Fix the OBO Foundry synchronization script

.gitignore

@@ -6,6 +6,7 @@ config/*.p12
 config/*.json
 data/
 projectFilesBackup/
+.bundle
 .ruby-version
 repo*
 *.turtle

Gemfile.lock

@@ -60,6 +60,8 @@ PATH
   specs:
     ncbo_cron (0.0.1)
       dante
+      faraday (~> 2)
+      faraday-follow_redirects (~> 0)
       goo
       google-analytics-data
       mlanett-redis-lock
@@ -98,6 +100,8 @@ GEM
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
+    faraday-follow_redirects (0.3.0)
+      faraday (>= 1, < 3)
     faraday-net_http (3.0.2)
     faraday-retry (2.2.1)
       faraday (~> 2.0)

lib/ncbo_cron/obofoundry_sync.rb

@@ -1,42 +1,39 @@
-require 'base64'
-require 'json'
-require 'net/http'
-require 'uri'
+require 'faraday'
+require 'faraday/follow_redirects'
+require 'multi_json'
 
 module NcboCron
   module Models
     class OBOFoundrySync
 
       def initialize
         @logger = Logger.new(STDOUT)
-        @oauth_token = Base64.decode64(NcboCron.settings.git_repo_access_token)
-        @graphql_uri = URI.parse("https://api.github.com/graphql")
-        @request_options = { use_ssl: @graphql_uri.scheme == "https" }
       end
 
       def run
         # Get a map of OBO ID spaces to BioPortal acronyms
         map = get_ids_to_acronyms_map
 
         onts = get_obofoundry_ontologies
-        @logger.info("Found #{onts.size} OBO Library ontologies")
+        @logger.info("Found #{onts.size} OBO Foundry ontologies")
 
-        # Are any OBO Library ontologies missing from BioPortal?
+        # Are any OBO Foundry ontologies missing from BioPortal?
         missing_onts = []
-        active_onts = onts.reject { |ont| ont.key?("is_obsolete") }
+        active_onts = onts.reject { |ont| ont.key?('is_obsolete') }
+        @logger.info("#{active_onts.size} OBO Foundry ontologies are currently active")
         active_onts.each do |ont|
-          if not map.key?(ont["id"])
+          if not map.key?(ont['id'])
             missing_onts << ont
-            @logger.info("Missing OBO Library ontology: #{ont['title']} (#{ont['id']})")
+            @logger.info("Missing OBO Foundry ontology: #{ont['title']} (#{ont['id']})")
           end
         end
 
-        # Have any of the OBO Library ontologies that BioPortal hosts become obsolete?
+        # Have any of the OBO Foundry ontologies that BioPortal hosts become obsolete?
         obsolete_onts = []
-        ids = active_onts.map{ |ont| ont["id"] }
+        ids = active_onts.map{ |ont| ont['id'] }
         obsolete_ids = map.keys - ids
         obsolete_ids.each do |id|
-          ont = onts.find{ |ont| ont["id"] == id }
+          ont = onts.find{ |ont| ont['id'] == id }
           @logger.info("Deprecated OBO Library ontology: #{ont['title']} (#{ont['id']})")
           obsolete_onts << ont
         end        
@@ -45,49 +42,19 @@ def run
       end
 
       def get_ids_to_acronyms_map
-        query = "query { 
-                  repository(name: \"ncbo.github.io\", owner: \"ncbo\") {
-                    object(expression: \"master:oboids_to_bpacronyms.json\") {
-                      ... on Blob {
-                        text
-                      }
-                    }
-                  }
-                }"
-
-        response = issue_request(query)
-        JSON.parse(response)
+        response = Faraday.get('https://ncbo.github.io/oboids_to_bpacronyms.json')
+        MultiJson.load(response.body)
       end
 
       def get_obofoundry_ontologies
-        query = "query { 
-                  repository(name: \"OBOFoundry.github.io\", owner: \"OBOFoundry\") {
-                    object(expression: \"master:registry/ontologies.jsonld\") {
-                      ... on Blob {
-                        text
-                      }
-                    }
-                  }
-                }"
-
-        response = issue_request(query)
-        ont_registry = JSON.parse(response)
-        ont_registry["ontologies"].to_a
-      end
-
-      def issue_request(query)
-        request = Net::HTTP::Post.new(@graphql_uri)
-        request["Authorization"] = "bearer #{@oauth_token}"
-        request.body = JSON.dump({"query" => query})
-
-        response = Net::HTTP.start(@graphql_uri.hostname, @graphql_uri.port, @request_options) do |http|
-          http.request(request)
+        conn = Faraday.new do |faraday|
+          faraday.response :follow_redirects
+          faraday.adapter Faraday.default_adapter
         end
+        response = conn.get('http://purl.obolibrary.org/meta/ontologies.jsonld')
 
-        parsed = JSON.parse(response.body)
-        parsed.dig("data", "repository", "object", "text")
+        MultiJson.load(response.body)['ontologies']
       end
-
     end
   end
 end

ncbo_cron.gemspec

@@ -15,6 +15,8 @@ Gem::Specification.new do |gem|
   gem.require_paths = ["lib"]
 
   gem.add_dependency("dante")
+  gem.add_dependency('faraday', '~> 2')
+  gem.add_dependency('faraday-follow_redirects', '~> 0')
   gem.add_dependency("goo")
   gem.add_dependency("google-analytics-data")
   gem.add_dependency("mlanett-redis-lock")