+    libxml-ruby (5.0.3)
     link_header (0.0.8)
     logger (1.6.0)
     macaddr (1.7.2)
@@ -269,11 +273,11 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
-    net-smtp (0.4.0.1)
+    net-smtp (0.5.0)
       net-protocol
-    net-ssh (7.2.1)
+    net-ssh (7.2.3)
     netrc (0.11.0)
-    newrelic_rpm (9.7.1)
+    newrelic_rpm (9.8.0)
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
@@ -285,7 +289,7 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.4)
+    public_suffix (5.0.5)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -342,7 +346,7 @@ GEM
       netrc (~> 0.8)
     retriable (3.1.2)
     rexml (3.2.6)
-    rsolr (2.5.0)
+    rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
     ruby-xxHash (0.4.0.2)
@@ -377,7 +381,8 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.22.0)
+    sshkit (1.22.1)
+      base64
       mutex_m
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
@@ -404,6 +409,7 @@ GEM
       hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
@@ -462,4 +468,4 @@ DEPENDENCIES
   webmock (~> 3.19.1)
 
 BUNDLED WITH
-   2.3.15
+   2.4.22

app.rb

@@ -11,8 +11,6 @@
 require 'oj'
 require 'multi_json'
 require 'cgi'
-require 'google/apis/analytics_v3'
-require 'google/api_client/auth/key_utils'
 
 # NCBO dependencies
 require 'ontologies_linked_data'

bin/ontoportal

@@ -76,7 +76,7 @@ build_docker_run_cmd() {
   local goo_path="$3"
   local sparql_client_path="$4"
 
-  local docker_run_cmd="docker compose run --rm -it"
+  local docker_run_cmd="docker compose -p ontoportal_docker run --rm -it --name api-service"
   local bash_cmd=""
 
   # Conditionally add bind mounts only if the paths are not empty
@@ -100,6 +100,7 @@ build_docker_run_cmd() {
   eval "$docker_run_cmd"
 }
 
+
 # Function to handle the "dev" and "test" options
 run_command() {
   local custom_command="$1"
@@ -177,7 +178,7 @@ run_command() {
 dev() {
   echo "Starting OntoPortal API development server..."
 
-  local custom_command="bundle exec shotgun --host 0.0.0.0  --env=development"
+  local custom_command="bundle exec shotgun --host 0.0.0.0  --env=development --port 9393"
   run_command "$custom_command" "$@"
 }
 

controllers/analytics_controller.rb

@@ -1,13 +1,13 @@
 require 'csv'
 
-class OntologyAnalyticsController < ApplicationController
+class AnalyticsController < ApplicationController
 
   ##
   # get all ontology analytics for a given year/month combination
   # TODO use a namespace analytics after migration the old OntologyAnalyticsController
   namespace "/data/analytics" do
 
-    get 'ontologies' do
+    get '/ontologies' do
       expires 86400, :public
       year = year_param(params)
       error 400, "The year you supplied is invalid. Valid years start with 2 and contain 4 digits." if params["year"] && !year
@@ -20,7 +20,7 @@ class OntologyAnalyticsController < ApplicationController
     end
 
 
-    get 'users' do
+    get '/users' do
       expires 86400, :public
       year = year_param(params)
       error 400, "The year you supplied is invalid. Valid years start with 2 and contain 4 digits." if params["year"] && !year
@@ -30,7 +30,7 @@ class OntologyAnalyticsController < ApplicationController
       reply analytics['all_users']
     end
 
-    get 'page_visits' do
+    get '/page_visits' do
       expires 86400, :public
       year = year_param(params)
       error 400, "The year you supplied is invalid. Valid years start with 2 and contain 4 digits." if params["year"] && !year

controllers/dereference_resource_controller.rb

@@ -0,0 +1,55 @@
+require_relative '../test/test_case'
+
+use Rack::ContentNegotiation
+
+class DereferenceResourceController < ApplicationController
+  namespace "/ontologies" do
+    get "/:acronym/resolve/:uri" do
+      acronym = params[:acronym]
+      uri = params[:uri]
+
+      if acronym.blank? || uri.blank?
+        error 500, "Usage: ontologies/:acronym/resolve/:uri?output_format= OR POST: acronym, uri, output_format parameters"
+      end
+
+      output_format = env["format"].presence || params[:output_format].presence || 'application/n-triples'
+
+      process_request(acronym, uri, output_format)
+    end
+
+    private
+
+    def process_request(acronym_param, uri_param, output_format)
+      acronym = acronym_param
+      uri = URI.decode_www_form_component(uri_param)
+
+      error 500, "INVALID URI" unless valid_url?(uri)
+      sub = LinkedData::Models::Ontology.find(acronym).first&.latest_submission
+
+      error 500, "Ontology not found" unless  sub
+
+      r = Resource.new(sub.id, uri)
+      case output_format
+      when 'application/ld+json', 'application/json'
+          r.to_json
+      when 'application/rdf+xml', 'application/xml'
+          r.to_xml
+      when 'text/turtle'
+          r.to_turtle
+      when 'application/n-triples'
+          r.to_ntriples
+      else
+          error 500, "Invalid output format, valid format are: application/json, application/ld+json,  application/xml, application/rdf+xml, text/turtle and application/n-triples"
+      end
+
+
+    end
+
+    def valid_url?(url)
+      uri = URI.parse(url)
+      uri.is_a?(URI::HTTP) || uri.is_a?(URI::HTTPS)
+    rescue URI::InvalidURIError
+      false
+    end
+  end
+end

controllers/slices_controller.rb

@@ -41,17 +41,20 @@ class SlicesController < ApplicationController
     ##
     # Create a new slice
     post do
+      error 403, "Access denied" unless current_user && current_user.admin?
       create_slice
     end
 
     # Delete a slice
     delete '/:slice' do
+      error 403, "Access denied" unless current_user && current_user.admin?
       LinkedData::Models::Slice.find(params[:slice]).first.delete
       halt 204
     end
 
     # Update an existing slice
     patch '/:slice' do
+      error 403, "Access denied" unless current_user && current_user.admin?
       slice = LinkedData::Models::Slice.find(params[:slice]).include(LinkedData::Models::Slice.attributes(:all)).first
       populate_from_params(slice, params)
       if slice.valid?
@@ -61,7 +64,7 @@ class SlicesController < ApplicationController
       end
       halt 204
     end
-    
+
     private
 
     def create_slice

controllers/users_controller.rb

@@ -80,6 +80,7 @@ class UsersController < ApplicationController
     # Update an existing submission of an user
     patch '/:username' do
       user = User.find(params[:username]).include(User.attributes).first
+      params.delete("role") unless current_user.admin?
       populate_from_params(user, params)
       if user.valid?
         user.save
@@ -102,6 +103,7 @@ def create_user
       params ||= @params
       user = User.find(params["username"]).first
       error 409, "User with username `#{params["username"]}` already exists" unless user.nil?
+      params.delete("role") unless current_user.admin?
       user = instance_from_params(User, params)
       if user.valid?
         user.save(send_notifications: false)

helpers/users_helper.rb

@@ -23,9 +23,7 @@ def send_reset_token(email, username)
         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