Upgrading ConText component to FastContext within annotator UI (cf. a…

…nnotators issue ncbo#28 : ontoportal-lirmm/annotators#28)

app/assets/javascripts/bp_annotator.js

@@ -79,7 +79,7 @@ function get_annotations() {
   params.expand_mappings = jQuery("#expand_mappings").is(':checked');
   params.ncbo_slice = (("ncbo_slice" in BP_CONFIG) ? BP_CONFIG.ncbo_slice : '');
 
-  params.fast_context = jQuery("#fast_context").is(':checked');
+  params.negation = params.experiencer = params.temporality = params.certainty = params.fast_context = jQuery("#fast_context").is(':checked');
 
   params.score_threshold = jQuery("#score_threshold").val();
   params.confidence_threshold = jQuery("#confidence_threshold").val();

app/controllers/annotator_controller.rb

@@ -50,9 +50,7 @@ def create
                 :exclude_numbers => params[:exclude_numbers] ||= "false",  # service default is false
                 :whole_word_only => params[:whole_word_only] ||= "true", # service default is true
                 :exclude_synonyms => params[:exclude_synonyms] ||= "false",  # service default is false
-                :negation => params[:negation] ||= "false",  # service default is false
-                #:experiencer => params[:experiencer] ||= "false",  # service default is false
-                :temporality => params[:temporality] ||= "false",  # service default is false
+                :fast_context => params[:fast_context] ||= "false",  # service default is false
                 :score => params[:score],
                 :lemmatize => params[:lemmatize] ||= "false",
                 :ncbo_slice => params[:ncbo_slice] || ''
@@ -67,9 +65,7 @@ def create
     query += "&expand_class_hierarchy=true" if options[:class_hierarchy_max_level] > 0
     query += "&class_hierarchy_max_level=" + options[:class_hierarchy_max_level].to_s if options[:class_hierarchy_max_level] > 0
     query += "&score=" + options[:score] unless options[:score] == ""
-    query += "&negation=" + options[:negation] unless options[:negation].empty?
-    #query += "&experiencer=" + options[:experiencer] unless options[:experiencer].empty?
-    query += "&temporality=" + options[:temporality] unless options[:temporality].empty?
+    query += "&fast_context=" + options[:fast_context] unless options[:fast_context].empty?
     query += "&ontologies=" + CGI.escape(options[:ontologies].join(',')) unless options[:ontologies].empty?
     query += "&semantic_types=" + options[:semantic_types].join(',') unless options[:semantic_types].empty?
     query += "&semantic_groups=" + options[:semantic_groups].join(',') unless options[:semantic_groups].empty?   

app/views/annotator/index.html.haml

@@ -91,19 +91,9 @@
 
           %div.form-group
             %div.custom-control.custom-checkbox
-              = check_box_tag("negation", :all, false, class: "custom-control-input")
-              %label.custom-control-label{for: "negation"} Detect negation  
-              %small#negationHelp.form-text.text-muted Detect if a concept has been negated (affirmed, negated, possible)
-
-            %div.custom-control.custom-checkbox
-              = check_box_tag("experiencer", :all, false, class: "custom-control-input")
-              %label.custom-control-label{for: "experiencer"} Detect experiencer
-              %small#experiencerHelp.form-text.text-muted Detect who experienced the each identified concept (patient, other)
-
-            %div.custom-control.custom-checkbox
-              = check_box_tag("temporality", :all, false, class: "custom-control-input")
-              %label.custom-control-label{for: "temporality"} Detect temporality
-              %small#temporalityHelp.form-text.text-muted Detect when the annotated concept occurred (recent, historical, hypothetical)
+              = check_box_tag("fast_context", :all, false, class: "custom-control-input")
+              %label.custom-control-label{for: "fast_context"} FastContext
+              %small#fast_contextnHelp.form-text.text-muted= t('annotator.index.fast_context.tooltip')
 
         %div.my-4
           = button_tag("Get annotations", type: "button", id: "annotator_button", class: "btn btn-primary btn-lg")
@@ -160,6 +150,7 @@
               %th Negation
               %th Experiencer
               %th Temporality
+              %th Certainty
           %tbody
         %div.my-3
           %b Format results as:

config/locales/en.yml

@@ -112,6 +112,8 @@ en:
     index:
       intro: Get annotations for biomedical text with classes from the ontologies
       annotatorplus_html: <em>Check out <a href="%{annotatorplus_href}">AnnotatorPlus</a> beta; a new version of the Annotator with added support for negation, and more!</em>
+      fast_context:
+        tooltip: "Enable FastContext to detect : if a concept has been negated (affirmed, negated), who experienced the found concept (patient, other), when the annotated concept occurred (recent, historical, hypothetical), and/or if the annotated concept is uncertain (certain, uncertain)."
       sample_text: Melanoma is a malignant tumor of melanocytes which are found predominantly in skin but also in the bowel and the eye.
 
   nbco_annotatosplus: