Merge pull request #2 from ncbo/master

Sync: merge releases 2.2.0 and 2.2.1 from ncbo

.github/workflows/ruby.yml

@@ -9,17 +9,19 @@ name: Ruby
 
 on:
   push:
-  pull_request:
+  pull_request_target:
+    types: [opened, reopened]
 
 jobs:
   test:
 
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         ruby-version: ['2.7', '3.0']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Ruby
     # To automatically get bug fixes and new Ruby versions for ruby/setup-ruby,
     # change this to (see https://github.com/ruby/setup-ruby#versioning):

Gemfile

@@ -3,5 +3,6 @@ source 'https://rubygems.org'
 gemspec
 
 gem 'rake'
+gem 'rubocop', '~> 1.43'
 gem 'pry'
 gem 'test-unit'

Gemfile.lock

@@ -1,11 +1,12 @@
 PATH
   remote: .
   specs:
-    ontologies_api_client (2.0.3)
-      activesupport (= 6.0.4.1)
+    ontologies_api_client (2.2.2)
+      activesupport (= 6.1.7.3)
+      addressable (~> 2.8)
       excon
       faraday
-      faraday-excon (~> 2.0.0)
+      faraday-excon
       faraday-multipart
       lz4-ruby
       multi_json
@@ -15,56 +16,82 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.0.4.1)
+    activesupport (6.1.7.3)
       concurrent-ruby (~> 1.0, >= 1.0.2)
-      i18n (>= 0.7, < 2)
-      minitest (~> 5.1)
-      tzinfo (~> 1.1)
-      zeitwerk (~> 2.2, >= 2.2.2)
+      i18n (>= 1.6, < 2)
+      minitest (>= 5.1)
+      tzinfo (~> 2.0)
+      zeitwerk (~> 2.3)
+    addressable (2.8.4)
+      public_suffix (>= 2.0.2, < 6.0)
+    ast (2.4.2)
     coderay (1.1.3)
-    concurrent-ruby (1.1.9)
-    excon (0.91.0)
-    faraday (2.0.1)
-      faraday-net_http (~> 2.0)
+    concurrent-ruby (1.2.2)
+    excon (0.100.0)
+    faraday (2.7.6)
+      faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
-    faraday-excon (2.0.0)
+    faraday-excon (2.1.0)
       excon (>= 0.27.4)
-      faraday (~> 2.0.0.alpha.pre.2)
-    faraday-multipart (1.0.3)
-      multipart-post (>= 1.2, < 3)
-    faraday-net_http (2.0.1)
-    i18n (1.10.0)
+      faraday (~> 2.0)
+    faraday-multipart (1.0.4)
+      multipart-post (~> 2)
+    faraday-net_http (3.0.2)
+    i18n (1.14.1)
       concurrent-ruby (~> 1.0)
+    json (2.6.3)
     lz4-ruby (0.3.3)
     method_source (1.0.0)
-    minitest (5.15.0)
+    minitest (5.18.1)
     multi_json (1.15.0)
-    multipart-post (2.1.1)
-    oj (3.13.11)
-    power_assert (2.0.1)
-    pry (0.14.1)
+    multipart-post (2.3.0)
+    oj (3.15.0)
+    parallel (1.22.1)
+    parser (3.2.0.0)
+      ast (~> 2.4.1)
+    power_assert (2.0.3)
+    pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
+    public_suffix (5.0.1)
+    rainbow (3.1.1)
     rake (13.0.6)
+    regexp_parser (2.6.2)
+    rexml (3.2.5)
+    rubocop (1.44.1)
+      json (~> 2.3)
+      parallel (~> 1.10)
+      parser (>= 3.2.0.0)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.8, < 3.0)
+      rexml (>= 3.2.5, < 4.0)
+      rubocop-ast (>= 1.24.1, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 2.4.0, < 3.0)
+    rubocop-ast (1.24.1)
+      parser (>= 3.1.1.0)
+    ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
     spawnling (2.1.5)
-    test-unit (3.5.3)
+    test-unit (3.5.7)
       power_assert
-    thread_safe (0.3.6)
-    tzinfo (1.2.10)
-      thread_safe (~> 0.1)
-    zeitwerk (2.5.4)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unicode-display_width (2.4.2)
+    zeitwerk (2.6.8)
 
 PLATFORMS
   ruby
   x86_64-darwin-16
   x86_64-darwin-17
+  x86_64-linux
 
 DEPENDENCIES
   ontologies_api_client!
   pry
   rake
+  rubocop (~> 1.43)
   test-unit
 
 BUNDLED WITH
-   2.1.4
+   2.3.22

config/config.test.rb

@@ -1,7 +1,8 @@
 # config.rb is required for testing
 # unit test makes calls to bioportal api so it needs a valid API key which can
 # be set via ENV variable UT_APIKEY
-abort('env variable UT_APIKEY is not set. Canceling tests...') unless ENV.include?('UT_APIKEY')
+abort('UT_APIKEY env variable is not set. Canceling tests') unless ENV.include?('UT_APIKEY')
+abort('UT_APIKEY env variable is set to an empty value. Canceling tests') unless ENV['UT_APIKEY'].size > 5
 
 LinkedData::Client.config do |config|
   config.rest_url   = 'https://data.bioontology.org'

lib/ontologies_api_client/http.rb

@@ -19,6 +19,7 @@ def members
   def length
     @table.keys.length
   end
+
   alias :size :length
 
   def to_a
@@ -37,7 +38,9 @@ def values_at(*selectors)
 module LinkedData
   module Client
     module HTTP
-      class Link < String; attr_accessor :media_type; end
+      class Link < String
+        attr_accessor :media_type;
+      end
 
       def self.conn
         unless LinkedData::Client.connection_configured?
@@ -53,7 +56,7 @@ def self.conn
       def self.get(path, params = {}, options = {})
         headers = options[:headers] || {}
         raw = options[:raw] || false # return the unparsed body of the request
-        params = params.delete_if {|k,v| v == nil || v.to_s.empty?}
+        params = params.delete_if { |k, v| v == nil || v.to_s.empty? }
         params[:ncbo_cache_buster] = Time.now.to_f if raw # raw requests don't get cached to ensure body is available
         invalidate_cache = params.delete(:invalidate_cache) || false
 
@@ -83,7 +86,7 @@ def self.get(path, params = {}, options = {})
           else
             obj = recursive_struct(load_json(response.body))
           end
-        rescue Exception => e
+        rescue StandardError => e
           puts "Problem getting #{path}" if $DEBUG
           raise e
         end
@@ -94,12 +97,12 @@ def self.get_batch(paths, params = {})
         responses = []
         if conn.in_parallel?
           conn.in_parallel do
-            paths.each {|p| responses << conn.get(p, params) }
+            paths.each { |p| responses << conn.get(p, params) }
           end
         else
           responses = threaded_request(paths, params)
         end
-        return responses
+        responses
       end
 
       def self.post(path, obj, options = {})
@@ -108,11 +111,12 @@ def self.post(path, obj, options = {})
           req.url path
           custom_req(obj, file, file_attribute, req)
         end
-        raise Exception, response.body if response.status >= 500
+        raise StandardError, response.body if response.status >= 500
+
         if options[:raw] || false # return the unparsed body of the request
-          return response.body
+          response.body
         else
-          return recursive_struct(load_json(response.body))
+          recursive_struct(load_json(response.body))
         end
       end
 
@@ -122,7 +126,8 @@ def self.put(path, obj)
           req.url path
           custom_req(obj, file, file_attribute, req)
         end
-        raise Exception, response.body if response.status >= 500
+        raise StandardError, response.body if response.status >= 500
+
         recursive_struct(load_json(response.body))
       end
 
@@ -132,13 +137,17 @@ def self.patch(path, obj)
           req.url path
           custom_req(obj, file, file_attribute, req)
         end
-        raise Exception, response.body if response.status >= 500
+        raise StandardError, response.body if response.status >= 500
+
+        response
       end
 
       def self.delete(id)
         puts "Deleting #{id}" if $DEBUG
         response = conn.delete id
-        raise Exception, response.body if response.status >= 500
+        raise StandardError, response.body if response.status >= 500
+
+        response
       end
 
       def self.object_from_json(json)
@@ -170,9 +179,11 @@ def self.custom_req(obj, file, file_attribute, req)
 
       def self.params_file_handler(params)
         return if params.nil?
+
         file, return_attribute = nil, nil
         params.dup.each do |attribute, value|
           next unless value.is_a?(File) || value.is_a?(Tempfile) || value.is_a?(ActionDispatch::Http::UploadedFile)
+
           filename = value.original_filename
           file = Faraday::UploadIO.new(value.path, "text/plain", filename)
           return_attribute = attribute
@@ -203,7 +214,7 @@ def self.recursive_struct(json_obj)
           context = json_obj.delete("@context") # strip context
 
           # Create a struct with the left-over attributes to store data
-          attributes = json_obj.keys.map {|k| k.to_sym}
+          attributes = json_obj.keys.map { |k| k.to_sym }
           attributes_always_present = value_cls.attrs_always_present || [] rescue []
           attributes = (attributes + attributes_always_present).uniq
 
@@ -233,7 +244,7 @@ def self.recursive_struct(json_obj)
             end
           else
             # Get the struct class
-            recursive_obj_hash = {links: nil, context: nil}
+            recursive_obj_hash = { links: nil, context: nil }
             json_obj.each do |key, value|
               recursive_obj_hash[key] = recursive_struct(value)
             end
@@ -260,6 +271,7 @@ def self.prep_links(obj)
 
         context = links.delete("@context")
         return if context.nil?
+
         links.keys.each do |link_type|
           link = Link.new(links[link_type])
           link.media_type = context[link_type]
@@ -270,6 +282,7 @@ def self.prep_links(obj)
 
       def self.load_json(json)
         return if json.nil? || json.empty?
+
         begin
           MultiJson.load(json)
         rescue Exception => e

lib/ontologies_api_client/link_explorer.rb

@@ -1,4 +1,4 @@
-require 'uri'
+require 'addressable/uri'
 require_relative 'http'
 
 module LinkedData
@@ -58,10 +58,11 @@ def combined_links
 
       def replace_template_elements(url, values = [])
         return url if values.nil? || values.empty?
+
         values = values.dup
         values = [values] unless values.is_a?(Array)
         return url.gsub(/(\{.*?\})/) do
-          URI.escape(values.shift, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))
+          Addressable::URI.encode_component(values.shift, Addressable::URI::CharacterClasses::UNRESERVED)
         end
       end
 

lib/ontologies_api_client/models/class.rb

@@ -1,3 +1,4 @@
+require 'addressable/uri'
 require "uri"
 require_relative "../base"
 
@@ -47,8 +48,10 @@ def to_jsonld
         def purl
           return "" if self.links.nil?
           return self.id if self.id.include?("purl.")
+
           ont = self.explore.ontology
-          "#{LinkedData::Client.settings.purl_prefix}/#{ont.acronym}?conceptid=#{URI.escape(self.id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}"
+          encoded_id = Addressable::URI.encode_component(self.id, Addressable::URI::CharacterClasses::UNRESERVED)
+          "#{LinkedData::Client.settings.purl_prefix}/#{ont.acronym}?conceptid=#{encoded_id}"
         end
 
         def ontology
@@ -57,7 +60,7 @@ def ontology
 
         def self.find(id, ontology, params = {})
           ontology = HTTP.get(ontology, params)
-          ontology.explore.class(URI.escape(id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")))
+          ontology.explore.single_class(id)
         end
 
         def self.search(*args)

lib/ontologies_api_client/models/mapping.rb

@@ -1,4 +1,4 @@
-require "uri"
+require 'addressable/template'
 require_relative "../base"
 
 module LinkedData
@@ -11,11 +11,13 @@ class Mapping < LinkedData::Client::Base
         @media_type = "http://data.bioontology.org/metadata/Mapping"
 
         def self.find(id, params = {})
-          HTTP.get(mappings_url_prefix + URI.escape(id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")), params)
+          template = Addressable::Template.new("#{mappings_url_prefix}/{mapping}")
+          HTTP.get(template.expand({mapping: id}), params)
         end
 
         def delete
-          HTTP.delete(mappings_url_prefix + URI.escape(self.id, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]")))
+          template = Addressable::Template.new("#{mappings_url_prefix}/{mapping}")
+          HTTP.delete(template.expand({mapping: self.id}))
         end
 
         private
@@ -24,7 +26,7 @@ def delete
         # This is in a method because the settings are configured after
         # the VM initialization, so the rest_url could be null or wrong
         def self.mappings_url_prefix
-          LinkedData::Client.settings.rest_url + "/mappings/"
+          LinkedData::Client.settings.rest_url + "/mappings"
         end
 
         def mappings_url_prefix