Update to current stable ruby and rails

.github/workflows/deploy.yml

@@ -37,7 +37,7 @@ jobs:
         uses: ruby/setup-ruby@v1
         with:
           working-directory: ./server
-          ruby-version: '3.1'
+          ruby-version: '4.0.3'
           bundler-cache: true
 
       - name: Deploy

.github/workflows/test_server.yaml

@@ -26,14 +26,14 @@ jobs:
         uses: ruby/setup-ruby@v1
         with:
           bundler-cache: true
-          ruby-version: '3.1.2'
+          ruby-version: '4.0.3'
           working-directory: ./server
 
       - name: 'Set up DB'
         env:
           CI_BUILD: true
           RAILS_ENV: test
-        run: bundle exec rails db:create db:structure:load
+        run: bundle exec rails db:create db:schema:load
         working-directory: ./server
 
       - name: 'Run tests'

README.md

@@ -8,9 +8,8 @@ A from-scratch rewrite of the [Drug-Gene Interaction Database](https://dgidb.org
 
 First, make sure you have all of the following installed:
 
-- [RVM](https://rvm.io/rvm/install#any-other-system) -- choose the stable version
+- [mise](https://mise.jdx.dev/). The easiest method is `brew install mise`. You will likely also want to [automatically activate it in your shell](https://mise.jdx.dev/getting-started.html#activate-mise).
 - PostgreSQL, either from [here](https://wiki.postgresql.org/wiki/Homebrew) or [here](http://postgresapp.com)
-- [NPM/Node](https://nodejs.org/en/download/)
 
 Clone and enter the repository:
 
@@ -19,29 +18,22 @@ git clone https://github.com/dgidb/dgidb-v5
 cd dgidb-v5
 ```
 
-### Server setup
-
-First, you may need to switch your Ruby version with RVM to match the version declared in the first few lines of the [Gemfile](server/Gemfile). For example, to switch to version 3.1.0:
+Then install the correct versions of node, ruby, and python by running the following:
 
 ```shell
-rvm install 3.1.0
-rvm 3.1.0
+mise trust
+mise install
 ```
+This will also automaticaly set up and activate a python virtualenv.
+
+### Server setup
 
 From the repo root, enter the [server subdirectory](server/):
 
 ```shell
 cd server
 ```
 
-If RVM is properly installed, you should expect to encounter a warning message here:
-
-```
-RVM used your Gemfile for selecting Ruby, it is all fine - Heroku does that too,
-you can ignore these warnings with 'rvm rvmrc warning ignore ./Gemfile'.
-To ignore the warning for all files run 'rvm rvmrc warning ignore allGemfiles'.
-```
-
 Next, install Rails and other required gems with `bundle`:
 
 ```shell
@@ -55,13 +47,13 @@ pg_ctl -D /opt/homebrew/var/postgres start
 # on older macs you may need to use a different path instead, eg "pg_ctl -D /usr/local/var/postgres start"
 ```
 
-The database must be constructed manually. This command will also vary, but it should be something like this:
+Create the database and load in the schema:
 
-```
-createdb -U postgres dgidb
+```shell
+rails db:setup
 ```
 
-Next, back in the main shell, import a database dump file (ask on Slack if you need the latest file):
+Next, import a database dump file (ask on Slack if you need the latest file):
 
 ```shell
 psql -d dgidb -f dgidb_dump_20220526.psql  # provide path to data dump
@@ -83,18 +75,16 @@ To perform a data load from scratch, first run the `reset` task to provide a cle
 rake db:reset
 ```
 
-Some Python libraries are required for importing data. From the repo root, create a Python virtual environment and install required dependencies:
+Some Python libraries are required for importing data. From the repo root, install required dependencies:
 
 ```shell
-python3 -m venv .venv
-source .venv/bin/activate
 pip install -r scripts/requirements.txt
 ```
 
 A Python script is supplied to ensure that primary source data is available. This can also be used to acquire new versions of data that supply discrete releases (like ChEMBL):
 
 ```
-python3 scripts/download_files.py
+python scripts/download_files.py
 ```
 
 Then, load claims:

mise.toml

@@ -0,0 +1,12 @@
+[tools]
+node = "24"
+ruby = "4.0.3"
+python = "3.14"
+
+
+[env]
+_.python.venv = {
+  path = ".venv",
+  create = true
+}
+

server/Gemfile

@@ -1,57 +1,51 @@
 source "https://rubygems.org"
 git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 
-ruby "~>3.1.0"
+ruby "4.0.3"
 gem "rack-cors"
 
-gem "rails", "~> 6.1.3", ">= 6.1.3.1"
-gem "pg", "~>1.2.3"
-gem "puma"
+gem "rails", "~> 8.1.3"
+gem "pg", "~> 1.6"
+gem "puma", "~> 7.2"
 gem "rufo"
+gem "propshaft"
 
-gem "graphql", "~> 2.3.14"
-gem 'graphql-batch', '~>0.5.3'
-gem "graphiql-rails", "~> 1.7.0"
+gem "graphql", "~> 2.6"
+gem "graphql-batch", "~> 0.6.1"
+gem "graphiql-rails", "~> 1.10"
 gem "search_object_graphql", "~> 1.0.5"
 
 # Reduces boot times through caching; required in config/boot.rb
 gem "bootsnap", ">= 1.4.4", require: false
 
 # Background job processing
-gem 'sidekiq', '~> 7.1.2'
+gem "sidekiq", "~> 8.1"
 
-# versions pinned for security vulnerability reasons
-gem "actionpack", ">= 6.1.4.6"
-gem "activestorage", ">= 6.1.4.7"
+# version pinned for security vulnerability reasons
 gem "nokogiri", ">= 1.13.2"
 
 # Importer dependencies
-gem "graphql-client", "~> 0.23.0"
+gem "graphql-client", "~> 0.26"
 gem "ruby-progressbar"
+gem "csv"
 gem "sqlite3", require: false
 gem "zlib", require: false
 gem "net-ftp", require: false
 gem "rubyzip", require: false
 
-# loading workaround until we update rails to 7
-gem "net-smtp", require: false
-gem "net-imap", require: false
-gem "net-pop", require: false
-
 # required for ssh tasks
-gem 'ed25519'
-gem 'bcrypt_pbkdf'
+gem "ed25519"
+gem "bcrypt_pbkdf"
 
 group :development, :test do
-  gem "byebug", platforms: [:mri, :mingw, :x64_mingw]
-  gem "rspec-rails", "~> 5.1"
+  gem "debug", platforms: [:mri, :windows]
+  gem "rspec-rails", "~> 8.0"
   gem "factory_bot", "~> 6.2"
   gem "capybara"
 end
 
 group :development do
   gem "listen", "~> 3.3"
-  gem "spring"
   gem "rack-mini-profiler"
 
   gem "capistrano"
@@ -60,4 +54,4 @@ group :development do
 end
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
-gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+gem "tzinfo-data", platforms: [:windows, :jruby]