Merge pull request #1 from lifewatch-eric/ecoportal-ontoportal-reset

Ontoportal align: Ecoportal ontoportal reset

.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):

.gitignore

@@ -1,3 +1,5 @@
+.bundle/
+
 *.gem
 .DS_Store
 config/config.rb

Gemfile.lock

@@ -1,8 +1,8 @@
 PATH
   remote: .
   specs:
-    ontologies_api_client (2.0.3)
-      activesupport (= 6.0.4.1)
+    ontologies_api_client (2.2.0)
+      activesupport
       excon
       faraday
       faraday-excon (~> 2.0.0)
@@ -15,50 +15,46 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.0.4.1)
+    activesupport (7.0.4)
       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)
     coderay (1.1.3)
-    concurrent-ruby (1.1.9)
-    excon (0.91.0)
+    concurrent-ruby (1.1.10)
+    excon (0.95.0)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
       ruby2_keywords (>= 0.0.4)
     faraday-excon (2.0.0)
       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-multipart (1.0.4)
+      multipart-post (~> 2)
+    faraday-net_http (2.1.0)
+    i18n (1.12.0)
       concurrent-ruby (~> 1.0)
     lz4-ruby (0.3.3)
     method_source (1.0.0)
-    minitest (5.15.0)
+    minitest (5.16.3)
     multi_json (1.15.0)
-    multipart-post (2.1.1)
-    oj (3.13.11)
-    power_assert (2.0.1)
+    multipart-post (2.2.3)
+    oj (3.13.23)
+    power_assert (2.0.2)
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
     rake (13.0.6)
     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 (2.0.5)
+      concurrent-ruby (~> 1.0)
 
 PLATFORMS
-  ruby
-  x86_64-darwin-16
-  x86_64-darwin-17
+  x86_64-darwin-21
+  x86_64-linux
 
 DEPENDENCIES
   ontologies_api_client!
@@ -67,4 +63,4 @@ DEPENDENCIES
   test-unit
 
 BUNDLED WITH
-   2.1.4
+   2.3.23

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/base.rb

@@ -6,7 +6,15 @@ class Base
       attr_accessor :context, :links
 
       class << self
-        attr_accessor :media_type, :act_as_media_type, :include_attrs, :include_attrs_full, :attrs_always_present
+        attr_accessor :act_as_media_type, :include_attrs, :include_attrs_full, :attrs_always_present
+        def media_types
+          Array(@media_type)
+        end
+
+        def media_type
+          media_types.first
+        end
+
       end
 
       ##
@@ -31,8 +39,11 @@ def self.map_classes
         map = {}
         classes = LinkedData::Client::Models.constants.map {|c| LinkedData::Client::Models.const_get(c)}
         classes.each do |media_type_cls|
-          next if map[media_type_cls] || !media_type_cls.respond_to?(:media_type) || !media_type_cls.ancestors.include?(LinkedData::Client::Base)
-          map[media_type_cls.media_type] = media_type_cls
+          next if map[media_type_cls] || !media_type_cls.respond_to?(:media_types) || !media_type_cls.ancestors.include?(LinkedData::Client::Base)
+          media_type_cls.media_types.each do |type|
+            next if map[type]
+            map[type] = media_type_cls
+          end
           media_type_cls.act_as_media_type.each {|mt| map[mt] = media_type_cls} if media_type_cls.act_as_media_type
         end
         return map

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
 
@@ -85,7 +88,7 @@ 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
@@ -96,30 +99,26 @@ 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 = {})
-        begin
-          file, file_attribute = params_file_handler(obj)
-          response = conn.post do |req|
-            req.url path
-            custom_req(obj, file, file_attribute, req)
-          end
-          raise Exception, response.body if response.status >= 500
-          if options[:raw] || false # return the unparsed body of the request
-            return response.body
-          else
-            return recursive_struct(load_json(response.body))
-          end
-        rescue => e
-          LOGGER.debug "\n\n\nRUBY API - LinkedData::Client::HTTP ->post: - ECCEZIONE: #{e.message}\n#{e.backtrace.join("\n")}"
-          raise e        
+        file, file_attribute = params_file_handler(obj)
+        response = conn.post do |req|
+          req.url path
+          custom_req(obj, file, file_attribute, req)
+        end
+        raise StandardError, response.body if response.status >= 500
+
+        if options[:raw] || false # return the unparsed body of the request
+          response.body
+        else
+          recursive_struct(load_json(response.body))
         end
 
       end
@@ -130,7 +129,8 @@ 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
 
@@ -140,13 +140,17 @@ 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)
@@ -178,9 +182,11 @@ 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
@@ -211,7 +217,7 @@ 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
 
@@ -241,7 +247,7 @@ 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
@@ -268,6 +274,7 @@ 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]
@@ -278,6 +285,7 @@ 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

@@ -60,9 +60,15 @@ 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}]"))
+        escaped_value = CGI.escape(values.shift)
+        if url.match(/(\{.*?\})/)
+          url.gsub(/(\{.*?\})/) do
+            escaped_value
+          end
+        else
+          url + '/' + escaped_value
         end
+
       end
 
       def linkable_attributes

lib/ontologies_api_client/models/agent.rb

@@ -0,0 +1,14 @@
+require_relative "../base"
+
+module LinkedData
+  module Client
+    module Models
+      class Agent < LinkedData::Client::Base
+        include LinkedData::Client::Collection
+        include LinkedData::Client::ReadWrite
+
+        @media_type = "http://xmlns.com/foaf/0.1/Agent"
+      end
+    end
+  end
+end

lib/ontologies_api_client/models/class.rb

@@ -1,16 +1,15 @@
-require "uri"
+require "cgi"
 require_relative "../base"
 
 module LinkedData
   module Client
     module Models
       class Class < LinkedData::Client::Base
         HTTP = LinkedData::Client::HTTP
-        @media_type = "http://www.w3.org/2002/07/owl#Class"
-        @include_attrs = "prefLabel,definition,synonym,obsolete,hasChildren"
-        @include_attrs_full = "prefLabel,definition,synonym,obsolete,properties,hasChildren,children"
-        @attrs_always_present = :prefLabel, :definition, :synonym, :obsolete, :properties, :hasChildren, :children
-
+        @media_type = %w[http://www.w3.org/2002/07/owl#Class http://www.w3.org/2004/02/skos/core#Concept]
+        @include_attrs = "prefLabel,definition,synonym,obsolete,hasChildren,inScheme,memberOf"
+        @include_attrs_full = "prefLabel,definition,synonym,obsolete,properties,hasChildren,childre,inScheme,memberOf"
+        @attrs_always_present = :prefLabel, :definition, :synonym, :obsolete, :properties, :hasChildren, :children, :inScheme, :memberOf
         alias :fullId :id
 
         # triple store predicate is <http://www.w3.org/2002/07/owl#deprecated>
@@ -48,7 +47,7 @@ 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}]"))}"
+          "#{LinkedData::Client.settings.purl_prefix}/#{ont.acronym}?conceptid=#{CGI.escape(self.id)}"
         end
 
         def ontology
@@ -57,7 +56,7 @@ 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.class(CGI.escape(id))
         end
 
         def self.search(*args)

lib/ontologies_api_client/models/collection.rb

@@ -0,0 +1,12 @@
+require_relative "../base"
+
+module LinkedData
+  module Client
+    module Models
+      class Collection < LinkedData::Client::Base
+        include LinkedData::Client::Collection
+        @media_type =  "http://www.w3.org/2004/02/skos/core#Collection"
+      end
+    end
+  end
+end