add :index_all_data step the process actions

ontoportal-lirmm · Apr 26, 2024 · abf1125 · abf1125
1 parent 95cde49
commit abf1125
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Showing 3 changed files with 11 additions and 9 deletions.
diff --git a/lib/ncbo_cron/ontology_helper.rb b/lib/ncbo_cron/ontology_helper.rb
@@ -10,6 +10,7 @@ module OntologyHelper
         :process_rdf => true,
         :generate_labels => true,
         :extract_metadata => true,
+        :index_all_data => true,
         :index_search => true,
         :index_properties => true,
         :run_metrics => true,

diff --git a/test/test_case.rb b/test/test_case.rb
@@ -60,10 +60,11 @@ def backend_triplestore_delete
     raise StandardError, 'Too many triples in KB, does not seem right to run tests' unless
           count_pattern('?s ?p ?o') < 400000
 
-    LinkedData::Models::Ontology.where.include(:acronym).each do |o|
-      query = "submissionAcronym:#{o.acronym}"
-      LinkedData::Models::Ontology.unindexByQuery(query)
-    end
+    # LinkedData::Models::Ontology.where.include(:acronym).each do |o|
+    #   query = "submissionAcronym:#{o.acronym}"
+    #   LinkedData::Models::Ontology.unindexByQuery(query)
+    # end
+    #
     LinkedData::Models::Ontology.indexCommit
     Goo.sparql_update_client.update('DELETE {?s ?p ?o } WHERE { ?s ?p ?o }')
     LinkedData::Models::SubmissionStatus.init_enum

diff --git a/test/test_ontology_submission_parser.rb b/test/test_ontology_submission_parser.rb
@@ -40,7 +40,7 @@ def test_queue_submission
     assert_nil val
 
     parser.queue_submission(o1.submissions[0], {
-        dummy_action: true, index_search: false, metrics: true,
+        dummy_action: true, index_all_data: false, index_search: false, metrics: true,
         process_annotator: true, another_dummy_action: true, all: true})
     val = @@redis.hget(NcboCron::Models::OntologySubmissionParser::QUEUE_HOLDER, parser.get_prefixed_id(o1.submissions[0].id.to_s))
     options = MultiJson.load(val, symbolize_keys: true)
@@ -49,11 +49,11 @@ def test_queue_submission
     o2 = @@ontologies[1]
     o2.bring(:submissions) if o2.bring?(:submissions)
     parser.queue_submission(o2.submissions[0], {
-        :process_rdf => false, :index_search => true, :metrics => true,
+        :process_rdf => false, :index_search => true, index_all_data: true, :metrics => true,
         :process_annotator => false})
     val = @@redis.hget(NcboCron::Models::OntologySubmissionParser::QUEUE_HOLDER, parser.get_prefixed_id(o2.submissions[0].id.to_s))
     options = MultiJson.load(val, symbolize_keys: true)
-    assert_equal({:process_rdf => false, :index_search => true, :process_annotator => false}, options)
+    assert_equal({:process_rdf => false, :index_search => true, index_all_data: true,  :process_annotator => false}, options)
   end
 
   def test_parse_submissions
@@ -76,13 +76,13 @@ def test_parse_submissions
     o2_sub2.bring(:submissionStatus)
 
     options_o1 = {
-      :dummy_action => true, :process_rdf => true, :index_search => true, :index_properties => true, :diff => true,
+      :dummy_action => true, :process_rdf => true, :index_all_data => true, :index_search => true, :index_properties => true, :diff => true,
       :dummy_metrics => false, :run_metrics => false, :process_annotator => false,
       :another_dummy_action => false, :all => false
     }
 
     options_o2 = {
-      dummy_action: false, process_rdf: true, index_search: false, index_properties: false, :diff => true,
+      dummy_action: false, process_rdf: true, index_search: false, :index_all_data => false, index_properties: false, :diff => true,
       dummy_metrics: true, run_metrics: false, process_annotator: true,
       another_dummy_action: true, all: false
     }