Merge pull request #43 from ncbo/develop

Develop to master merge, release v5.33.4
ncbo · Nov 27, 2024 · 1709cce · 1709cce
2 parents b6d50eb + 11838eb
commit 1709cce
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diff --git a/Gemfile b/Gemfile
@@ -15,6 +15,6 @@ group :development do
 end
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
diff --git a/Gemfile.lock b/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/ontologies_linked_data.git
-  revision: 0ce77f2781ac3353716407c22d8fc16d9bfd2c8f
-  branch: master
+  revision: 6389fa2052e06ff8e21c64fd1be0030beca4c828
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -36,8 +36,8 @@ 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)

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -80,7 +80,7 @@ services:
       retries: 10
 
   mgrep-ut:
-    image: ontoportal/mgrep:0.0.2
+    image: ontoportal/mgrep:0.0.3
     platform: linux/amd64
     healthcheck:
       test: ["CMD", "nc", "-z", "-v", "127.0.0.1", "55556"]

diff --git a/test/test_annotator.rb b/test/test_annotator.rb
@@ -251,16 +251,17 @@ def test_annotate
           with_synonyms: true
       })
       direct = annotations
-      assert direct.length >= size && direct.length > 0
+      assert_operator 0, :<, direct.length
+      assert_operator size, :<, direct.length
       found = 0
       class_page.each do |cls|
         if cls.prefLabel.length > 2
           #TODO: This assertion may fail if the dictionary file on mgrep server does not contain the terms from the test ontologies
-          assert (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length > 0
+          assert_operator 0, :<, (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length, "expected to find #{cls.id}"
           found += 1
         end
       end
-      assert found >= size
+      assert_operator size, :<=, found
     end
 
     # test for a specific class annotation
@@ -279,12 +280,12 @@ def test_annotate
         with_synonyms: true
     })
 
-    assert annotations.length == 1
-    assert annotations.first.annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Storage"
-    assert annotations.first.annotations.length == 1
-    assert annotations.first.annotations.first[:from] == 1
-    assert annotations.first.annotations.first[:to] == term_text.length
-    assert text[annotations.first.annotations.first[:from] - 1, annotations.first.annotations.first[:to]] == term_text
+    assert_equal 1, annotations.length
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Storage", annotations.first.annotatedClass.id.to_s
+    assert_equal 1, annotations.first.annotations.length
+    assert_equal 1, annotations.first.annotations.first[:from]
+    assert_equal term_text.length, annotations.first.annotations.first[:to]
+    assert_equal term_text, text[annotations.first.annotations.first[:from] - 1, annotations.first.annotations.first[:to]]
 
     # check for a non-existent ontology
     non_existent_ont = ["DOESNOTEXIST"]
@@ -370,14 +371,15 @@ def test_annotate_minsize_term
     })
     direct = annotations
 
-    assert direct.length >= size && direct.length > 0
+    assert_operator 0, :<, direct.length
+    assert_operator size, :<, direct.length
     found = 0
     filter_out_next = []
     must_be_next = []
     class_page.each do |cls|
       if cls.prefLabel.length > 2
         #TODO: This assertion may fail if the dictionary file on mgrep server does not contain the terms from the test ontologies
-        assert (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length > 0
+        assert_operator 0, :<, (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length
         found += 1
         if cls.prefLabel.length < 10
           filter_out_next << cls
@@ -403,12 +405,13 @@ def test_annotate_minsize_term
 
     direct = annotations
     filter_out_next.each do |cls|
-      assert (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length == 0
+      assert_equal 0, (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length
     end
     must_be_next.each do |cls|
-      assert (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length > 0
+      assert_operator 0, :<, (direct.select { |x| x.annotatedClass.id.to_s == cls.id.to_s }).length
     end
-    assert must_be_next.length > 0 && filter_out_next.length > 0
+    assert_operator 0, :<, must_be_next.length
+    assert_operator 0, :<, filter_out_next.length
   end
 
   def test_annotate_stop_words
@@ -430,7 +433,7 @@ def test_annotate_stop_words
                 "http://purl.obolibrary.org/obo/MCBCC_0000296#Deletion"]
 
     not_show.each do |cls|
-      assert (annotations.select { |x| x.annotatedClass.id.to_s == cls }).length > 0
+      assert_operator 0, :<, (annotations.select { |x| x.annotatedClass.id.to_s == cls }).length
     end
 
     #annotation should not show up
@@ -449,7 +452,7 @@ def test_annotate_stop_words
     })
 
     not_show.each do |cls|
-      assert (annotations.select { |x| x.annotatedClass.id.to_s == cls }).length == 0
+      assert_equal 0, (annotations.select { |x| x.annotatedClass.id.to_s == cls }).length
     end
 
     #empty array must annotate all
@@ -468,7 +471,7 @@ def test_annotate_stop_words
     })
 
     not_show.each do |cls|
-      assert (annotations.select { |x| x.annotatedClass.id.to_s == cls }).length > 0
+      assert_operator 0, :<, (annotations.select { |x| x.annotatedClass.id.to_s == cls }).length
     end
   end
 
@@ -477,16 +480,16 @@ def test_annotate_hierarchy
     text = "Aggregate Human Data Aggregate Human Data"
     annotator = Annotator::Models::NcboAnnotator.new
     annotations = annotator.annotate(text)
-    assert annotations.length == 1
-    assert annotations.first.annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data"
-    assert annotations.first.annotatedClass.submission.ontology.acronym == "BROTEST-0"
-    assert annotations.first.annotations.length == 2
-    assert annotations.first.annotations.first[:from] = 1
-    assert annotations.first.annotations.first[:to] = 1+("Aggregate Human Data".length)
-    assert annotations.first.annotations[1][:from] = 2 + ("Aggregate Human Data".length)
-    assert text[annotations.first.annotations.first[:from]-1,annotations.first.annotations.first[:to]-1] == "Aggregate Human Data"
-    assert annotations.first.annotations[1][:to] == (1 + ("Aggregate Human Data".length)) + ("Aggregate Human Data".length)
-    assert text[annotations.first.annotations[1][:from]-1,annotations.first.annotations[1][:to]-1] == "Aggregate Human Data"
+    assert_equal 1, annotations.length
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data", annotations.first.annotatedClass.id.to_s
+    assert_equal "BROTEST-0", annotations.first.annotatedClass.submission.ontology.acronym
+    assert_equal 2, annotations.first.annotations.length
+    assert_equal 1, annotations.first.annotations.first[:from]
+    assert_equal "Aggregate Human Data".length, annotations.first.annotations.first[:to]
+    assert_equal 2 + ("Aggregate Human Data".length), annotations.first.annotations[1][:from]
+    assert_equal "Aggregate Human Data", text[annotations.first.annotations.first[:from]-1,annotations.first.annotations.first[:to]]
+    assert_equal (1 + ("Aggregate Human Data".length)) + ("Aggregate Human Data".length), annotations.first.annotations[1][:to]
+    assert_equal "Aggregate Human Data", text[annotations.first.annotations[1][:from]-1,annotations.first.annotations[1][:to]-1]
     annotations = annotator.annotate(text, {
         ontologies: [],
         semantic_types: [],
@@ -499,16 +502,16 @@ def test_annotate_hierarchy
         with_synonyms: true
     })
 
-    assert annotations.length == 1
-    assert annotations.first.annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data"
-    assert annotations.first.annotatedClass.submission.ontology.acronym == "BROTEST-0"
-    assert annotations.first.annotations.length == 2
-    assert annotations.first.annotations.first[:from] = 1
-    assert annotations.first.annotations.first[:to] = 1+("Aggregate Human Data".length)
+    assert_equal 1, annotations.length
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data", annotations.first.annotatedClass.id.to_s
+    assert_equal "BROTEST-0", annotations.first.annotatedClass.submission.ontology.acronym
+    assert_equal 2, annotations.first.annotations.length
+    assert_equal 1, annotations.first.annotations.first[:from]
+    assert_equal "Aggregate Human Data".length, annotations.first.annotations.first[:to]
 
-    assert annotations.first.hierarchy.length == 1
-    assert annotations.first.hierarchy.first.annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Care_Data"
-    assert annotations.first.hierarchy.first.distance == 1
+    assert_equal 1, annotations.first.hierarchy.length
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Care_Data", annotations.first.hierarchy.first.annotatedClass.id.to_s
+    assert_equal 1, annotations.first.hierarchy.first.distance
     annotations = annotator.annotate(text, {
         ontologies: [],
         semantic_types: [],
@@ -521,13 +524,13 @@ def test_annotate_hierarchy
         with_synonyms: true
     })
 
-    assert annotations.first.hierarchy.length == 3
-    assert annotations.first.hierarchy.first.annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Care_Data"
-    assert annotations.first.hierarchy.first.distance == 1
-    assert annotations.first.hierarchy[1].annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Resource"
-    assert annotations.first.hierarchy[1].distance == 2
-    assert annotations.first.hierarchy[2].annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Information_Resource"
-    assert annotations.first.hierarchy[2].distance == 3
+    assert_equal 3, annotations.first.hierarchy.length
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Care_Data", annotations.first.hierarchy.first.annotatedClass.id.to_s
+    assert_equal 1, annotations.first.hierarchy.first.distance
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Resource", annotations.first.hierarchy[1].annotatedClass.id.to_s
+    assert_equal 2, annotations.first.hierarchy[1].distance
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Information_Resource", annotations.first.hierarchy[2].annotatedClass.id.to_s
+    assert_equal 3, annotations.first.hierarchy[2].distance
   end
 
   def test_annotate_hierachy_terms_multiple
@@ -546,56 +549,56 @@ def test_annotate_hierachy_terms_multiple
         with_synonyms: true
     })
 
-    assert annotations[0].annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data"
-    assert annotations[0].annotations.length == 3
-    assert annotations[0].hierarchy.length == 4
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Aggregate_Human_Data", annotations[0].annotatedClass.id.to_s
+    assert_equal 3, annotations[0].annotations.length
+    assert_equal 4, annotations[0].hierarchy.length
     hhh = annotations[0].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
     hhh.sort!
 
-    assert hhh == [
+    assert_equal [
       "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource",
       "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Information_Resource",
       "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Clinical_Care_Data",
       "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Resource"
-    ].sort
+    ].sort, hhh
 
-    assert annotations[1].annotatedClass.id.to_s == "http://purl.obolibrary.org/obo/MCBCC_0000288#ChromosomalMutation"
-    assert annotations[1].annotations.length == 2
+    assert_equal "http://purl.obolibrary.org/obo/MCBCC_0000288#ChromosomalMutation", annotations[1].annotatedClass.id.to_s
+    assert_equal 2, annotations[1].annotations.length
     hhh = annotations[1].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
-    hhh == ["http://purl.obolibrary.org/obo/MCBCC_0000287#GeneticVariation"]
+    assert_equal ["http://purl.obolibrary.org/obo/MCBCC_0000287#GeneticVariation"], hhh
 
-    assert annotations[2].annotatedClass.id.to_s == "http://purl.obolibrary.org/obo/MCBCC_0000289#ChromosomalDeletion"
-    assert annotations[2].annotations.length == 1
+    assert_equal "http://purl.obolibrary.org/obo/MCBCC_0000289#ChromosomalDeletion", annotations[2].annotatedClass.id.to_s
+    assert_equal 1, annotations[2].annotations.length
     hhh = annotations[2].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
     assert hhh == ["http://purl.obolibrary.org/obo/MCBCC_0000287#GeneticVariation",
             "http://purl.obolibrary.org/obo/MCBCC_0000288#ChromosomalMutation"]
 
-    assert annotations[3].annotatedClass.id.to_s == "http://purl.obolibrary.org/obo/MCBCC_0000296#Deletion"
+    assert_equal "http://purl.obolibrary.org/obo/MCBCC_0000296#Deletion", annotations[3].annotatedClass.id.to_s
     hhh = annotations[3].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
-    assert hhh = ["http://purl.obolibrary.org/obo/MCBCC_0000287#GeneticVariation",
-     "http://purl.obolibrary.org/obo/MCBCC_0000295#GeneMutation"]
+    assert_equal ["http://purl.obolibrary.org/obo/MCBCC_0000287#GeneticVariation",
+     "http://purl.obolibrary.org/obo/MCBCC_0000295#GeneMutation"], hhh
 
-    assert annotations[4].annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Resource"
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Data_Resource", annotations[4].annotatedClass.id.to_s
     hhh = annotations[4].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
-    assert hhh == ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource",
- "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Information_Resource"]
+    assert_equal ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource",
+ "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Information_Resource"], hhh
 
-    assert annotations[5].annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource"
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource", annotations[5].annotatedClass.id.to_s
     hhh = annotations[5].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
-    assert hhh == [] #root
+    assert_empty hhh
 
-    assert annotations[6].annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Federal_Funding_Resource"
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Federal_Funding_Resource", annotations[6].annotatedClass.id.to_s
     hhh = annotations[6].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
-    assert hhh == ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource",
- "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Funding_Resource"]
+    assert_equal ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource",
+ "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Funding_Resource"], hhh
 
-    assert annotations[7].annotatedClass.id.to_s == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Funding_Resource"
+    assert_equal "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Funding_Resource", annotations[7].annotatedClass.id.to_s
     hhh = annotations[7].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
-    assert hhh == ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource" ]
+    assert_equal ["http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Resource" ], hhh
 
-    assert annotations[8].annotatedClass.id.to_s == "http://purl.obolibrary.org/obo/MCBCC_0000275#ReceptorAntagonists"
+    assert_equal "http://purl.obolibrary.org/obo/MCBCC_0000275#ReceptorAntagonists", annotations[8].annotatedClass.id.to_s
     hhh = annotations[8].hierarchy.sort {|x| x.distance }.map { |x| x.annotatedClass.id.to_s }
-    assert hhh == ["http://purl.obolibrary.org/obo/MCBCC_0000256#ChemicalsAndDrugs"]
+    assert_equal ["http://purl.obolibrary.org/obo/MCBCC_0000256#ChemicalsAndDrugs"], hhh
 
   end