Merge pull request #7 from ncbo/master

Sync with BioPortal release 2.5.0

.github/workflows/ruby.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        ruby-version: ['3.0', '3.1']
+        ruby-version: ['3.1']
     steps:
     - uses: actions/checkout@v3
     - name: Set up Ruby

Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    ontologies_api_client (2.4.0)
+    ontologies_api_client (2.5.0)
       activesupport (= 7.0.8)
       addressable (~> 2.8)
       excon
@@ -23,73 +23,75 @@ GEM
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
     ast (2.4.2)
-    bigdecimal (3.1.8)
+    bigdecimal (3.1.9)
     coderay (1.1.3)
-    concurrent-ruby (1.3.3)
-    excon (0.111.0)
-    faraday (2.10.0)
-      faraday-net_http (>= 2.0, < 3.2)
+    concurrent-ruby (1.3.5)
+    excon (1.2.3)
+    faraday (2.12.2)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
       logger
-    faraday-excon (2.1.0)
-      excon (>= 0.27.4)
-      faraday (~> 2.0)
+    faraday-excon (2.3.0)
+      excon (>= 1.0.0)
+      faraday (>= 2.11.0, < 3)
     faraday-follow_redirects (0.3.0)
       faraday (>= 1, < 3)
-    faraday-multipart (1.0.4)
-      multipart-post (~> 2)
-    faraday-net_http (3.1.0)
-      net-http
-    i18n (1.14.5)
+    faraday-multipart (1.1.0)
+      multipart-post (~> 2.0)
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
+    i18n (1.14.7)
       concurrent-ruby (~> 1.0)
-    json (2.7.2)
-    language_server-protocol (3.17.0.3)
-    logger (1.6.0)
+    json (2.9.1)
+    language_server-protocol (3.17.0.4)
+    logger (1.6.5)
     lz4-ruby (0.3.3)
     method_source (1.1.0)
-    minitest (5.25.1)
-    minitest-hooks (1.5.1)
+    minitest (5.25.4)
+    minitest-hooks (1.5.2)
       minitest (> 5.3)
     multi_json (1.15.0)
     multipart-post (2.4.1)
-    net-http (0.4.1)
+    net-http (0.6.0)
       uri
-    oj (3.16.4)
+    oj (3.16.9)
       bigdecimal (>= 3.0)
-    parallel (1.25.1)
-    parser (3.3.4.0)
+      ostruct (>= 0.2)
+    ostruct (0.6.1)
+    parallel (1.26.3)
+    parser (3.3.7.1)
       ast (~> 2.4.1)
       racc
-    pry (0.14.2)
+    pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (6.0.0)
-    racc (1.8.0)
+    public_suffix (6.0.1)
+    racc (1.8.1)
     rainbow (3.1.1)
     rake (13.2.1)
-    regexp_parser (2.9.2)
-    rexml (3.3.2)
-      strscan
-    rubocop (1.65.0)
+    regexp_parser (2.10.0)
+    rubocop (1.71.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 2.4, < 3.0)
-      rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.31.1, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.38.0, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.31.3)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.38.0)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
-    strscan (3.1.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.5.0)
-    uri (0.13.0)
+    unicode-display_width (3.1.4)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
+    uri (1.0.2)
 
 PLATFORMS
+  arm64-darwin-24
   ruby
   x86_64-darwin-16
   x86_64-darwin-17
@@ -105,4 +107,4 @@ DEPENDENCIES
   rubocop (~> 1.43)
 
 BUNDLED WITH
-   2.4.18
+   2.5.11

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2021, The Board of Trustees of Leland Stanford Junior University
+Copyright (c) 2025, The Board of Trustees of Leland Stanford Junior University
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are

README.md

@@ -153,14 +153,4 @@ For questions please email [[email protected]]([email protected].)
 
 ## License
 
-Copyright (c) 2024, The Board of Trustees of Leland Stanford Junior University All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-
-Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-
-Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE BOARD OF TRUSTEES OF LELAND STANFORD JUNIOR UNIVERSITY ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL The Board of Trustees of Leland Stanford Junior University OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-The views and conclusions contained in the software and documentation are those of the authors and should not be interpreted as representing official policies, either expressed or implied, of The Board of Trustees of Leland Stanford Junior University.
+This project is licensed under the [FreeBSD License](LICENSE.txt) © 2025 The Board of Trustees of Leland Stanford Junior University.

lib/ontologies_api_client/link_explorer.rb

@@ -61,9 +61,15 @@ def replace_template_elements(url, values = [])
 
         values = values.dup
         values = [values] unless values.is_a?(Array)
-        return url.gsub(/(\{.*?\})/) do
-          Addressable::URI.encode_component(values.shift, Addressable::URI::CharacterClasses::UNRESERVED)
+        escaped_value = Addressable::URI.encode_component(values.shift, Addressable::URI::CharacterClasses::UNRESERVED)
+        if url.match(/(\{.*?\})/)
+          url.gsub(/(\{.*?\})/) do
+            escaped_value
+          end
+        else
+          url + '/' + escaped_value
         end
+
       end
 
       def linkable_attributes

lib/ontologies_api_client/version.rb

@@ -2,6 +2,6 @@
 
 module LinkedData
   module Client
-    VERSION = '2.4.0'
+    VERSION = '2.5.0'
   end
 end

test/test_link_explorer.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+require_relative 'test_case'
+
+class LinkExplorerTest < LinkedData::Client::TestCase
+  def test_explore_ontology_submission_by_id
+    ont = LinkedData::Client::Models::Ontology.get('FMA')
+    sub = ont.explore.submissions('29')
+    refute_nil(sub)
+    assert_instance_of(LinkedData::Client::Models::OntologySubmission, sub)
+    assert_equal(29, sub.submissionId)
+  end
+
+  def test_explore_ontology_class_by_id
+    ont = LinkedData::Client::Models::Ontology.get('FMA')
+    cls = ont.explore.classes('http://purl.org/sig/ont/fma/fma70742')
+    refute_nil(cls)
+    assert_instance_of(LinkedData::Client::Models::Class, cls)
+    assert_equal('http://purl.org/sig/ont/fma/fma70742', cls.id)
+    assert_equal('Set of eyelashes', cls.prefLabel)
+  end
+
+  def test_explore_ontology_single_class
+    ont = LinkedData::Client::Models::Ontology.get('FMA')
+    cls = ont.explore.single_class('http://purl.org/sig/ont/fma/fma322428')
+    refute_nil(cls)
+    assert_instance_of(LinkedData::Client::Models::Class, cls)
+    assert_equal('http://purl.org/sig/ont/fma/fma322428', cls.id)
+    assert_equal('Set of salivary glands', cls.prefLabel)
+  end
+end