changes related to ncbo/ontologies_api#134 and ncbo/ontologies_api#135

ncbo · Feb 13, 2024 · c0f9d00 · c0f9d00
1 parent 4b6b7f4
commit c0f9d00
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Showing 3 changed files with 50 additions and 7 deletions.
diff --git a/config/solr/term_search/schema.xml b/config/solr/term_search/schema.xml
@@ -140,7 +140,19 @@
     <field name="synonymSuggestEdge"    type="text_suggest_edge"  indexed="true"  stored="true"  multiValued="true" />
     <field name="synonymSuggestNgram"   type="text_suggest_ngram" indexed="true"  stored="true"  omitNorms="true" multiValued="true" />
 
-    <field name="notation"              type="text_general"       indexed="true"  stored="true"  multiValued="false" />
+
+
+    <field name="notation"              type="string_ci"          indexed="true"  stored="true"  multiValued="false" />
+
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+
+    <field name="shortId"              type="string_ci"          indexed="true"  stored="true"  multiValued="false" />
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+
 
     <field name="definition"            type="string"             indexed="true"  stored="true"  multiValued="true" />
     <field name="submissionAcronym"     type="string"             indexed="true"  stored="true"  multiValued="false" />
@@ -151,8 +163,8 @@
     <field name="childCount"            type="int"                indexed="true"  stored="true"  multiValued="false" />
 
     <!-- Added cui and tui (semanticType) - NCBO-695 -->
-    <field name="cui"                   type="text_general"       indexed="true"  stored="true"  multiValued="true" />
-    <field name="semanticType"          type="text_general"       indexed="true"  stored="true"  multiValued="true" />
+    <field name="cui"                   type="string_ci"          indexed="true"  stored="true"  multiValued="true" />
+    <field name="semanticType"          type="string_ci"          indexed="true"  stored="true"  multiValued="true" />
 
     <field name="property"              type="text_general"       indexed="true"  stored="true"  multiValued="true" />
     <field name="propertyRaw"           type="text_general"       indexed="false" stored="true"  multiValued="false" />

diff --git a/lib/ontologies_linked_data/models/class.rb b/lib/ontologies_linked_data/models/class.rb
@@ -199,6 +199,15 @@ def index_doc(to_set=nil)
             doc[:semanticType] = []
             all_attrs[:semanticType].each { |semType| doc[:semanticType] << semType.split("/").last }
           end
+
+          # special handling for :notation field because some ontologies have it defined as :prefixIRI
+          if !doc[:notation] || doc[:notation].empty?
+            if all_attrs[:prefixIRI] && !all_attrs[:prefixIRI].empty?
+              doc[:notation] = all_attrs[:prefixIRI].strip
+            else
+              doc[:notation] = LinkedData::Utils::Triples::last_iri_fragment(doc[:id])
+            end
+          end
         end
 
         if to_set.nil? || (to_set.is_a?(Array) && to_set.include?(:properties))
@@ -210,9 +219,26 @@ def index_doc(to_set=nil)
           end
         end
 
+        # binding.pry
+
         doc
       end
 
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       def properties_for_indexing()
         self_props = self.properties
         return nil if self_props.nil?

diff --git a/lib/ontologies_linked_data/sample_data/ontology.rb b/lib/ontologies_linked_data/sample_data/ontology.rb
@@ -20,6 +20,9 @@ def self.create_ontologies_and_submissions(options = {})
         process_submission = options[:process_submission] || false
         submissions_to_process = options[:submissions_to_process]
         acronym = options[:acronym] || "TEST-ONT"
+        pref_label_property = options[:pref_label_property] || false
+        synonym_property = options[:synonym_property] || false
+        definition_property = options[:synonym_property] || false
         name = options[:name]
         # set ontology type
         ontology_type = nil
@@ -60,14 +63,17 @@ def self.create_ontologies_and_submissions(options = {})
           max.times do
             #refresh submission to get new next submission ID after saving in a loop
             o.bring(:submissions)
-            os = LinkedData::Models::OntologySubmission.new({
+            sub_options = {
               ontology: o,
               hasOntologyLanguage: of,
               submissionId: o.next_submission_id,
-              definitionProperty: (RDF::IRI.new "http://bioontology.org/ontologies/biositemap.owl#definition"),
               contact: [contact],
               released: DateTime.now - 3
-            })
+            }
+            sub_options[:prefLabelProperty] = RDF::IRI.new(pref_label_property) if pref_label_property
+            sub_options[:synonymProperty] = RDF::IRI.new(synonym_property) if synonym_property
+            sub_options[:definitionProperty] = RDF::IRI.new(definition_property) if definition_property
+            os = LinkedData::Models::OntologySubmission.new(sub_options)
 
             if (submissions_to_process.nil? || submissions_to_process.include?(os.submissionId))
               file_path = options[:file_path]
@@ -88,7 +94,6 @@ def self.create_ontologies_and_submissions(options = {})
               o.summaryOnly = true
               o.save
             end
-
             os.save unless os.exist?
           end
         end