Staging (#465)

* Dev (#457)

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: add 404 error page to drugs, genes, and interactions that have no data (#456)

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: add error message when data not found and fixing footer position

* feat: add error message when data not found

* style: removing console log

* cleaning up code

* refactor: extracting variable for interaction

* feat: add 404 error page to drugs, genes, and interactions that have no data

* Automated frontend build

* Automated frontend build

* Dev (#464)

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: add 404 error page to drugs, genes, and interactions that have no data (#456)

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: update API page to show users endpoint for graphql requests

* feat: add error message when data not found and fixing footer position

* feat: add error message when data not found

* style: removing console log

* cleaning up code

* refactor: extracting variable for interaction

* feat: add 404 error page to drugs, genes, and interactions that have no data

* add public/data as shared, linked dir

* Update dgidb:load_local method (#463)

* update file download location for dgidb_v5_latest in load_local methods

* update download instructions with rake dgidb:load_local method

* removed psql command in favor of just dgidb:load_local

* fix spacing issue

* prettier

* add December 2023 download links

---------

Co-authored-by: Katie Stahl <[email protected]>
Co-authored-by: Adam Coffman <[email protected]>

* Automated frontend build

* Automated frontend build

---------

Co-authored-by: Katie Stahl <[email protected]>
Co-authored-by: katiestahl <[email protected]>
Co-authored-by: Adam Coffman <[email protected]>
Co-authored-by: mcannon068nw <[email protected]>

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

@@ -24,6 +24,13 @@ function createData(
 }
 
 const rows = [
+  createData(
+    '2023-Dec',
+    'interactions.tsv',
+    'genes.tsv',
+    'drugs.tsv',
+    'categories.tsv'
+  ),
   createData(
     '2022-Feb',
     'interactions.tsv',

client/src/pages/Downloads/Info/Info.tsx

@@ -11,19 +11,12 @@ export const Info = () => {
         information for each source.
       </p>
       <p>
-        You may load the{' '}
-        <Link
-          href="https://nch-igm-wagner-lab-public.s3.us-east-2.amazonaws.com/dgidb_v5_latest.sql"
-          target="_blank"
-          rel="noopener"
-        >
-          latest data dump
-        </Link>{' '}
-        into your local database instance by running the following command while
-        in your local checkout of the DGIdb repository:
+        You may instantiate your local database instance by running the
+        following command while in the 'server' directory of your local checkout
+        of the DGIdb repository:
       </p>
       <Box sx={{ ml: 2 }} className="code-text-container">
-        <code className="code-text">psql -d dgidb -f dgidb_v5_latest.sql</code>
+        <code className="code-text">rake dgidb:load_local</code>
       </Box>
       <p>
         This will recreate the local database and import the latest data dump

server/config/deploy.rb

@@ -11,7 +11,7 @@
 
 set :rbenv_type, :user
 
-set :linked_dirs, fetch(:linked_dirs, []).push('log', 'tmp/pids', 'tmp/cache', 'tmp/sockets', 'vendor/bundle', 'public/system', 'public/uploads', 'storage')
+set :linked_dirs, fetch(:linked_dirs, []).push('log', 'tmp/pids', 'tmp/cache', 'tmp/sockets', 'vendor/bundle', 'public/system', 'public/uploads', 'public/data', 'storage')
 set :linked_files, fetch(:linked_files, []).push('config/master.key')
 
 set :repo_tree, 'server'

server/lib/tasks/db_bootstrapping.rake

@@ -9,7 +9,7 @@ namespace :dgidb do
   else
     data_submodule_path = File.join(Rails.root, 'data')
   end
-  data_file = File.join(data_submodule_path, 'data.sql')
+  data_file = File.join(data_submodule_path, 'dgidb_v5_latest.sql')
   version_file = File.join(Rails.root, 'VERSION')
   database_name = Rails.configuration.database_configuration[Rails.env]['database']
   host = Rails.configuration.database_configuration[Rails.env]['host']

server/lib/utils/snapshot_helpers.rb

@@ -52,7 +52,7 @@ def download_data_dump(destination)
     unless Dir.exist? 'data'
       Dir.mkdir('data')
     end
-    system_or_die("wget -O #{destination} http://dgidb.org/data/data.sql")
+    system_or_die("wget -O #{destination} https://nch-igm-wagner-lab-public.s3.us-east-2.amazonaws.com/dgidb_v5_latest.sql")
   end
 
   private

server/public/asset-manifest.json

@@ -1,7 +1,7 @@
 {
   "files": {
     "main.css": "/static/css/main.8868957b.css",
-    "main.js": "/static/js/main.6d739da6.js",
+    "main.js": "/static/js/main.52d838b3.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.8868957b.css.map": "/static/css/main.8868957b.css.map",
-    "main.6d739da6.js.map": "/static/js/main.6d739da6.js.map",
+    "main.52d838b3.js.map": "/static/js/main.52d838b3.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.8868957b.css",
-    "static/js/main.6d739da6.js"
+    "static/js/main.52d838b3.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.6d739da6.js"></script><link href="/static/css/main.8868957b.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.52d838b3.js"></script><link href="/static/css/main.8868957b.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>