Dev (#483) (#484)

* Dev (#483)

* switch multiple drug matching to use left anchored, case insensitive search

* Update citations with V5 citation (#477)

* update citations for v5

* fixed link

* prettier

* rudimentary support for querying current data_version

* implement ga4gh service service info spec

* update griffith lab affiliation

* run prettier

* fix: categories.tsv was downloading interactions (#475)

* fix: categories.tsv was downloading interactions

* feat: change top row of data downloads to latest

* feat: change top row of data downloads to latest

---------

Co-authored-by: Adam Coffman <[email protected]>
Co-authored-by: Matthew Cannon <[email protected]>
Co-authored-by: Adam Coffman <[email protected]>

* Automated frontend build

* Automated frontend build

---------

Co-authored-by: Adam Coffman <[email protected]>
Co-authored-by: Matthew Cannon <[email protected]>
Co-authored-by: Adam Coffman <[email protected]>
Co-authored-by: katiestahl <[email protected]>

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>

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

@@ -3,6 +3,16 @@ import { Link } from '@mui/material';
 export const Publications = () => {
   return (
     <div className="publications-section-container">
+      <div className="about-pub-item">
+        <Link href="https://pubmed.ncbi.nlm.nih.gov/37953380/" target="_blank">
+          DGIdb 5.0: rebuilding the drug-gene interaction database for precision
+          medicine and drug discovery platforms.
+        </Link>{' '}
+        Cannon M, Stevenson J, Stahl K, Basu R, Coffman A, Kiwala S, McMichael
+        JF, Kuzma K, Morrisey D, Cotto KC, Mardis ER, Griffith OL, Griffith M,
+        Wagner AH. Nucleic Acids Research. 2024 Jan 5; doi:
+        https://doi.org/10.1093/nar/gkad1040. PMID: 37953380.
+      </div>
       <div className="about-pub-item">
         <Link href="https://pubmed.ncbi.nlm.nih.gov/33237278/" target="_blank">
           Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with

client/src/pages/Downloads/Files/Files.tsx

@@ -13,66 +13,24 @@ import Paper from '@mui/material/Paper';
 // style
 import './Files.scss';
 
-function createData(
-  date: string,
-  interactions: string,
-  genes: string,
-  drugs: string,
-  categories: string
-) {
-  return { date, interactions, genes, drugs, categories };
+function getDataObj(date: string) {
+  return {
+    date,
+    interactions: 'interactions.tsv',
+    genes: 'genes.tsv',
+    drugs: 'drugs.tsv',
+    categories: 'categories.tsv',
+  };
 }
 
 const rows = [
-  createData(
-    '2023-Dec',
-    'interactions.tsv',
-    'genes.tsv',
-    'drugs.tsv',
-    'categories.tsv'
-  ),
-  createData(
-    '2022-Feb',
-    'interactions.tsv',
-    'genes.tsv',
-    'drugs.tsv',
-    'categories.tsv'
-  ),
-  createData(
-    '2021-May',
-    'interactions.tsv',
-    'genes.tsv',
-    'drugs.tsv',
-    'categories.tsv'
-  ),
-  createData(
-    '2021-Jan',
-    'interactions.tsv',
-    'genes.tsv',
-    'drugs.tsv',
-    'categories.tsv'
-  ),
-  createData(
-    '2020-Nov',
-    'interactions.tsv',
-    'genes.tsv',
-    'drugs.tsv',
-    'categories.tsv'
-  ),
-  createData(
-    '2020-Oct',
-    'interactions.tsv',
-    'genes.tsv',
-    'drugs.tsv',
-    'categories.tsv'
-  ),
-  createData(
-    '2020-Sep',
-    'interactions.tsv',
-    'genes.tsv',
-    'drugs.tsv',
-    'categories.tsv'
-  ),
+  getDataObj('latest'),
+  getDataObj('2022-Feb'),
+  getDataObj('2021-May'),
+  getDataObj('2021-Jan'),
+  getDataObj('2020-Nov'),
+  getDataObj('2020-Oct'),
+  getDataObj('2020-Sep'),
 ];
 
 export const Files = () => {
@@ -123,10 +81,7 @@ export const Files = () => {
                   </a>
                 </TableCell>
                 <TableCell align="center">
-                  <a
-                    download
-                    href={'data/' + row.date + '/' + row.interactions}
-                  >
+                  <a download href={'data/' + row.date + '/' + row.categories}>
                     {row.categories}
                   </a>
                 </TableCell>

server/app/graphql/resolvers/drugs.rb

@@ -13,8 +13,10 @@ class Resolvers::Drugs < GraphQL::Schema::Resolver
     scope.where(id: value)
   end
 
-  option(:names, type: [String], description: 'Substring filtering on a list of drug names.') do |scope, value|
-    scope.where(name: value.map(&:upcase))
+  option(:names, type: [String], description: 'Left anchored filtering on a list of drug names.') do |scope, value|
+    text = 'name ILIKE ?'
+    clause = Array.new(value.size, text).join(" OR ")
+    scope.where(clause, *value.map {|v| "#{v}%"})
   end
 
   option(:name, type: String, description: 'Left anchored string search on drug name') do |scope, value|

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

server/public/asset-manifest.json

@@ -1,7 +1,7 @@
 {
   "files": {
     "main.css": "/static/css/main.090445a8.css",
-    "main.js": "/static/js/main.4948a2ff.js",
+    "main.js": "/static/js/main.5c213655.js",
     "static/js/461.86214142.chunk.js": "/static/js/461.86214142.chunk.js",
     "static/js/80.a852d8b5.chunk.js": "/static/js/80.a852d8b5.chunk.js",
     "static/js/990.d59bee53.chunk.js": "/static/js/990.d59bee53.chunk.js",
@@ -28,7 +28,7 @@
     "static/js/925.a41f4405.chunk.js": "/static/js/925.a41f4405.chunk.js",
     "index.html": "/index.html",
     "main.090445a8.css.map": "/static/css/main.090445a8.css.map",
-    "main.4948a2ff.js.map": "/static/js/main.4948a2ff.js.map",
+    "main.5c213655.js.map": "/static/js/main.5c213655.js.map",
     "461.86214142.chunk.js.map": "/static/js/461.86214142.chunk.js.map",
     "80.a852d8b5.chunk.js.map": "/static/js/80.a852d8b5.chunk.js.map",
     "990.d59bee53.chunk.js.map": "/static/js/990.d59bee53.chunk.js.map",
@@ -56,6 +56,6 @@
   },
   "entrypoints": [
     "static/css/main.090445a8.css",
-    "static/js/main.4948a2ff.js"
+    "static/js/main.5c213655.js"
   ]
 }

server/public/index.html

@@ -1 +1 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/favicon.png"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="DGIdb, The Drug Gene Interaction Database, is a research resource that can be used to search candidate genes or drugs against the known and potentially druggable genome."/><link rel="preconnect" href="https://fonts.googleapis.com"><link rel="preconnect" href="https://fonts.gstatic.com" crossorigin><link href="https://fonts.googleapis.com/css2?family=Fira+Sans:wght@300;350;400;500;700;800&display=swap" rel="stylesheet"><link href="https://fonts.googleapis.com/css2?family=Lato:wght@100;300;350;400;700&display=swap" rel="stylesheet"><link href="https://fonts.googleapis.com/css2?family=Work+Sans:wght@200;300;350;400;500;600&display=swap" rel="stylesheet"><link rel="apple-touch-icon" href="/dgidb-icon_48.png"/><link rel="manifest" href="/manifest.json"/><title>DGIdb</title><script defer="defer" src="/static/js/main.4948a2ff.js"></script><link href="/static/css/main.090445a8.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>
+<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/favicon.png"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="DGIdb, The Drug Gene Interaction Database, is a research resource that can be used to search candidate genes or drugs against the known and potentially druggable genome."/><link rel="preconnect" href="https://fonts.googleapis.com"><link rel="preconnect" href="https://fonts.gstatic.com" crossorigin><link href="https://fonts.googleapis.com/css2?family=Fira+Sans:wght@300;350;400;500;700;800&display=swap" rel="stylesheet"><link href="https://fonts.googleapis.com/css2?family=Lato:wght@100;300;350;400;700&display=swap" rel="stylesheet"><link href="https://fonts.googleapis.com/css2?family=Work+Sans:wght@200;300;350;400;500;600&display=swap" rel="stylesheet"><link rel="apple-touch-icon" href="/dgidb-icon_48.png"/><link rel="manifest" href="/manifest.json"/><title>DGIdb</title><script defer="defer" src="/static/js/main.5c213655.js"></script><link href="/static/css/main.090445a8.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>