Feature: create graphs endpoints to list, create and delete (#115)

* fix: docker-compose app volume * fix ncbo_ontology_recommender version * add admin graphs controller to list triple store graphs and delete them * update gemfile * extract graph count path in a constant * add graphs admin action unit tests
ontoportal-lirmm · Jan 23, 2025 · 07290db · 07290db
1 parent 909a8aa
commit 07290db
Show file tree

Hide file tree

Showing 8 changed files with 151 additions and 60 deletions.
diff --git a/.ruby-version b/.ruby-version
@@ -1 +1 @@
-3.0.6
+2.7.5
diff --git a/Gemfile b/Gemfile
@@ -47,8 +47,8 @@ gem 'redcarpet'
 
 # 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'
-gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
-gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
+gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'development'
+gem 'ncbo_ontology_recommender', git: 'https://github.com/ontoportal-lirmm/ncbo_ontology_recommender.git', branch: 'development'
 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'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,17 +1,6 @@
-GIT
-  remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 9dbd4f179e42c52095129d353a5ac584e9bd47f3
-  branch: master
-  specs:
-    ncbo_ontology_recommender (0.0.1)
-      goo
-      ncbo_annotator
-      ontologies_linked_data
-      redis
-
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: f8ac7b00e8d8b46d1eea04de014175525c1cdd83
+  revision: 27300f28ca6c656c7e78af65013d88b792a6312f
   branch: development
   specs:
     goo (0.0.2)
@@ -40,8 +29,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: bed0ff08408ad1241db3513992ad025a253eeef0
-  branch: master
+  revision: dd736917974f13ac7558e0d2a61a84030d82acaa
+  branch: development
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -55,9 +44,20 @@ GIT
       redis
       rufus-scheduler (~> 2.0.24)
 
+GIT
+  remote: https://github.com/ontoportal-lirmm/ncbo_ontology_recommender.git
+  revision: a0e36c89e6e2f8502cac288df2992625649dad7a
+  branch: development
+  specs:
+    ncbo_ontology_recommender (0.0.1)
+      goo
+      ncbo_annotator
+      ontologies_linked_data
+      redis
+
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 312ef426eeaa461e88fa23124ea5fd531f4276ba
+  revision: 6cb18910e322645e3cc3490951d10f19468da52f
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -77,7 +77,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/sparql-client.git
-  revision: 59251e59346c9a69a67c88552ba55a1244eec602
+  revision: 4364d34e9e4c411f1dd0ea706bf052465bf0b467
   branch: development
   specs:
     sparql-client (3.2.2)
@@ -117,9 +117,9 @@ GEM
     base64 (0.2.0)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
-    bigdecimal (3.1.8)
+    bigdecimal (3.1.9)
     builder (3.3.0)
-    capistrano (3.19.1)
+    capistrano (3.19.2)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -132,13 +132,13 @@ GEM
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.3.4)
-    connection_pool (2.4.1)
+    concurrent-ruby (1.3.5)
+    connection_pool (2.5.0)
     crack (0.4.5)
       rexml
     cube-ruby (0.0.3)
     dante (0.2.0)
-    date (3.3.4)
+    date (3.4.1)
     declarative (0.0.20)
     docile (1.4.1)
     domain_name (0.6.20240107)
@@ -164,12 +164,12 @@ GEM
     google-analytics-data (0.6.1)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.13.1)
+    google-analytics-data-v1beta (0.14.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
       google-apis-core (>= 0.15.0, < 2.a)
-    google-apis-core (0.15.1)
+    google-apis-core (0.16.0)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (~> 1.9)
       httpclient (>= 2.8.3, < 3.a)
@@ -188,7 +188,7 @@ GEM
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
-    googleapis-common-protos-types (1.16.0)
+    googleapis-common-protos-types (1.18.0)
       google-protobuf (>= 3.18, < 5.a)
     googleauth (1.11.2)
       faraday (>= 1.0, < 3.a)
@@ -203,27 +203,27 @@ GEM
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
-    hashdiff (1.1.1)
+    hashdiff (1.1.2)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.7)
+    http-cookie (1.0.8)
       domain_name (~> 0.5)
     httpclient (2.8.3)
-    i18n (1.14.6)
+    i18n (1.14.7)
       concurrent-ruby (~> 1.0)
-    json (2.7.5)
+    json (2.9.1)
     json-ld (3.0.2)
       multi_json (~> 1.12)
       rdf (>= 2.2.8, < 4.0)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    jwt (2.9.3)
+    jwt (2.10.1)
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.3)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.1)
+    logger (1.6.5)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -235,49 +235,49 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1001)
+    mime-types-data (3.2025.0107)
     mini_mime (1.1.5)
-    minitest (5.25.1)
+    minitest (5.25.4)
     minitest-hooks (1.5.2)
       minitest (> 5.3)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    mutex_m (0.2.0)
-    net-http-persistent (4.0.4)
+    mutex_m (0.3.0)
+    net-http-persistent (4.0.5)
       connection_pool (~> 2.2)
-    net-imap (0.4.17)
+    net-imap (0.4.18)
       date
       net-protocol
     net-pop (0.1.2)
       net-protocol
     net-protocol (0.2.2)
       timeout
-    net-scp (4.0.0)
+    net-scp (4.1.0)
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
     net-smtp (0.5.0)
       net-protocol
     net-ssh (7.3.0)
     netrc (0.11.0)
-    newrelic_rpm (9.14.0)
-    oj (3.16.6)
+    newrelic_rpm (9.16.1)
+    oj (3.16.9)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
-    ostruct (0.6.0)
+    ostruct (0.6.1)
     parallel (1.26.3)
     parseconfig (1.1.2)
-    parser (3.3.5.0)
+    parser (3.3.7.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
       mail (>= 2.0)
-    pry (0.14.2)
+    pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
@@ -295,7 +295,7 @@ GEM
       rack (>= 1.2.0)
     rack-protection (1.5.5)
       rack
-    rack-test (2.1.0)
+    rack-test (2.2.0)
       rack (>= 1.3)
     rack-timeout (0.7.0)
     rainbow (3.1.1)
@@ -319,14 +319,14 @@ GEM
     redcarpet (3.6.0)
     redis (5.3.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.2)
+    redis-client (0.23.2)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
     redis-store (1.11.0)
       redis (>= 4, < 6)
-    regexp_parser (2.9.2)
+    regexp_parser (2.10.0)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
@@ -339,26 +339,26 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.3.9)
+    rexml (3.4.0)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.67.0)
+    rubocop (1.71.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 2.4, < 3.0)
-      rubocop-ast (>= 1.32.2, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.36.2, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.33.0)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.37.0)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
     ruby2_keywords (0.0.5)
-    rubyzip (2.3.2)
+    rubyzip (2.4.1)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
     signet (0.19.0)
@@ -397,13 +397,15 @@ GEM
     systemu (2.6.5)
     temple (0.10.3)
     thread_safe (0.3.6)
-    tilt (2.4.0)
-    timeout (0.4.1)
+    tilt (2.6.0)
+    timeout (0.4.3)
     trailblazer-option (0.1.2)
     tzinfo (1.2.11)
       thread_safe (~> 0.1)
     uber (0.1.0)
-    unicode-display_width (2.6.0)
+    unicode-display_width (3.1.4)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
@@ -416,7 +418,7 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.8.2)
+    webrick (1.9.1)
 
 PLATFORMS
   x86_64-linux

diff --git a/config/environments/test.rb b/config/environments/test.rb
@@ -102,5 +102,6 @@
 NcboCron.config do |config|
   config.redis_host = REDIS_PERSISTENT_HOST.to_s
   config.redis_port = REDIS_PORT.to_i
+  config.graphs_counts_report_path = './test/ontologies_report.json'
 #  config.ontology_report_path = REPORT_PATH
 end
diff --git a/controllers/admin_graphs_controller.rb b/controllers/admin_graphs_controller.rb
@@ -0,0 +1,34 @@
+require 'ncbo_cron/graphs_counts'
+class AdminGraphsController < ApplicationController
+
+  namespace '/admin' do
+    GRAPH_COUNT_REPORT_PATH = NcboCron.settings.graphs_counts_report_path
+    before do
+      if LinkedData.settings.enable_security && (!env['REMOTE_USER'] || !env['REMOTE_USER'].admin?)
+        error 403, 'Access denied'
+      end
+    end
+
+    get '/graphs' do
+      output = NcboCron::GraphsCounts.new(nil, GRAPH_COUNT_REPORT_PATH).read_graph_counts
+      reply output
+    end
+
+    post '/graphs' do
+      generate_graphs_counts
+      reply({ message: 'Graph counts generated', status: 200 })
+    end
+
+    delete '/graphs' do
+      url = params['url']
+      error 400, 'You must provide a valid URL for the graph to delete' if url.blank?
+      Goo.sparql_data_client.delete_graph(url)
+      generate_graphs_counts
+      reply({ message: "Graph #{url} deleted", status: 200 })
+    end
+
+    def generate_graphs_counts
+      NcboCron::GraphsCounts.new(nil, GRAPH_COUNT_REPORT_PATH).run
+    end
+  end
+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
-      - .:/srv/ontoportal/ontologies_api
+      - app_api:/srv/ontoportal/ontologies_api
       - repository:/srv/ontoportal/data/repository
 
   ncbo_cron:
@@ -199,4 +199,3 @@ volumes:
   mgrep:
   logs:
   history:
-
diff --git a/mise.toml b/mise.toml
@@ -0,0 +1,2 @@
+[tools]
+ruby = "2.7.8"