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fix the annotator call to get mappings #7

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fix the annotator call to get mappings #7

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9 changes: 2 additions & 7 deletions app/assets/javascripts/bp_annotator.js
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Original file line number Diff line number Diff line change
Expand Up @@ -55,15 +55,15 @@ function get_annotations() {
ajax_process_halt();

var params = {},
ont_select = jQuery("#ontology_ontologyId"),
mappings = [];
ont_select = jQuery("#ontology_ontologyId");

params.text = jQuery("#annotation_text").val();
params.ontologies = (ont_select.val() === null) ? [] : ont_select.val();
params.longest_only = jQuery("#longest_only").is(':checked');
params.exclude_numbers = jQuery("#exclude_numbers").is(':checked');
params.whole_word_only = !jQuery("#match_partial_words").is(':checked');
params.exclude_synonyms = jQuery("#exclude_synonyms").is(':checked');
params.expand_mappings = jQuery("#expand_mappings").is(':checked');
params.ncbo_slice = (("ncbo_slice" in BP_CONFIG) ? BP_CONFIG.ncbo_slice : '');

var maxLevel = parseInt(jQuery("#class_hierarchy_max_level").val());
Expand All @@ -83,11 +83,6 @@ function get_annotations() {
// params.wholeWordOnly = jQuery("#wholeWordOnly:checked").val();
//}

jQuery("[name='mappings']:checked").each(function() {
mappings.push(jQuery(this).val());
});
params.mappings = mappings;

if (jQuery("#semantic_types").val() !== null) {
params.semantic_types = jQuery("#semantic_types").val();
annotationsTable.fnSetColumnVis(BP_COLUMNS.sem_types, true);
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9 changes: 5 additions & 4 deletions app/controllers/annotator_controller.rb
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Expand Up @@ -31,7 +31,7 @@ def create
:class_hierarchy_max_level => params[:class_hierarchy_max_level].to_i,
:expand_class_hierarchy => params[:class_hierarchy_max_level].to_i > 0,
:semantic_types => params[:semantic_types],
:mappings => params[:mappings],
:expand_mappings => params[:expand_mappings],
:longest_only => params[:longest_only],
:exclude_numbers => params[:exclude_numbers] ||= "false", # service default is false
:whole_word_only => params[:whole_word_only] ||= "true", # service default is true
Expand All @@ -42,19 +42,20 @@ def create
start = Time.now
query = ANNOTATOR_URI
query += "?text=" + CGI.escape(text_to_annotate)
query += "&include=prefLabel"
#query += "&include=prefLabel"
# Include= prefLabel causes an internal error when retrieving mappings
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 += "&ontologies=" + CGI.escape(options[:ontologies].join(',')) unless options[:ontologies].empty?
query += "&semantic_types=" + options[:semantic_types].join(',') unless options[:semantic_types].empty?
query += "&mappings=" + options[:mappings].join(',') unless options[:mappings].empty?
query += "&expand_mappings=" + options[:expand_mappings].to_s unless options[:expand_mappings].empty?
query += "&longest_only=#{options[:longest_only]}"
query += "&recognizer=#{params[:recognizer]}"
query += "&exclude_numbers=" + options[:exclude_numbers].to_s unless options[:exclude_numbers].empty?
query += "&whole_word_only=" + options[:whole_word_only].to_s unless options[:whole_word_only].empty?
query += "&exclude_synonyms=" + options[:exclude_synonyms].to_s unless options[:exclude_synonyms].empty?
query += "&ncbo_slice=" + options[:ncbo_slice].to_s unless options[:ncbo_slice].empty?

annotations = parse_json(query) # See application_controller.rb
#annotations = LinkedData::Client::HTTP.get(query)
LOG.add :debug, "Retrieved #{annotations.length} annotations: #{Time.now - start}s"
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4 changes: 2 additions & 2 deletions app/views/annotator/index.html.haml
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Expand Up @@ -21,8 +21,8 @@
= label_tag :longest_only, "Match Longest Only"
  
/ TODO: When the REST API supports different mapping types, revise this section of the UI.
= check_box_tag :mappings, :all, false, :id => "mappings_all"
= label_tag :mappings_all, "Include Mappings"
= check_box_tag :expand_mappings, :all, false, :id => "expand_mappings"
= label_tag :expand_mappings, "Include Mappings"
%p
= check_box_tag :exclude_numbers, :all, false, :id => "exclude_numbers"
= label_tag :exclude_numbers, "Exclude Numbers"
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