refactor test to be faster by doing the indexation only if needed

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)
@@ -260,16 +265,16 @@ def test_default_properties_output
     assert last_response.ok?
     annotations = MultiJson.load(last_response.body)
     assert_equal 9, annotations.length
-    annotations.sort! { |a,b| a["annotatedClass"]["prefLabel"].downcase <=> b["annotatedClass"]["prefLabel"].downcase }
+    annotations.sort! { |a,b| a["annotatedClass"]["prefLabel"].first.downcase <=> b["annotatedClass"]["prefLabel"].first.downcase }
     assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data", annotations.first["annotatedClass"]["@id"]
-    assert_equal "Aggregate Human Data", annotations.first["annotatedClass"]["prefLabel"]
+    assert_equal "Aggregate Human Data", Array(annotations.first["annotatedClass"]["prefLabel"]).first
 
     params = {text: text, include: "prefLabel,definition"}
     get "/annotator", params
     assert last_response.ok?
     annotations = MultiJson.load(last_response.body)
     assert_equal 9, annotations.length
-    annotations.sort! { |a,b| a["annotatedClass"]["prefLabel"].downcase <=> b["annotatedClass"]["prefLabel"].downcase }
+    annotations.sort! { |a,b| Array(a["annotatedClass"]["prefLabel"]).first.downcase <=> Array(b["annotatedClass"]["prefLabel"]).first.downcase }
     assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data", annotations.first["annotatedClass"]["@id"]
     assert_equal ["A resource that provides data from clinical care that comprises combined data from multiple individual human subjects."], annotations.first["annotatedClass"]["definition"]
   end
@@ -348,15 +353,15 @@ 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)
         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)

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

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
 

test/controllers/test_metrics_controller.rb

@@ -18,11 +18,12 @@ def self.before_suite
               "individuals"=>124,
               "properties"=>63,
               "maxDepth"=> 7 }
-    @@options = {ont_count: 2,
-               submission_count: 3,
-               submissions_to_process: [1, 2],
-               process_submission: true,
-               random_submission_count: false}
+    @@options = { ont_count: 2,
+                  submission_count: 3,
+                  submissions_to_process: [1, 2],
+                  process_submission: true,
+                  process_options: { process_rdf: true, extract_metadata: false, run_metrics: true, index_properties: true },
+                  random_submission_count: false }
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions(@@options)
   end
 
@@ -78,18 +79,18 @@ def test_metrics_missing
     get '/metrics/missing'
     assert last_response.ok?
     ontologies = MultiJson.load(last_response.body)
-    assert_equal(0, ontologies.length, msg='Failure to detect 0 ontologies with missing metrics.')
+    assert_equal(0, ontologies.length, msg = 'Failure to detect 0 ontologies with missing metrics.')
     # create ontologies with latest submissions that have no metrics
     delete_ontologies_and_submissions
-    options = {ont_count: 2,
-               submission_count: 1,
-               process_submission: false,
-               random_submission_count: false}
+    options = { ont_count: 2,
+                submission_count: 1,
+                process_submission: false,
+                random_submission_count: false }
     create_ontologies_and_submissions(options)
     get '/metrics/missing'
     assert last_response.ok?
     ontologies = MultiJson.load(last_response.body)
-    assert_equal(2, ontologies.length, msg='Failure to detect 2 ontologies with missing metrics.')
+    assert_equal(2, ontologies.length, msg = 'Failure to detect 2 ontologies with missing metrics.')
     # recreate the before_suite data (this test might not be the last one to run in the suite)
     delete_ontologies_and_submissions
     create_ontologies_and_submissions(@@options)

test/controllers/test_ontologies_controller.rb

@@ -188,7 +188,9 @@ def test_download_ontology
   end
 
   def test_download_ontology_csv
-    num_onts_created, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true)
+    num_onts_created, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 1,
+                                                                                     process_submission: true,
+                                                                                     process_options:{process_rdf: true, extract_metadata: true, index_search: true})
     ont = onts.first
     acronym = created_ont_acronyms.first
 
@@ -220,13 +222,13 @@ def test_download_acl_only
     begin
       allowed_user = User.new({
         username: "allowed",
-        email: "test@example.org",
+        email: "test1@example.org",
         password: "12345"
       })
       allowed_user.save
       blocked_user = User.new({
         username: "blocked",
-        email: "test@example.org",
+        email: "test2@example.org",
         password: "12345"
       })
       blocked_user.save
@@ -296,6 +298,32 @@ def test_on_demand_ontology_pull
     end
   end
 
+  def test_detach_a_view
+    view = Ontology.find(@@view_acronym).include(:viewOf).first
+    ont =  view.viewOf
+    refute_nil view
+    refute_nil ont
+
+    remove_view_of = {viewOf: ''}
+    patch "/ontologies/#{@@view_acronym}", MultiJson.dump(remove_view_of), "CONTENT_TYPE" => "application/json"
+
+    assert last_response.status == 204
+
+    get "/ontologies/#{@@view_acronym}"
+    onto = MultiJson.load(last_response.body)
+    assert_nil onto["viewOf"]
+
+
+    add_view_of = {viewOf: @@acronym}
+    patch "/ontologies/#{@@view_acronym}", MultiJson.dump(add_view_of), "CONTENT_TYPE" => "application/json"
+
+    assert last_response.status == 204
+
+    get "/ontologies/#{@@view_acronym}?include=all"
+    onto = MultiJson.load(last_response.body)
+    assert_equal onto["viewOf"], ont.id.to_s
+  end
+
   private
 
   def start_server

test/controllers/test_ontology_submissions_controller.rb

@@ -18,7 +18,10 @@ def self._set_vars
       administeredBy: "tim",
       "file" => Rack::Test::UploadedFile.new(@@test_file, ""),
       released: DateTime.now.to_s,
-      contact: [{name: "test_name", email: "[email protected]"}]
+      contact: [{name: "test_name", email: "[email protected]"}],
+      URI: 'https://test.com/test',
+      status: 'production',
+      description: 'ontology description'
     }
     @@status_uploaded = "UPLOADED"
     @@status_rdf = "RDF"
@@ -36,6 +39,12 @@ def self._create_onts
     ont.save
   end
 
+  def setup
+    delete_ontologies_and_submissions
+    ont = Ontology.new(acronym: @@acronym, name: @@name, administeredBy: [@@user])
+    ont.save
+  end
+
   def test_submissions_for_given_ontology
     num_onts_created, created_ont_acronyms = create_ontologies_and_submissions(ont_count: 1)
     ontology = created_ont_acronyms.first
@@ -156,13 +165,13 @@ def test_download_acl_only
     begin
       allowed_user = User.new({
         username: "allowed",
-        email: "test@example.org",
+        email: "test4@example.org",
         password: "12345"
       })
       allowed_user.save
       blocked_user = User.new({
         username: "blocked",
-        email: "test@example.org",
+        email: "test5@example.org",
         password: "12345"
       })
       blocked_user.save
@@ -235,5 +244,4 @@ def test_ontology_submissions_access_controller
       del.delete if del
     end
   end
-
 end

test/controllers/test_properties_controller.rb

@@ -5,6 +5,7 @@ class TestPropertiesController < TestCase
   def self.before_suite
     count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                   process_submission: true,
+                                                                                                  process_options:{process_rdf: true, extract_metadata: false},
                                                                                                   acronym: "BROSEARCHTEST",
                                                                                                   name: "BRO Search Test",
                                                                                                   file_path: "./test/data/ontology_files/BRO_v3.2.owl",
@@ -15,6 +16,7 @@ def self.before_suite
 
     count, acronyms, mccl = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                    process_submission: true,
+                                                                                                   process_options:{process_rdf: true, extract_metadata: true},
                                                                                                    acronym: "MCCLSEARCHTEST",
                                                                                                    name: "MCCL Search Test",
                                                                                                    file_path: "./test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl",

test/controllers/test_properties_search_controller.rb

@@ -5,6 +5,7 @@ class TestPropertiesSearchController < TestCase
   def self.before_suite
     count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                   process_submission: true,
+                                                                                                  process_options:{process_rdf: true, extract_metadata: false, index_properties: true},
                                                                                                   acronym: "BROSEARCHTEST",
                                                                                                   name: "BRO Search Test",
                                                                                                   file_path: "./test/data/ontology_files/BRO_v3.2.owl",
@@ -15,6 +16,7 @@ def self.before_suite
 
     count, acronyms, mccl = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                    process_submission: true,
+                                                                                                   process_options:{process_rdf: true, extract_metadata: false, index_properties: true},
                                                                                                    acronym: "MCCLSEARCHTEST",
                                                                                                    name: "MCCL Search Test",
                                                                                                    file_path: "./test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl",

test/controllers/test_recommender_controller.rb

@@ -14,7 +14,7 @@ def self.before_suite
       @@redis.del(mappings)
     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)
     annotator = Annotator::Models::NcboAnnotator.new
     annotator.init_redis_for_tests()
     annotator.create_term_cache_from_ontologies(@@ontologies, false)

test/controllers/test_recommender_v1_controller.rb

@@ -1,10 +1,10 @@
 require_relative '../test_case'
 
-class TestRecommenderController < TestCase
+class TestRecommenderV1Controller < 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)
     @@text = <<eos
 Ginsenosides chemistry, biosynthesis, analysis, and potential health effects in software concept or data." "Ginsenosides are a special group of triterpenoid saponins that can be classified into two groups by the skeleton of their aglycones, namely dammarane- and oleanane-type. Ginsenosides are found nearly exclusively in Panax species (ginseng) and up to now more than 150 naturally occurring ginsenosides have been isolated from roots, leaves/stems, fruits, and/or flower heads of ginseng. The same concept indicates Ginsenosides have been the target of a lot of research as they are believed to be the main active principles behind the claims of ginsengs efficacy. The potential health effects of ginsenosides that are discussed in this chapter include anticarcinogenic, immunomodulatory, anti-inflammatory, antiallergic, antiatherosclerotic, antihypertensive, and antidiabetic effects as well as antistress activity and effects on the central nervous system. Ginsensoides can be metabolized in the stomach (acid hydrolysis) and in the gastrointestinal tract (bacterial hydrolysis) or transformed to other ginsenosides by drying and steaming of ginseng to more bioavailable and bioactive ginsenosides. The metabolization and transformation of intact ginsenosides, which seems to play an important role for their potential health effects, are discussed. Qualitative and quantitative analytical techniques for the analysis of ginsenosides are important in relation to quality control of ginseng products and plant material and for the determination of the effects of processing of plant material as well as for the determination of the metabolism and bioavailability of ginsenosides. Analytical techniques for the analysis of ginsenosides that are described in this chapter are thin-layer chromatography (TLC), high-performance liquid chromatography (HPLC) combined with various detectors, gas chromatography (GC), colorimetry, enzyme immunoassays (EIA), capillary electrophoresis (CE), nuclear magnetic resonance (NMR) spectroscopy, and spectrophotometric methods.
 eos

test/middleware/test_rack_attack.rb

@@ -18,14 +18,14 @@ def self.before_suite
     LinkedData::OntologiesAPI.settings.req_per_second_per_ip = 1
     LinkedData::OntologiesAPI.settings.safe_ips = Set.new(["1.2.3.4", "1.2.3.5"])
 
-    @@user = LinkedData::Models::User.new({username: "user", password: "test_password", email: "test_email@example.org"})
+    @@user = LinkedData::Models::User.new({username: "user", password: "test_password", email: "test_email1@example.org"})
     @@user.save
 
-    @@bp_user = LinkedData::Models::User.new({username: "ncbobioportal", password: "test_password", email: "test_email@example.org"})
+    @@bp_user = LinkedData::Models::User.new({username: "ncbobioportal", password: "test_password", email: "test_email2@example.org"})
     @@bp_user.save
 
     admin_role = LinkedData::Models::Users::Role.find("ADMINISTRATOR").first
-    @@admin = LinkedData::Models::User.new({username: "admin", password: "test_password", email: "test_email@example.org", role: [admin_role]})
+    @@admin = LinkedData::Models::User.new({username: "admin", password: "test_password", email: "test_email3@example.org", role: [admin_role]})
     @@admin.save
 
     # Redirect output or we get a bunch of noise from Rack (gets reset in the after_suite method).
@@ -34,8 +34,8 @@ def self.before_suite
     $stdout = File.open("/dev/null", "w")
     $stderr = File.open("/dev/null", "w")
 
-    # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports
-    @@port1 = Random.rand(55000..65535)
+
+    @@port1 = self.new('').unused_port
 
     # Fork the process to create two servers. This isolates the Rack::Attack configuration, which makes other tests fail if included.
     @@pid1 = fork do
@@ -47,7 +47,7 @@ def self.before_suite
       Signal.trap("HUP") { Process.exit! }
     end
 
-    @@port2 = Random.rand(55000..65535) # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports
+    @@port2 =  self.new('').unused_port
     @@pid2 = fork do
       require_relative '../../config/rack_attack'
       Rack::Server.start(

test/test_case.rb

@@ -21,7 +21,9 @@
 require_relative 'test_log_file'
 require_relative '../app'
 require 'minitest/unit'
+require 'webmock/minitest'
 MiniTest::Unit.autorun
+WebMock.allow_net_connect!
 require 'rack/test'
 require 'multi_json'
 require 'oj'
@@ -144,6 +146,9 @@ 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
 
@@ -214,4 +219,24 @@ def self.reset_to_not_admin(user)
     user.save
   end
 
+  def unused_port
+    max_retries = 5
+    retries = 0
+    server_port = Random.rand(55000..65535)
+    while port_in_use?(server_port)
+      retries += 1
+      break if retries >= max_retries
+      server_port = Random.rand(55000..65535)
+    end
+    server_port
+  end
+  private
+  def port_in_use?(port)
+    server = TCPServer.new(port)
+    server.close
+    false
+  rescue Errno::EADDRINUSE
+    true
+  end
+
 end