optimize api tests

ontoportal-lirmm · Oct 26, 2023 · faf3848 · faf3848
1 parent f3bb98a
commit faf3848
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Showing 13 changed files with 61 additions and 11 deletions.
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -53,7 +53,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 189f5898e1e2422a647f3937495c3ea1c9894350
+  revision: 0b0414dc1af8ddac39642ce23be5970de5acc00c
   branch: feature/migrate-to-virtuoso
   specs:
     ontologies_linked_data (0.0.1)

diff --git a/config/environments/test.rb b/config/environments/test.rb
@@ -12,12 +12,14 @@
 SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8984/solr/prop_search_core1"
 MGREP_HOST = ENV.include?("MGREP_HOST") ? ENV["MGREP_HOST"] : "localhost"
 MGREP_PORT = ENV.include?("MGREP_PORT") ? ENV["MGREP_PORT"] : 55556
+GOO_SLICES = ENV["GOO_SLICES"] || 500
 
 begin
   # For prefLabel extract main_lang first, or anything if no main found.
   # For other properties only properties with a lang that is included in main_lang are used
   Goo.main_languages = ['en']
   Goo.use_cache = false
+  Goo.slice_loading_size = GOO_SLICES.to_i
 rescue NoMethodError
   puts "(CNFG) >> Goo.main_lang not available"
 end

diff --git a/test/controllers/test_annotator_controller.rb b/test/controllers/test_annotator_controller.rb
@@ -16,7 +16,12 @@ def self.before_suite
     end
 
     LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
-    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies
+    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true,
+                                                                          process_options: {
+                                                                            process_rdf: true,
+                                                                            extract_metadata: false,
+                                                                            index_search: true
+                                                                          })
     annotator = Annotator::Models::NcboAnnotator.new
     annotator.init_redis_for_tests()
     annotator.create_term_cache_from_ontologies(@@ontologies, false)
@@ -348,15 +353,16 @@ def self.mapping_test_set
         classes = []
         class_id = terms_a[i]
         ont_acr = onts_a[i]
-        sub = LinkedData::Models::Ontology.find(ont_acr).first.latest_submission
+        sub = LinkedData::Models::Ontology.find(ont_acr).first.latest_submission(status: :any)
+        binding.pry if sub.nil?
         sub.bring(ontology: [:acronym])
         c = LinkedData::Models::Class.find(RDF::URI.new(class_id))
                                     .in(sub)
                                     .first
         classes << c
         class_id = terms_b[i]
         ont_acr = onts_b[i]
-        sub = LinkedData::Models::Ontology.find(ont_acr).first.latest_submission
+        sub = LinkedData::Models::Ontology.find(ont_acr).first.latest_submission(status: :any)
         sub.bring(ontology: [:acronym])
         c = LinkedData::Models::Class.find(RDF::URI.new(class_id))
                                     .in(sub)

diff --git a/test/controllers/test_batch_controller.rb b/test/controllers/test_batch_controller.rb
@@ -2,8 +2,7 @@
 
 class TestBatchController < TestCase
   def self.before_suite
-    LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
-    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies
+    @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true)
   end
 
   def test_class_batch_one_ontology

diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb
@@ -7,7 +7,9 @@ def self.before_suite
                submission_count: 3,
                submissions_to_process: [1, 2],
                process_submission: true,
-               random_submission_count: false}
+               random_submission_count: false,
+               process_options: {process_rdf: true, extract_metadata: false}
+    }
     return LinkedData::SampleData::Ontology.create_ontologies_and_submissions(options)
   end
 

diff --git a/test/controllers/test_collections_controller.rb b/test/controllers/test_collections_controller.rb
@@ -5,6 +5,7 @@ class TestCollectionsController < TestCase
   def self.before_suite
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
       process_submission: true,
+      process_options: {process_rdf: true, extract_metadata: false},
       acronym: 'INRAETHES',
       name: 'INRAETHES',
       file_path: './test/data/ontology_files/thesaurusINRAE_nouv_structure.rdf',

diff --git a/test/controllers/test_external_mappings_controller.rb b/test/controllers/test_external_mappings_controller.rb
@@ -14,6 +14,7 @@ def self.before_suite
     end
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                          process_submission: true,
+                                                                         process_options: {process_rdf: true, extract_metadata: false},
                                                                          acronym: "BRO-TEST-MAP",
                                                                          name: "BRO-TEST-MAP",
                                                                          file_path: "./test/data/ontology_files/BRO_v3.2.owl",
@@ -22,6 +23,7 @@ def self.before_suite
                                                                        })
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                          process_submission: true,
+                                                                         process_options: {process_rdf: true, extract_metadata: false},
                                                                          acronym: "CNO-TEST-MAP",
                                                                          name: "CNO-TEST-MAP",
                                                                          file_path: "./test/data/ontology_files/CNO_05.owl",
@@ -30,6 +32,7 @@ def self.before_suite
                                                                        })
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                          process_submission: true,
+                                                                         process_options: {process_rdf: true, extract_metadata: false},
                                                                          acronym: "FAKE-TEST-MAP",
                                                                          name: "FAKE-TEST-MAP",
                                                                          file_path: "./test/data/ontology_files/fake_for_mappings.owl",

diff --git a/test/controllers/test_instances_controller.rb b/test/controllers/test_instances_controller.rb
@@ -5,6 +5,7 @@ class TestInstancesController < TestCase
   def self.before_suite
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
       process_submission: true,
+      process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
       acronym: 'XCT-TEST-INST',
       name: 'XCT-TEST-INST',
       file_path: './test/data/ontology_files/XCTontologyvtemp2.owl',
@@ -13,9 +14,6 @@ def self.before_suite
     })
   end
 
-  def self.after_suite
-    LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
-  end
 
   def test_first_default_page
     ont = Ontology.find('XCT-TEST-INST-0').include(:acronym).first
@@ -52,6 +50,7 @@ def test_all_instance_pages
       assert last_response.ok?
       instance_count = instance_count + response['collection'].size
     end while response['nextPage']
+
     assert_equal 714, instance_count
 
     # Next page should have no results.

diff --git a/test/controllers/test_mappings_controller.rb b/test/controllers/test_mappings_controller.rb
@@ -15,6 +15,7 @@ def self.before_suite
     end
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                          process_submission: true,
+                                                                         process_options: { process_rdf: true, extract_metadata: false},
                                                                          acronym: "BRO-TEST-MAP",
                                                                          name: "BRO-TEST-MAP",
                                                                          file_path: "./test/data/ontology_files/BRO_v3.2.owl",
@@ -23,6 +24,7 @@ def self.before_suite
                                                                        })
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                          process_submission: true,
+                                                                         process_options: { process_rdf: true, extract_metadata: false},
                                                                          acronym: "CNO-TEST-MAP",
                                                                          name: "CNO-TEST-MAP",
                                                                          file_path: "./test/data/ontology_files/CNO_05.owl",
@@ -31,6 +33,7 @@ def self.before_suite
                                                                        })
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                          process_submission: true,
+                                                                         process_options: { process_rdf: true, extract_metadata: false},
                                                                          acronym: "FAKE-TEST-MAP",
                                                                          name: "FAKE-TEST-MAP",
                                                                          file_path: "./test/data/ontology_files/fake_for_mappings.owl",

diff --git a/test/data/graphdb-repo-config.ttl b/test/data/graphdb-repo-config.ttl
@@ -0,0 +1,33 @@
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix rep: <http://www.openrdf.org/config/repository#> .
+@prefix sail: <http://www.openrdf.org/config/sail#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<#ontoportal> a rep:Repository;
+  rep:repositoryID "ontoportal";
+  rep:repositoryImpl [
+      rep:repositoryType "graphdb:SailRepository";
+      <http://www.openrdf.org/config/repository/sail#sailImpl> [
+          <http://www.ontotext.com/trree/owlim#base-URL> "http://example.org/owlim#";
+          <http://www.ontotext.com/trree/owlim#check-for-inconsistencies> "false";
+          <http://www.ontotext.com/trree/owlim#defaultNS> "";
+          <http://www.ontotext.com/trree/owlim#disable-sameAs> "true";
+          <http://www.ontotext.com/trree/owlim#enable-context-index> "false";
+          <http://www.ontotext.com/trree/owlim#enable-literal-index> "true";
+          <http://www.ontotext.com/trree/owlim#enablePredicateList> "true";
+          <http://www.ontotext.com/trree/owlim#entity-id-size> "32";
+          <http://www.ontotext.com/trree/owlim#entity-index-size> "10000000";
+          <http://www.ontotext.com/trree/owlim#imports> "";
+          <http://www.ontotext.com/trree/owlim#in-memory-literal-properties> "true";
+          <http://www.ontotext.com/trree/owlim#owlim-license> "";
+          <http://www.ontotext.com/trree/owlim#query-limit-results> "0";
+          <http://www.ontotext.com/trree/owlim#query-timeout> "0";
+          <http://www.ontotext.com/trree/owlim#read-only> "false";
+          <http://www.ontotext.com/trree/owlim#repository-type> "file-repository";
+          <http://www.ontotext.com/trree/owlim#ruleset> "rdfsplus-optimized";
+          <http://www.ontotext.com/trree/owlim#storage-folder> "storage";
+          <http://www.ontotext.com/trree/owlim#throw-QueryEvaluationException-on-timeout> "false";
+          sail:sailType "owlim:Sail"
+        ]
+    ];
+  rdfs:label "" .
diff --git a/test/data/graphdb-test-load.nt b/test/data/graphdb-test-load.nt
diff --git a/test/helpers/test_http_cache_helper.rb b/test/helpers/test_http_cache_helper.rb
@@ -4,7 +4,6 @@ class TestHTTPCacheHelper < TestCaseHelpers
 
   def self.before_suite
     raise Exception, "Redis is unavailable, caching will not function" if LinkedData::HTTPCache.redis.ping.nil?
-    self.new("before_suite").delete_ontologies_and_submissions
     ontologies = self.new("before_suite")._ontologies
     @@ontology = ontologies.shift
     @@ontology_alt = ontologies.shift

diff --git a/test/test_case.rb b/test/test_case.rb
@@ -149,6 +149,9 @@ def app
   # @option options [TrueClass, FalseClass] :random_submission_count Use a random number of submissions between 1 and :submission_count
   # @option options [TrueClass, FalseClass] :process_submission Parse the test ontology file
   def create_ontologies_and_submissions(options = {})
+    if options[:process_submission] && options[:process_options].nil?
+      options[:process_options] =  { process_rdf: true, extract_metadata: false, generate_missing_labels: false }
+    end
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions(options)
   end