Merge pull request #482 from dgidb/dataset-version

Add support for GA4GH service info query

Author: acoffman

client/src/pages/About/SubSections/Contact.tsx

@@ -6,10 +6,10 @@ export const Contact = () => {
     <div className="contact-section-container doc-section">
       <div>
         <p>
-          DGIdb was developed at The McDonnell Genome Institute, Washington
-          University School of Medicine. If you have a source of information
-          related to the druggable genome you would like us to incorporate,
-          please contact us at{' '}
+          DGIdb was initially developed at The McDonnell Genome Institute,
+          Washington University School of Medicine. If you have a source of
+          information related to the druggable genome you would like us to
+          incorporate, please contact us at{' '}
           <Link href="mailto:[email protected]">[email protected].</Link>
         </p>
         <p>
@@ -24,12 +24,8 @@ export const Contact = () => {
 
       <div className="left-section">
         <h4>
-          <Link
-            href="http://genome.wustl.edu/"
-            target="_blank"
-            rel="noreferrer"
-          >
-            The McDonnell Genome Institute
+          <Link href="https://griffithlab.org" target="_blank" rel="noreferrer">
+            The Griffith Laboratory
           </Link>
         </h4>
         <p>Washington University</p>

server/app/graphql/types/meta_type.rb

@@ -0,0 +1,70 @@
+module Types
+  class MetaType < Types::BaseObject
+    field :id, String, null: false, description: 'Unique identifier for service.'
+    field :data_version, String, null: false, description: 'Version of the data being served by DGIdb'
+    field :name, String, null: false, description: 'Human readable name of the service'
+    field :type, Types::ServiceType, null: false
+    field :description, String, null: false
+    field :organization, Types::OrganizationType, null: false
+    field :contact_url, String, null: false, description: 'URL of the contact for the provider of this service'
+    field :documentation_url, String, null: false, description: 'URL of the documentation of this service'
+    field :created_at, GraphQL::Types::ISO8601DateTime, null: false, description: 'Timestamp describing when the service was first deployed and available'
+    field :updated_at, GraphQL::Types::ISO8601DateTime, null: false, description: 'Timestamp describing when the service was last updated'
+    field :environment, String, null: false, description: 'Environment the service is running in'
+    field :version, String, null: false, description: 'Version of the service being described'
+
+    def id
+      'org.dgidb.graphql'
+    end
+
+    def data_version
+      DATA_VERSION
+    end
+
+    def name
+      'DGIdb'
+    end
+
+     def type
+       {}
+     end
+
+     def description
+       "An open-source search engine for drug-gene interactions and the druggable genome."
+     end
+
+     def organization
+       {}
+     end
+
+     def contact_url
+       "mailto:[email protected]"
+     end
+
+     def documentation_url
+       'https://dgidb.org/api/graphiql'
+     end
+
+     def created_at
+       #version 5.0.0 initial release on GitHub
+       DateTime.parse("October 20, 2023 8:51 AM CDT")
+     end
+
+     def updated_at
+       DateTime.parse(github_release&.dig("published_at"))
+     end
+
+     def environment
+       Rails.env
+     end
+
+     def version
+       github_release&.dig("tag_name")
+     end
+
+     private
+     def github_release
+       @rel ||= GithubRelease.current
+     end
+  end
+end

server/app/graphql/types/organization_type.rb

@@ -0,0 +1,14 @@
+module Types
+  class OrganizationType < Types::BaseObject
+    field :name, String, null: false, description: 'Name of the organization responsible for the service'
+    field :url, String, null: false, description: 'URL of the website of the organization'
+
+    def name
+      'Wagner and Griffith laboratories'
+    end
+
+    def url
+      'https://dgidb.org/about#contact'
+    end
+  end
+end

server/app/graphql/types/query_type.rb

@@ -13,6 +13,8 @@ class QueryType < Types::BaseObject
     field :categories, resolver: Resolvers::Categories
     field :interaction_claim_types, resolver: Resolvers::InteractionClaimTypes
 
+    field :service_info, Types::MetaType, null: false
+
     field :drug_suggestions, [Types::DrugSuggestionType], null: true do
       description "A searchable drug name or alias that can be completed from the supplied term"
       argument :term, String, required: true
@@ -331,5 +333,9 @@ def interaction(id:)
     def publication(id:)
       Publication.find_by(id: id)
     end
+
+    def service_info
+      {}
+    end
   end
 end

server/app/graphql/types/service_type.rb

@@ -0,0 +1,19 @@
+module Types
+  class ServiceType < Types::BaseObject
+    field :group, String, null: false, description: 'Namespace in reverse domain name format.'
+    field :artifact, String, null: false, description: 'Name of the API or GA4GH specification implemented.'
+    field :version, String, null: false, description: 'API Version (semantic)'
+
+    def group
+      'org.dgidb'
+    end
+
+    def artifact
+      'DGIdb GraphQL'
+    end
+
+    def version
+      GithubRelease.current&.dig("tag_name")
+    end
+  end
+end

server/app/models/github_release.rb

@@ -0,0 +1,18 @@
+class GithubRelease
+  def self.current
+    Rails.cache.fetch("current_github_release", expires_in: 12.hours) do
+      fetch_release
+    end
+  end
+
+  private
+  def self.fetch_release
+    uri = URI.parse('https://api.github.com/repos/dgidb/dgidb-v5/releases?per_page=1')
+    resp = Net::HTTP.get_response(uri)
+    if resp.code == '200'
+      JSON.parse(resp.body).first
+    else
+      nil
+    end
+  end
+end

server/config/initializers/dataset_version.rb

@@ -0,0 +1,8 @@
+file = File.join(Rails.root, 'data_version.yml')
+data = YAML.load_file(file)
+
+DATA_VERSION = data.dig('version')
+
+if DATA_VERSION.nil?
+  raise StandardError.new("Missing or malformed data_version.yml. Expect file at Rails.root with a version: key")
+end

server/data_version.yml

@@ -0,0 +1 @@
+version: Dec-2023