chore: update bin/setup, config/database.yml, and capybara_setup.rb t…

…o be compatible for devcontainer

bin/setup

@@ -13,7 +13,8 @@ FileUtils.chdir APP_ROOT do
   # Add necessary setup steps to this file.
 
   puts "== Installing dependencies =="
-  system("bundle check") || system!("bundle install")
+  system("bin/bundle check") || system!("bin/bundle install")
+  system("pnpm install --frozen-lockfile")
 
   # puts "\n== Copying sample files =="
   # unless File.exist?("config/database.yml")

config/database.yml

@@ -1,43 +1,42 @@
-# PostgreSQL configuration options for development, production,
-# and test profiles. Currently using postgres version 14.6
+# PostgreSQL. Versions 9.3 and up are supported.
 #
-#   Ensure the PostgreSQL gem is defined in your Gemfile
-#   gem "pg"
+# Install the pg driver:
+#   gem install pg
+# On macOS with Homebrew:
+#   gem install pg -- --with-pg-config=/usr/local/bin/pg_config
+# On Windows:
+#   gem install pg
+#       Choose the win32 build.
+#       Install PostgreSQL and put its /bin directory on your path.
 #
-#   Also, ensure you have postgresql installed on your machine
-#   and/or dev/prod server either using asdf or using the OS
-#   package manager (such as apt-get for Ubuntu)
+# Configure Using Gemfile
+# gem "pg"
 #
 default: &default
   adapter: postgresql
   encoding: unicode
   # For details on connection pooling, see Rails configuration guide
-  # http://guides.rubyonrails.org/configuring.html#database-pooling
+  # https://guides.rubyonrails.org/configuring.html#database-pooling
   pool: <%= ENV.fetch("RAILS_MAX_THREADS") { 5 } %>
-  username: test
-  password: test
+  <% if ENV["DB_HOST"] %>
+  host: <%= ENV["DB_HOST"] %>
+  username: postgres
+  password: postgres
+  <% else %>
   host: localhost
-  timeout: 5000
-
-jobs: &jobs
-  adapter: postgresql
-  encoding: unicode
-  # For details on connection pooling, see Rails configuration guide
-  # http://guides.rubyonrails.org/configuring.html#database-pooling
-  pool: <%= ENV.fetch("RAILS_MAX_THREADS") { 5 } %>
   username: test
   password: test
-  host: localhost
-  timeout: 5000
-  migrations_paths: db/jobs_migrate
+  <% end %>
+
 
 development:
   primary:
     <<: *default
     database: irida_next_development
   jobs:
-    <<: *jobs
+    <<: *default
     database: irida_next_jobs_development
+    migrations_paths: db/jobs_migrate
 
 # Warning: The database defined as "test" will be erased and
 # re-generated from your development database when you run "rake".
@@ -47,17 +46,38 @@ test:
     <<: *default
     database: irida_next_test
   jobs:
-    <<: *jobs
+    <<: *default
     database: irida_next_jobs_test
+    migrations_paths: db/jobs_migrate
 
+# As with config/credentials.yml, you never want to store sensitive information,
+# like your database password, in your source code. If your source code is
+# ever seen by anyone, they now have access to your database.
+#
+# Instead, provide the password or a full connection URL as an environment
+# variable when you boot the app. For example:
 #
 #   DATABASE_URL="postgres://myuser:mypass@localhost/somedatabase"
 #   JOBS_DATABASE_URL="postgres://myuser:mypass@localhost/someotherdatabase"
 #
+# If the connection URL is provided in the special DATABASE_URL environment
+# variable, Rails will automatically merge its configuration values on top of
+# the values provided in this file. Alternatively, you can specify a connection
+# URL environment variable explicitly:
+#
+#   production:
+#     url: <%= ENV["MY_APP_DATABASE_URL"] %>
+#
+# Read https://guides.rubyonrails.org/configuring.html#configuring-a-database
+# for a full overview on how database connection configuration can be specified.
+#
 production:
-  primary:
+  primary: &primary_production
     <<: *default
-    url: <%= ENV['DATABASE_URL'] %>
+    database: irida_next_production
+    username: irida_next
+    password: <%= ENV["IRIDA_NEXT_DATABASE_PASSWORD"] %>
   jobs:
-    <<: *jobs
-    url: <%= ENV['JOBS_DATABASE_URL'] %>
+    <<: *primary_production
+    database: irida_next_jobs_production
+    migrations_paths: db/jobs_migrate

test/test_helpers/capybara_setup.rb

@@ -4,19 +4,6 @@
 
 Capybara.server = :puma, { Silent: true }
 
-# Make server listening on all hosts
-Capybara.server_host = '0.0.0.0'
-# Use a hostname accessible from the outside world
-Capybara.app_host = 'http://localhost'
-
-# Which domain to use when setting cookies directly in tests.
-CAPYBARA_COOKIE_DOMAIN = URI.parse(Capybara.app_host).host.then do |host|
-  # If host is a top-level domain
-  next host unless host.include?('.')
-
-  ".#{host}"
-end
-
 # Don't wait too long in `have_xyz` matchers
 Capybara.default_max_wait_time = 20.seconds