Updating to newest base image, Ruby 3.4 (SCP-5959)

Dockerfile

@@ -1,8 +1,8 @@
 # use SCP base Rails image, configure only project-specific items here
-FROM gcr.io/broad-singlecellportal-staging/rails-baseimage:2.3.0
+FROM gcr.io/broad-singlecellportal-staging/rails-baseimage:3.0.0
 
 # Set ruby version
-RUN bash -lc 'rvm --default use ruby-3.2.2'
+RUN bash -lc 'rvm --default use ruby-3.4.2'
 RUN bash -lc 'rvm rvmrc warning ignore /home/app/webapp/Gemfile'
 
 # Set up project dir, install gems, set up script to migrate database and precompile static assets on run

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 
-ruby '3.2.2'
+ruby '3.4.2'
 
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
 gem 'rails', '6.1.7.9'
@@ -29,7 +29,7 @@ gem 'sdoc', group: :doc
 # gem 'capistrano-rails', group: :development
 
 gem 'bootsnap', require: false
-gem 'minitest', '5.15.0'
+gem 'minitest'
 gem 'minitest-rails'
 gem 'minitest-reporters'
 
@@ -71,7 +71,6 @@ gem 'rack-brotli'
 gem 'time_difference'
 gem 'sys-filesystem', require: 'sys/filesystem'
 gem 'browser'
-gem 'ruby-prof'
 gem 'carrierwave', '~> 2.2'
 gem 'carrierwave-mongoid', :require => 'carrierwave/mongoid'
 gem 'uuid'
@@ -81,6 +80,14 @@ gem 'net-imap'
 gem 'net-pop'
 gem 'exponential-backoff'
 gem 'concurrent-ruby', '1.3.4'
+# gems removed from stdlib in 3.4
+gem 'bigdecimal'
+gem 'mutex_m'
+gem 'observer'
+gem 'ostruct'
+gem 'logger'
+gem 'benchmark'
+gem 'drb'
 
 group :development, :test do
   # Access an IRB console on exception pages or by using <%= console %> in views
@@ -93,6 +100,7 @@ group :development, :test do
   gem 'puma'
   gem 'rubocop', require: false
   gem 'rubocop-rails', require: false
+  gem 'csv'
 
   # Profiling
   gem 'rack-mini-profiler'

Gemfile.lock

@@ -99,6 +99,8 @@ GEM
       execjs
     base64 (0.2.0)
     bcrypt (3.1.16)
+    benchmark (0.4.0)
+    bigdecimal (3.1.9)
     bootsnap (1.13.0)
       msgpack (~> 1.2)
     brakeman (5.0.1)
@@ -129,6 +131,7 @@ GEM
     coffee-script-source (1.12.2)
     concurrent-ruby (1.3.4)
     crass (1.0.6)
+    csv (3.3.2)
     daemons (1.4.0)
     date (3.4.1)
     declarative (0.0.20)
@@ -146,9 +149,10 @@ GEM
       warden (~> 1.2.3)
     digest-crc (0.6.4)
       rake (>= 12.0.0, < 14.0.0)
-    docile (1.3.5)
+    docile (1.4.1)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
+    drb (2.2.1)
     dry-cli (0.7.0)
     easy_diff (1.0.0)
     erubi (1.13.1)
@@ -258,6 +262,7 @@ GEM
     listen (3.5.1)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
+    logger (1.6.6)
     loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
@@ -277,7 +282,7 @@ GEM
     mime-types-data (3.2021.0225)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
-    minitest (5.15.0)
+    minitest (5.25.5)
     minitest-hooks (1.5.0)
       minitest (> 5.3)
     minitest-rails (6.1.0)
@@ -317,6 +322,7 @@ GEM
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.3.0)
+    mutex_m (0.3.0)
     naturally (2.2.1)
     net-imap (0.5.6)
       date
@@ -341,6 +347,7 @@ GEM
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
+    observer (0.1.2)
     omniauth (2.0.4)
       hashie (>= 3.4.6)
       rack (>= 1.6.2, < 3)
@@ -358,6 +365,7 @@ GEM
       omniauth (~> 2.0)
     orm_adapter (0.5.0)
     os (1.1.4)
+    ostruct (0.6.1)
     parallel (1.22.1)
     parser (3.1.2.1)
       ast (~> 2.4.1)
@@ -446,7 +454,6 @@ GEM
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.7.0, < 2.0)
-    ruby-prof (1.7.0)
     ruby-progressbar (1.11.0)
     ruby-vips (2.2.1)
       ffi (~> 1.12)
@@ -473,13 +480,13 @@ GEM
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
       multi_json (~> 1.10)
-    simplecov (0.21.2)
+    simplecov (0.22.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov-lcov (0.8.0)
-    simplecov_json_formatter (0.1.3)
+    simplecov_json_formatter (0.1.4)
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
@@ -541,9 +548,12 @@ PLATFORMS
   x86_64-darwin-20
   x86_64-darwin-21
   x86_64-darwin-23
+  x86_64-darwin-24
   x86_64-linux
 
 DEPENDENCIES
+  benchmark
+  bigdecimal
   bootsnap
   bootstrap-sass!
   brakeman
@@ -554,10 +564,12 @@ DEPENDENCIES
   carrierwave-mongoid
   coffee-rails
   concurrent-ruby (= 1.3.4)
+  csv
   daemons
   delayed_job
   delayed_job_mongoid
   devise
+  drb
   exponential-backoff
   factory_bot_rails
   flamegraph
@@ -573,22 +585,26 @@ DEPENDENCIES
   jquery-fileupload-rails
   jquery-rails
   listen
+  logger
   memory_profiler
-  minitest (= 5.15.0)
+  minitest
   minitest-hooks
   minitest-rails
   minitest-reporters
   mongoid
   mongoid-encrypted-fields
   mongoid-history
   mongoid_rails_migrations
+  mutex_m
   naturally
   nested_form!
   net-imap
   net-pop
   net-smtp
+  observer
   omniauth-google-oauth2
   omniauth-rails_csrf_protection
+  ostruct
   parallel
   puma
   rack-brotli
@@ -597,7 +613,6 @@ DEPENDENCIES
   rest-client
   rubocop
   rubocop-rails
-  ruby-prof
   ruby_native_statistics
   rubyzip
   sass-rails (>= 6)
@@ -619,7 +634,7 @@ DEPENDENCIES
   will_paginate_mongoid
 
 RUBY VERSION
-   ruby 3.2.2p53
+   ruby 3.4.2p28
 
 BUNDLED WITH
-   2.6.1
+   2.6.2

app/models/batch_api_client.rb

@@ -1,5 +1,3 @@
-# frozen_string_literal: true
-#
 # Wrapper around Google Batch API for submitting for submitting/reporting scp-ingest-service jobs
 class BatchApiClient
   extend ServiceAccountManager

bin/docker-compose-setup.sh

@@ -12,16 +12,18 @@ $0 [OPTION]
 -i  {IMAGE_TAG}  override default GCR image tag of development
 -p  {PORTAL_RAM_GB}  specify as integer the amount of RAM in GB for the single_cell container
 -v  {VITE_RAM_GB}  specify as integer the amount of RAM in GB for the single_cell_vite container
+-l  use a local copy of GCR_IMAGE (for testing build updates)
 -h  print this text
 EOF
 )
 
 DETACHED=""
 VITE_FRONTEND_SERVICE_WORKER_CACHE="false"
 IMAGE_TAG="development"
+LOCAL="false"
 export PORTAL_RAM_GB="6"
 export VITE_RAM_GB="2"
-while getopts "dchi:p:v:" OPTION; do
+while getopts "dchi:p:v:l" OPTION; do
 case $OPTION in
   d)
     echo "### SETTING DETACHED ###"
@@ -48,6 +50,9 @@ case $OPTION in
     echo "### SETTING VITE_RAM_GB TO $OPTARG ###"
     VITE_RAM_GB="$OPTARG"
     ;;
+  l)
+    LOCAL="true"
+    ;;
   *)
     echo "unrecognized option"
     echo "$usage"
@@ -66,9 +71,11 @@ CHANGED=$(git diff "$LOCAL_BRANCH" development --name-only -- Dockerfile)
 if [[ "$CHANGED" = "Dockerfile" ]]; then
   echo "### DOCKERFILE CHANGES DETECTED, BUILDING $GCR_IMAGE LOCALLY ###"
   docker build -t "$GCR_IMAGE" .
-else
+elif [[ "$LOCAL" = "false" ]]; then
   echo "### PULLING UPDATED IMAGE FOR $GCR_IMAGE ###"
   docker pull "$GCR_IMAGE"
+else
+  echo "### USING LOCAL COPY OF $GCR_IMAGE ###"
 fi
 echo "### STARTING SERVICES ###"
 VITE_FRONTEND_SERVICE_WORKER_CACHE="$VITE_FRONTEND_SERVICE_WORKER_CACHE" \

bin/run_tests.sh

@@ -29,29 +29,8 @@ RETURN_CODE=0
 THIS_DIR="$(cd "$(dirname "$BASH_SOURCE")"; pwd)"
 BASE_DIR="$(dirname $THIS_DIR)"
 
-function setup_burp_cert {
-  if [ -n "$BURP_PROXY" ]; then
-    # we will store Burp certificate here
-    local BURP_CERT="/usr/local/share/ca-certificates/burp.crt"
-
-    # fetch Burp certificate from Burp proxy localhost endpoint and store it into $BURP_CERT
-    curl -s --proxy "$BURP_PROXY" burp/cert | openssl x509 -inform DER -out "$BURP_CERT"
-
-    # update system-wide certificate store
-    update-ca-certificates
-
-    # override cacert store for httpclient package (used by Google libraries)
-    ln -sf "$BURP_CERT" /usr/local/rvm/gems/default/gems/httpclient-*/lib/httpclient/cacert.pem
-
-    # override cafile for Yarn (used during package fetching)
-    yarn config set cafile "$BURP_CERT" -g
-
-    # set http_proxy variable, which will make HTTP connections go through the Burp proxy
-    export http_proxy="$BURP_PROXY"
-  fi
-}
-
 export PASSENGER_APP_ENV=test
+export RUBYOPT=--disable-frozen-string-literal
 
 function clean_up {
   echo "Cleaning up..."
@@ -90,7 +69,6 @@ else
   rm -f "$TMP_PIDS_DIR/delayed_job.*.pid"
 fi
 
-setup_burp_cert
 clean_up
 
 echo "*** STARTING DELAYED_JOB for $PASSENGER_APP_ENV env ***"