Merge branch 'development' into feature/add-query-logs-endpoints

.ruby-version

@@ -1 +1 @@
-3.0.6
+2.7.5

Gemfile

@@ -47,11 +47,11 @@ 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_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: 'feature/add-triple-store-logging'
+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: 'feature/add-queries-logging-'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
 
 
 group :development do

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: e7831230455c5d72447d38537049ff5b8ec8d4ce
-  branch: feature/add-triple-store-logging
+  revision: 5825dc1f9d0ff439b1ba9d8f78fa7bb20b1c65d0
+  branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -29,8 +29,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: d50c624868dec11cb0afcc88ba422d021c77926c
-  branch: master
+  revision: dd736917974f13ac7558e0d2a61a84030d82acaa
+  branch: development
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -57,8 +57,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 32c1aed4221e1b5f50a7931137092ee4ba62ca94
-  branch: feature/add-queries-logging-
+  revision: 6cb18910e322645e3cc3490951d10f19468da52f
+  branch: development
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -77,7 +77,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/sparql-client.git
-  revision: d4737ff08f33517cf93b4d82c78a471017991d97
+  revision: d4a226e75eb4aeaaf42720eac4f23f55380a0bd3
   branch: development
   specs:
     sparql-client (3.2.2)
@@ -254,7 +254,7 @@ GEM
       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)
@@ -343,7 +343,7 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.70.0)
+    rubocop (1.71.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)

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

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

mise.toml

@@ -0,0 +1,2 @@
+[tools]
+ruby = "2.7.8"

test/controllers/test_graphs_admin_controller.rb

@@ -0,0 +1,53 @@
+require_relative '../test_case'
+
+class TestGraphAdminController < TestCase
+  def setup
+    ontologies = LinkedData::Models::Ontology.all
+    if ontologies.empty?
+      LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
+      @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: false)
+    end
+    file_path = AdminGraphsController::GRAPH_COUNT_REPORT_PATH
+    File.delete(file_path) if File.exist?(file_path)
+  end
+
+  def test_initial_graphs_admin_actions
+    get '/admin/graphs'
+    assert last_response.ok?
+    response = MultiJson.load(last_response.body)
+    assert_empty response
+  end
+
+  def test_graph_creation_and_retrieval
+    post '/admin/graphs'
+
+    get '/admin/graphs'
+    assert last_response.ok?
+    response = MultiJson.load(last_response.body)
+    refute_empty response
+
+    response.each do |graph, count|
+      assert graph.is_a?(String)
+      assert count.is_a?(Array)
+      assert count[0].is_a?(Integer)
+      assert count[1].is_a?(TrueClass) || count[1].is_a?(FalseClass)
+    end
+  end
+
+  def test_graph_deletion
+    post '/admin/graphs'
+
+    get '/admin/graphs'
+    response = MultiJson.load(last_response.body)
+    refute_empty response
+
+    graph = 'http://data.bioontology.org/metadata/OntologySubmission'
+
+    delete '/admin/graphs', url: graph
+
+    get '/admin/graphs'
+    assert last_response.ok?
+    response = MultiJson.load(last_response.body)
+    assert_nil response[graph]
+  end
+end

test/controllers/test_logging_controller.rb

@@ -20,26 +20,30 @@ def test_logging_endpoint
     (1..10).each do |_i|
       LinkedData::Models::Ontology.where.include(:acronym).all
     end
-    get '/admin/latest_day_query_logs?page=1&pagesize=10'
+
+    get '/admin/latest_day_query_logs?page=1&pagesize=9'
     assert last_response.ok?
     logs = MultiJson.load(last_response.body)
-    assert_equal 10, logs['collection'].size
+    assert_equal 9, logs['collection'].size
 
-    get '/admin/latest_day_query_logs?page=2&pagesize=10'
+    get '/admin/latest_day_query_logs?page=2&pagesize=9'
     assert last_response.ok?
     logs = MultiJson.load(last_response.body)
     assert_equal 1, logs['collection'].size
 
-    get '/admin/latest_day_query_logs?page=3&pagesize=10'
+    get '/admin/latest_day_query_logs?page=3&pagesize=9'
     assert last_response.ok?
     logs = MultiJson.load(last_response.body)
     assert_empty logs['collection']
   end
 
   def test_n_last_seconds_logs
+    Goo.logger.info("Test log")
     (1..10).each do |_i|
       LinkedData::Models::Ontology.where.include(:acronym).all
     end
+
+    Goo.logger.info("Test log")
     get '/admin/last_n_s_query_logs?seconds=2&page=1&pagesize=10'
     assert last_response.ok?
     logs = MultiJson.load(last_response.body)
@@ -51,6 +55,5 @@ def test_n_last_seconds_logs
     assert last_response.ok?
     logs = MultiJson.load(last_response.body)
     assert_equal 1, logs['collection'].size
-    binding.pry
   end
 end