Develop to master merge, release v5.33.4

Gemfile

@@ -42,13 +42,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
-gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
-
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
+gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop'
+gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 39f67ab7fae7675b6ff417ace0ab923e40ffcbcd
-  branch: master
+  revision: 35721855ba808517698d8b94eb38d4553001c4b6
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: b6d50ebb79f114bf81a1cd89d0f8b4d4cbcddda2
-  branch: master
+  revision: 2abcd54c148d0983570d681506002d9d3782d2eb
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -27,8 +27,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 095ee0fab70b0fe0f2486655811cc8347b6a63ff
-  branch: master
+  revision: 8fa7a03a5a6ca63ebb3675fb9f7b2f1e1f408e2f
+  branch: develop
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -45,8 +45,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 9dbd4f179e42c52095129d353a5ac584e9bd47f3
-  branch: master
+  revision: 084cfc74a78b1c6334f3b74e228ddbf80d36e30a
+  branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -56,8 +56,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 0ce77f2781ac3353716407c22d8fc16d9bfd2c8f
-  branch: master
+  revision: 6389fa2052e06ff8e21c64fd1be0030beca4c828
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -76,8 +76,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
-  branch: master
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -235,7 +235,7 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.1105)
     mini_mime (1.1.5)
-    minitest (5.25.1)
+    minitest (5.25.2)
     minitest-hooks (1.5.2)
       minitest (> 5.3)
     minitest-stub_any_instance (1.0.3)
@@ -260,7 +260,7 @@ GEM
       net-protocol
     net-ssh (7.3.0)
     netrc (0.11.0)
-    newrelic_rpm (9.15.0)
+    newrelic_rpm (9.16.0)
     oj (3.16.7)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
@@ -456,4 +456,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.5.7
+   2.5.20

test/controllers/test_classes_controller.rb

@@ -106,8 +106,7 @@ def test_all_class_pages
       assert last_response.ok?
       count_terms = count_terms + page_response["collection"].length
     end while page_response["nextPage"]
-    #bnodes thing got fixed. changed to 486.
-    assert_equal 486, count_terms
+    assert_equal 487, count_terms
 
     #one more page should bring no results
     call = "/ontologies/#{ont.acronym}/classes"
@@ -295,42 +294,43 @@ def test_descendants_for_cls
     descendants_data = {}
     descendants_data['http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research'] =[
       "http://bioontology.org/ontologies/ResearchArea.owl#Behavioral_Science",
- "http://bioontology.org/ontologies/ResearchArea.owl#Bioinformatics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Biostatistics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Clinical_Studies",
- "http://bioontology.org/ontologies/ResearchArea.owl#Computational_Biology",
- "http://bioontology.org/ontologies/ResearchArea.owl#Epidemiology",
- "http://bioontology.org/ontologies/ResearchArea.owl#Genomics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Metabolomics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Nursing",
- "http://bioontology.org/ontologies/ResearchArea.owl#Outcomes_Research",
- "http://bioontology.org/ontologies/ResearchArea.owl#Pathology",
- "http://bioontology.org/ontologies/ResearchArea.owl#Pediatrics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Pharmacokinetics_Pharmacodynamics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Physiology",
- "http://bioontology.org/ontologies/ResearchArea.owl#Preclinical",
- "http://bioontology.org/ontologies/ResearchArea.owl#Proteomics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Psychometrics",
- "http://bioontology.org/ontologies/ResearchArea.owl#Research_IT",
- "http://bioontology.org/ontologies/ResearchArea.owl#Toxicology"]
+       "http://bioontology.org/ontologies/ResearchArea.owl#Bioinformatics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Biostatistics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Clinical_Studies",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Computational_Biology",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Epidemiology",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Genomics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Metabolomics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Nursing",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Outcomes_Research",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Pathology",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Pediatrics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Pharmacokinetics_Pharmacodynamics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Physiology",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Preclinical",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Proteomics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Psychometrics",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Research_IT",
+       "http://bioontology.org/ontologies/ResearchArea.owl#Toxicology"]
 
     descendants_data['http://bioontology.org/ontologies/Activity.owl#Activity'] =
       ["http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management",
- "http://bioontology.org/ontologies/Activity.owl#Community_Engagement",
- "http://bioontology.org/ontologies/Activity.owl#Gene_Therapy",
- "http://bioontology.org/ontologies/Activity.owl#Health_Services",
- "http://bioontology.org/ontologies/Activity.owl#IRB",
- "http://bioontology.org/ontologies/Activity.owl#Medical_Device_Development",
- "http://bioontology.org/ontologies/Activity.owl#Regulatory_Compliance",
- "http://bioontology.org/ontologies/Activity.owl#Research_Funding",
- "http://bioontology.org/ontologies/Activity.owl#Research_Lab_Management",
- "http://bioontology.org/ontologies/Activity.owl#Resource_Inventory",
- "http://bioontology.org/ontologies/Activity.owl#Small_Molecule",
- "http://bioontology.org/ontologies/Activity.owl#Social_Networking",
- "http://bioontology.org/ontologies/Activity.owl#Software_Development",
- "http://bioontology.org/ontologies/Activity.owl#Surgical_Procedure",
- "http://bioontology.org/ontologies/Activity.owl#Therapeutics",
- "http://bioontology.org/ontologies/Activity.owl#Training"]
+       "http://bioontology.org/ontologies/Activity.owl#Catalog",
+       "http://bioontology.org/ontologies/Activity.owl#Community_Engagement",
+       "http://bioontology.org/ontologies/Activity.owl#Gene_Therapy",
+       "http://bioontology.org/ontologies/Activity.owl#Health_Services",
+       "http://bioontology.org/ontologies/Activity.owl#IRB",
+       "http://bioontology.org/ontologies/Activity.owl#Medical_Device_Development",
+       "http://bioontology.org/ontologies/Activity.owl#Regulatory_Compliance",
+       "http://bioontology.org/ontologies/Activity.owl#Research_Funding",
+       "http://bioontology.org/ontologies/Activity.owl#Research_Lab_Management",
+       "http://bioontology.org/ontologies/Activity.owl#Resource_Inventory",
+       "http://bioontology.org/ontologies/Activity.owl#Small_Molecule",
+       "http://bioontology.org/ontologies/Activity.owl#Social_Networking",
+       "http://bioontology.org/ontologies/Activity.owl#Software_Development",
+       "http://bioontology.org/ontologies/Activity.owl#Surgical_Procedure",
+       "http://bioontology.org/ontologies/Activity.owl#Therapeutics",
+       "http://bioontology.org/ontologies/Activity.owl#Training"]
 
     clss_ids = [ 'http://bioontology.org/ontologies/Activity.owl#Activity',
             "http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research" ]
@@ -514,8 +514,7 @@ def test_class_page_with_metric_count
       assert last_response.ok?
       count_terms = count_terms + page_response["collection"].length
     end while page_response["nextPage"]
-    #bnodes thing got fixed. changed to 486.
-    assert_equal 486, count_terms
+    assert_equal 487, count_terms
 
     #one more page should bring no results
     call = "/ontologies/#{ont.acronym}/classes"
@@ -526,7 +525,7 @@ def test_class_page_with_metric_count
     assert page_response["collection"].length == 0
   end
 
-  def test_default_multilingual
+  def test_multilingual
     ont = Ontology.find("TEST-ONT-0").include(:acronym).first
     sub = ont.latest_submission
     sub.bring_remaining
@@ -561,10 +560,54 @@ def test_default_multilingual
     assert last_response.ok?
     page_response = MultiJson.load(last_response.body)
     # show french value as specified in submission naturalLanguage
-    assert_equal 'Biospecimen Management', page_response["prefLabel"]
+    assert_equal 'Gestion des échantillons biologiques', page_response["prefLabel"]
 
     sub.naturalLanguage = []
     sub.save
+
+    # prefLabel NOT present, rdfs:label is defined in multiple languages, default portal language
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Catalog')}?lang=all"
+    assert last_response.ok?
+    page_response = MultiJson.load(last_response.body)
+    assert_equal 'Catalog', page_response["prefLabel"]["en"]
+    assert_equal 'Catalogo', page_response["prefLabel"]["it"]
+    assert_equal 'Catalogue', page_response["prefLabel"]["fr"]
+    assert_equal 'Catálogo', page_response["prefLabel"]["es"]
+    assert_equal 'カタログ', page_response["prefLabel"]["ja"]
+
+    # prefLabel NOT present, rdfs:label is defined in multiple languages,
+    # portal language is set to one of the defined languages
+    sub.naturalLanguage = ['ja']
+    sub.save
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Catalog')}"
+    assert last_response.ok?
+    page_response = MultiJson.load(last_response.body)
+    # show Japanese value as specified in submission naturalLanguage
+    assert_equal 'カタログ', page_response["prefLabel"]
+
+    sub.naturalLanguage = []
+    sub.save
+
+    # prefLabel NOT present, multiple rdfs:label(s) are defined with no language designation
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Regulatory_Compliance')}"
+    assert last_response.ok?
+    page_response = MultiJson.load(last_response.body)
+    assert_equal 'Regulatory Compliance', page_response["prefLabel"]
+
+    # prefLabel is defined in a non-language format as well as in French and Italian - default check with no language requested
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Research_Lab_Management')}"
+    assert last_response.ok?
+    page_response = MultiJson.load(last_response.body)
+    assert_equal 'Research Lab Management', page_response["prefLabel"]
+
+    # prefLabel is defined in a non-language format as well as in French and Italian - all languages are requested
+    get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Research_Lab_Management')}?lang=all"
+    assert last_response.ok?
+    page_response = MultiJson.load(last_response.body)
+
+    assert_equal 'Research Lab Management', page_response["prefLabel"]["none"]
+    assert_equal 'Gestion du laboratoire de recherche', page_response["prefLabel"]["fr"]
+    assert_equal 'Gestione del laboratorio di ricerca', page_response["prefLabel"]["it"]
   end
 
 end

test/controllers/test_metrics_controller.rb

@@ -9,15 +9,15 @@ def before_suite
     end
     OntologySubmission.all.each {|s| s.delete }
     Ontology.all.each {|o| o.delete }
-    @@data = {"classes"=>486,
-              "averageChildCount"=>5,
-              "maxChildCount"=>65,
-              "classesWithOneChild"=>14,
-              "classesWithMoreThan25Children"=>2,
-              "classesWithNoDefinition"=>11,
-              "individuals"=>124,
-              "properties"=>63,
-              "maxDepth"=> 7 }
+    @@data = {"classes" => 487,
+              "averageChildCount" => 5,
+              "maxChildCount" => 65,
+              "classesWithOneChild" => 14,
+              "classesWithMoreThan25Children" => 2,
+              "classesWithNoDefinition" => 11,
+              "individuals" => 124,
+              "properties" => 63,
+              "maxDepth" => 7 }
     @@options = { ont_count: 2,
                   submission_count: 3,
                   submissions_to_process: [1, 2],
@@ -35,8 +35,8 @@ def test_all_metrics
     #TODO: improve this test and test for two different ontologies
     #though this is tested in LD
     metrics.each do |m|
-      @@data.each do |k,v|
-        assert_equal(m[k], v)
+      @@data.each do |k, v|
+        assert_equal(v, m[k])
       end
       assert m["@id"] == m["submission"].first + "/metrics"
     end
@@ -49,27 +49,29 @@ def test_single_metrics
     metrics = MultiJson.load(last_response.body)
 
     @@data.each do |k,v|
-      assert_equal(metrics[k], v)
+      assert_equal(v, metrics[k])
     end
   end
 
   def test_metrics_with_submission_id
     ontology = 'TEST-ONT-0'
-    get "/ontologies/#{ontology}/submissions/1/metrics"
+    get "/ontologies/#{ontology}/submissions/2/metrics"
     assert last_response.ok?
     metrics = MultiJson.load(last_response.body)
+
     @@data.each do |k,v|
-      assert_equal(metrics[k], v)
+      assert_equal(v, metrics[k])
     end
   end
 
   def test_metrics_with_submission_id_as_param
     ontology = 'TEST-ONT-0'
-    get "/ontologies/#{ontology}/metrics?submissionId=1"
+    get "/ontologies/#{ontology}/metrics?ontology_submission_id=2"
     assert last_response.ok?
     metrics = MultiJson.load(last_response.body)
+
     @@data.each do |k,v|
-      assert_equal(metrics[k], v)
+      assert_equal(v, metrics[k])
     end
   end