Feature: add Annotator UI tests (#627)

* setup annotator page UI tests * check if all the inputs and filters are present in annotator page test * add annotator http requests to test fixtures * test annotator results and count them * test annotator empty illustration * add comments in annotator page tests * use dynamic api in recommender tests * test that we have the exact correct annotations in the annotator test * undo adding ids for elements to run annotator tests * add a default ANNOTATOR_URL value for test config --------- Co-authored-by: Syphax bouazzouni <[email protected]>
ontoportal-lirmm · Jun 14, 2024 · e80cf79 · e80cf79
1 parent a4417a7
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diff --git a/app/controllers/annotator_controller.rb b/app/controllers/annotator_controller.rb
@@ -72,7 +72,7 @@ def annotator_results(uri)
       else
         @results_table_header.push(t('annotator.score'))
       end
-      annotations = LinkedData::Client::HTTP.get(uri, api_params)
+      annotations = LinkedData::Client::HTTP.get(uri.dup.to_s, api_params)
       @ontologies = get_simplified_ontologies_hash
       @semantic_types = get_semantic_types 
       @results = []

diff --git a/app/views/annotator/index.html.haml b/app/views/annotator/index.html.haml
@@ -37,6 +37,7 @@
             = render Input::SelectComponent.new(label: t('annotator.include_ancestors'), id: 'ancestors_level', name: 'class_hierarchy_max_level', value: @ancestors_levels, selected: params[:class_hierarchy_max_level])
           .filters_line
             - include_score_helper = 'Score annotations following previous NCBO 2009 measure (old) or Score annotations following C-Value measure (cvalue) or Score annotations following C-Value measure with hierarchy expansion (cvalueh).'
+
             = render Input::SelectComponent.new(label: t('annotator.include_score'), id: 'include_score', name: 'score', value: @include_score, tooltip: include_score_helper, selected: params[:score])
             = render Input::NumberComponent.new(label: t('annotator.score_threshold'), name: "score_threshold", value: params[:score_threshold] || 0, tooltip: 'Specify minimum score value for annotations.')
             = render Input::NumberComponent.new(label: t('annotator.confidence_threshold'), name: 'confidence_threshold', value: params[:confidence_threshold] || 0, tooltip: 'Specify the minimum position in the score distribution (between 1 and 100).')

diff --git a/config/bioportal_config_test.rb b/config/bioportal_config_test.rb
@@ -8,7 +8,7 @@
 $API_KEY = ENV['API_KEY']
 $REST_URL = ENV['API_URL']
 $BIOMIXER_URL = ENV['BIOMIXER_URL']
-$ANNOTATOR_URL = $PROXY_URL = ENV['ANNOTATOR_URL']
+$ANNOTATOR_URL = $PROXY_URL = ENV['ANNOTATOR_URL'].blank? ? "https://services.tesportal.lirmm.fr/annotator" : ENV['ANNOTATOR_URL']
 $FAIRNESS_URL = ENV['FAIRNESS_URL']
 
 # Resource term
@@ -218,7 +218,4 @@
   }
 ]
 
-$UI_THEME = :stageportal
-if File.exist?('config/bioportal_config_development_testportal.lirmm.fr.rb')
-  require_relative 'bioportal_config_development_testportal.lirmm.fr' # local credentials
-end
+$UI_THEME = :stageportal
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -103,9 +103,10 @@ services:
   chrome-server:
     image: selenium/standalone-chrome:112.0-chromedriver-112.0-grid-4.9.0-20230421
     shm_size: 2g
-    ports:
-      - "4444:4444"
-      - "7900:7900"
+    network_mode: 'host'
+#    ports:
+#      - "4444:4444"
+#      - "7900:7900"
 
 volumes:
   mysql-data:

diff --git a/test/fixtures/annotator.yml b/test/fixtures/annotator.yml
@@ -0,0 +1,181 @@
+yaml_structure: regular
+sample_response:
+  - annotatedClass:
+      prefLabel: Melanom
+      synonym:
+      - cilt kanseri
+      "@id": http://aims.fao.org/aos/agrovoc/c_4713
+      "@type": http://www.w3.org/2002/07/owl#Class
+      links:
+        self: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713
+        ontology: http://localhost:9393/ontologies/STY
+        children: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/children
+        parents: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/parents
+        descendants: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/descendants
+        ancestors: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/ancestors
+        instances: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/instances
+        tree: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/tree
+        notes: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/notes
+        mappings: https://data.stageportal.lirmm.fr/ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713/mappings
+        ui: http://stageportal.lirmm.fr/ontologies/AGROVOC?p=classes&conceptid=http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713
+        "@context":
+          self: http://www.w3.org/2002/07/owl#Class
+          ontology: http://localhost:9393/ontologies/STY
+          children: http://www.w3.org/2002/07/owl#Class
+          parents: http://www.w3.org/2002/07/owl#Class
+          descendants: http://www.w3.org/2002/07/owl#Class
+          ancestors: http://www.w3.org/2002/07/owl#Class
+          instances: http://data.bioontology.org/metadata/Instance
+          tree: http://www.w3.org/2002/07/owl#Class
+          notes: http://data.bioontology.org/metadata/Note
+          mappings: http://data.bioontology.org/metadata/Mapping
+          ui: http://www.w3.org/2002/07/owl#Class
+      "@context":
+        "@vocab": http://data.bioontology.org/metadata/
+        prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel
+        synonym: http://www.w3.org/2004/02/skos/core#altLabel
+        "@language": en
+    hierarchy: []
+    annotations:
+    - from: 1
+      to: 8
+      matchType: PREF
+      text: MELANOMA
+    mappings: []
+  - annotatedClass:
+      prefLabel: Melanom
+      synonym:
+      - malignant melanoma
+      - melanoma patient
+      - melanocytes
+      "@id": http://data.europa.eu/8mn/euroscivoc/276b8c99-a318-48df-aa31-1f9f3e0ba910
+      "@type": http://www.w3.org/2002/07/owl#Class
+      links:
+        self: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910
+        ontology: http://localhost:9393/ontologies/STY
+        children: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/children
+        parents: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/parents
+        descendants: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/descendants
+        ancestors: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/ancestors
+        instances: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/instances
+        tree: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/tree
+        notes: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/notes
+        mappings: https://data.stageportal.lirmm.fr/ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910/mappings
+        ui: http://stageportal.lirmm.fr/ontologies/EUROSCIVOC?p=classes&conceptid=http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910
+        "@context":
+          self: http://www.w3.org/2002/07/owl#Class
+          ontology: http://localhost:9393/ontologies/STY
+          children: http://www.w3.org/2002/07/owl#Class
+          parents: http://www.w3.org/2002/07/owl#Class
+          descendants: http://www.w3.org/2002/07/owl#Class
+          ancestors: http://www.w3.org/2002/07/owl#Class
+          instances: http://data.bioontology.org/metadata/Instance
+          tree: http://www.w3.org/2002/07/owl#Class
+          notes: http://data.bioontology.org/metadata/Note
+          mappings: http://data.bioontology.org/metadata/Mapping
+          ui: http://www.w3.org/2002/07/owl#Class
+      "@context":
+        "@vocab": http://data.bioontology.org/metadata/
+        prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel
+        synonym: http://www.w3.org/2004/02/skos/core#altLabel
+        "@language": en
+    hierarchy: []
+    annotations:
+    - from: 1
+      to: 8
+      matchType: PREF
+      text: MELANOMA
+    - from: 34
+      to: 44
+      matchType: SYN
+      text: MELANOCYTES
+    mappings: []
+  - annotatedClass:
+      definition:
+      - http://opendata.inrae.fr/thesaurusINRAE/note_f18c0fe1
+      prefLabel: mélanome
+      synonym:
+      - malignant melanoma
+      - mélanome malin
+      "@id": http://opendata.inrae.fr/thesaurusINRAE/c_11970
+      "@type": http://www.w3.org/2002/07/owl#Class
+      links:
+        self: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970
+        ontology: http://localhost:9393/ontologies/STY
+        children: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/children
+        parents: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/parents
+        descendants: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/descendants
+        ancestors: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/ancestors
+        instances: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/instances
+        tree: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/tree
+        notes: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/notes
+        mappings: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970/mappings
+        ui: http://stageportal.lirmm.fr/ontologies/INRAETHES?p=classes&conceptid=http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970
+        "@context":
+          self: http://www.w3.org/2002/07/owl#Class
+          ontology: http://localhost:9393/ontologies/STY
+          children: http://www.w3.org/2002/07/owl#Class
+          parents: http://www.w3.org/2002/07/owl#Class
+          descendants: http://www.w3.org/2002/07/owl#Class
+          ancestors: http://www.w3.org/2002/07/owl#Class
+          instances: http://data.bioontology.org/metadata/Instance
+          tree: http://www.w3.org/2002/07/owl#Class
+          notes: http://data.bioontology.org/metadata/Note
+          mappings: http://data.bioontology.org/metadata/Mapping
+          ui: http://www.w3.org/2002/07/owl#Class
+      "@context":
+        "@vocab": http://data.bioontology.org/metadata/
+        prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel
+        synonym: http://www.w3.org/2004/02/skos/core#altLabel
+        definition: http://www.w3.org/2004/02/skos/core#definition
+        "@language": en
+    hierarchy: []
+    annotations:
+    - from: 1
+      to: 8
+      matchType: PREF
+      text: MELANOMA
+    mappings: []
+  - annotatedClass:
+      prefLabel: tumeur
+      synonym:
+      - néoplasme
+      - néoplasie
+      "@id": http://opendata.inrae.fr/thesaurusINRAE/c_11887
+      "@type": http://www.w3.org/2002/07/owl#Class
+      links:
+        self: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887
+        ontology: http://localhost:9393/ontologies/STY
+        children: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/children
+        parents: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/parents
+        descendants: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/descendants
+        ancestors: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/ancestors
+        instances: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/instances
+        tree: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/tree
+        notes: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/notes
+        mappings: https://data.stageportal.lirmm.fr/ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887/mappings
+        ui: http://stageportal.lirmm.fr/ontologies/INRAETHES?p=classes&conceptid=http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887
+        "@context":
+          self: http://www.w3.org/2002/07/owl#Class
+          ontology: http://localhost:9393/ontologies/STY
+          children: http://www.w3.org/2002/07/owl#Class
+          parents: http://www.w3.org/2002/07/owl#Class
+          descendants: http://www.w3.org/2002/07/owl#Class
+          ancestors: http://www.w3.org/2002/07/owl#Class
+          instances: http://data.bioontology.org/metadata/Instance
+          tree: http://www.w3.org/2002/07/owl#Class
+          notes: http://data.bioontology.org/metadata/Note
+          mappings: http://data.bioontology.org/metadata/Mapping
+          ui: http://www.w3.org/2002/07/owl#Class
+      "@context":
+        "@vocab": http://data.bioontology.org/metadata/
+        prefLabel: http://www.w3.org/2004/02/skos/core#prefLabel
+        synonym: http://www.w3.org/2004/02/skos/core#altLabel
+        "@language": en
+    hierarchy: []
+    annotations:
+    - from: 25
+      to: 29
+      matchType: PREF
+      text: TUMOR
+    mappings: []
diff --git a/test/system/annotator_page_test.rb b/test/system/annotator_page_test.rb
@@ -0,0 +1,108 @@
+require "application_system_test_case"
+require 'webmock/minitest'
+
+class AnnotatorPageTest < ApplicationSystemTestCase
+    def setup
+        WebMock.disable!
+        @apikey = LinkedData::Client.settings.apikey
+        @annotator_api = $ANNOTATOR_URL
+        @host = "#{@annotator_api.split('/')[-2]}:443"
+        @annotator_text_area = ".annotator-page-text-area > textarea"
+        @sample_response = fixtures(:annotator)["sample_response"]
+    end
+
+    def teardown
+        WebMock.disable!
+    end
+
+    test "go to annotator page and check if all the inputs and filters are there" do
+        visit root_url
+        click_link(href: '/annotator')
+        assert_selector @annotator_text_area
+        assert_selector 'div.insert-sample-text-button'
+        # Check if there are the annotator's options
+        assert_selector 'label[for="chips-whole_word_only-check"]'
+        assert_selector 'label[for="chips-longest_only-check"]'
+        assert_selector 'label[for="chips-expand_mappings-check"]'
+        assert_selector 'label[for="chips-exclude_numbers-check"]'
+        assert_selector 'label[for="chips-exclude_synonyms-check"]'
+        assert_selector 'div.select-ontologies'
+
+        # Open the advanced options
+        find('div.advanced-options-button').click
+
+        # Check if there are the advanced options
+        assert_selector 'input#select_umls_semantic_types-ts-control', visible: :all
+        assert_selector 'input#select_umls_semantic_groups-ts-control', visible: :all
+        assert_selector 'input#select_ancestors_level-ts-control', visible: :all
+        assert_selector 'input#select_include_score-ts-control', visible: :all
+        assert_selector 'input[name="score_threshold"]'
+        assert_selector 'input[name="confidence_threshold"]'
+        assert_selector 'label[for="chips-fast_context-check"]'
+        assert_selector 'label[for="chips-lemmatize-check"]'
+    end
+
+    test "go to annotator page insert sample text and get annotations" do
+        visit root_url
+        click_link(href: '/annotator')
+
+        # Fill the annotator's text area input by a sample text
+        find(@annotator_text_area).fill_in(with: 'Melanoma is a malignant tumor of melanocytes found mainly')
+
+        # Mock the api call for the annotator with the entered text
+        WebMock.enable!
+        stub_request(:get, "#{@annotator_api}?class_hierarchy_max_level=None&confidence_threshold=0&score_threshold=0&text=Melanoma%20is%20a%20malignant%20tumor%20of%20melanocytes%20found%20mainly&whole_word_only=true")
+            .with(
+                headers: {
+                        'Accept'=>'application/json',
+                        'Authorization'=>"apikey token=#{@apikey}",
+                        'Host'=> @host,
+                        'User-Agent'=>'NCBO API Ruby Client v0.1.0'
+                })
+            .to_return(status: 200, body: @sample_response.to_json, headers: {})
+
+
+        find(".annotator-page-button #annotator").click
+
+        # Check if we get the table of annotations
+        assert_selector 'table#annotator-table'
+
+        # Check if the number of annotations is 4
+        assert_equal 5, page.all('tr').count
+
+        # Check if we got the correct annotations
+        assert_selector 'a[href="ontologies/AGROVOC/classes/http%3A%2F%2Faims.fao.org%2Faos%2Fagrovoc%2Fc_4713"]', text: 'Melanom'
+        assert_selector 'a[href="ontologies/EUROSCIVOC/classes/http%3A%2F%2Fdata.europa.eu%2F8mn%2Feuroscivoc%2F276b8c99-a318-48df-aa31-1f9f3e0ba910"]', text: 'Melanom'
+        assert_selector 'a[href="ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11970"]', text: 'mélanome'
+        assert_selector 'a[href="ontologies/INRAETHES/classes/http%3A%2F%2Fopendata.inrae.fr%2FthesaurusINRAE%2Fc_11887"]', text: 'tumeur'
+
+        # Check if the action buttons below the table are there (json, rdf, cite us and api doc buttons)
+        assert_selector '#annotator_json'
+        assert_selector '#annotator_rdf'
+        assert_selector '#annotator_cite_us'
+        assert_selector '#annotator_api_doc'
+
+        # Clear the sample text in the annotator text area
+        find(@annotator_text_area).native.clear
+
+        # Fill it with a text that will return an empty state
+        find(@annotator_text_area).fill_in(with: 'mainly')
+
+        # Mock the api call of the annotator to get and return an empty result
+        stub_request(:get, "#{@annotator_api}?class_hierarchy_max_level=None&confidence_threshold=0&score_threshold=0&text=mainly&whole_word_only=true")
+            .with(
+                headers: {
+                        'Accept'=>'application/json',
+                        'Authorization'=>"apikey token=#{@apikey}",
+                        'Host'=> @host,
+                        'User-Agent'=>'NCBO API Ruby Client v0.1.0'
+                })
+            .to_return(status: 200, body: ([]).to_json, headers: {})
+
+        find(".annotator-page-button #annotator").click
+
+        # Check if we got the empty state correctly
+        assert_selector 'div.browse-empty-illustration'
+    end
+
+end
diff --git a/test/test_helper.rb b/test/test_helper.rb
@@ -2,6 +2,7 @@
 require_relative '../config/environment'
 require 'rails/test_help'
 require 'simplecov'
+require 'webmock/minitest'
 
 SimpleCov.start 'rails' do
   add_filter '/bin/'
@@ -16,6 +17,7 @@ class ActiveSupport::TestCase
 
   # Add more helper methods to be used by all tests here...
 
+  WebMock.allow_net_connect!
 
   Capybara.server_host = "0.0.0.0"
   Capybara.app_host = "http://#{Socket.gethostname}:#{Capybara.server_port}"