Upgrade to Ruby 3.2.0 (from Ruby 2.4)

.github/workflows/GeneValidator.yml

@@ -19,15 +19,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        ruby-version: ['2.4.10', '2.5', '2.6', '2.7']
+        ruby-version: ['3.2']
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Ruby
-    # To automatically get bug fixes and new Ruby versions for ruby/setup-ruby,
-    # change this to (see https://github.com/ruby/setup-ruby#versioning):
-    # uses: ruby/setup-ruby@v1
-      uses: ruby/setup-ruby@473e4d8fe5dd94ee328fdfca9f8c9c7afc9dae5e
+      uses: ruby/setup-ruby@v1
       with:
         ruby-version: ${{ matrix.ruby-version }}
         bundler-cache: true # runs 'bundle install' and caches installed gems automatically

.ruby-version

@@ -1 +1 @@
-2.4.10
+3.2.2

.tool-versions

@@ -1 +1 @@
-ruby 2.4.0
+ruby 3.2.2

Gemfile.lock

@@ -1,20 +1,25 @@
 PATH
   remote: .
   specs:
-    genevalidator (2.1.11)
+    genevalidator (2.2.0)
       bio (~> 1.4)
       bio-blastxmlparser (~> 2.0)
       genevalidatorapp (~> 2.1.8)
-      ncbi-blast-dbs (= 0.0.6)
+      matrix (~> 0.4.2)
+      net-ftp (~> 0.1.3)
+      prime (~> 0.1.2)
       rack (~> 2.0)
+      rexml (~> 3.2, >= 3.2.6)
       slim (~> 3.0)
       statsample (= 2.1.0)
+      webrick (~> 1.8)
 
 GEM
   remote: http://rubygems.org/
   specs:
     awesome_print (1.9.2)
-    backports (3.21.0)
+    backports (3.24.1)
+    bigdecimal (3.1.6)
     bio (1.5.2)
     bio-blastxmlparser (2.0.4)
       bio-logger
@@ -24,27 +29,33 @@ GEM
     clbustos-rtf (0.4.2)
     daru (0.1.6)
       backports
+    date (3.3.4)
     dirty-memoize (0.0.4)
     distribution (0.8.0)
-    docile (1.3.1)
+    docile (1.4.0)
     extendmatrix (0.4)
+    forwardable (1.3.3)
     genevalidatorapp (2.1.8)
       bio (~> 1.4)
       sinatra (~> 2.0)
       sinatra-cross_origin (~> 0.3)
       slim (~> 3.0)
-    json (2.1.0)
     log4r (1.1.10)
-    mini_portile2 (2.4.0)
+    matrix (0.4.2)
+    mini_portile2 (2.8.5)
     minimization (0.2.5)
       text-table (~> 1.2)
-    minitest (5.11.3)
-    mustermann (1.1.1)
+    minitest (5.21.2)
+    mustermann (2.0.2)
       ruby2_keywords (~> 0.0.1)
-    ncbi-blast-dbs (0.0.6)
-      rake (~> 10.3, >= 10.3.2)
-    nokogiri (1.10.10)
-      mini_portile2 (~> 2.4.0)
+    net-ftp (0.1.4)
+      net-protocol
+      time
+    net-protocol (0.2.2)
+      timeout
+    nokogiri (1.16.2)
+      mini_portile2 (~> 2.8.2)
+      racc (~> 1.4)
     prawn (0.8.4)
       prawn-core (>= 0.8.4, < 0.9)
       prawn-layout (>= 0.8.4, < 0.9)
@@ -54,34 +65,42 @@ GEM
     prawn-security (0.8.4)
     prawn-svg (0.9.1.11)
       prawn (>= 0.8.4)
-    rack (2.2.3)
-    rack-protection (2.1.0)
+    prime (0.1.2)
+      forwardable
+      singleton
+    racc (1.7.3)
+    rack (2.2.8)
+    rack-protection (2.2.4)
       rack
-    rake (10.5.0)
+    rake (13.1.0)
     reportbuilder (1.4.2)
       clbustos-rtf (~> 0.4.0)
       prawn (~> 0.8.4)
       prawn-svg (~> 0.9.1)
       text-table (~> 1.2)
+    rexml (3.2.6)
     rserve-client (0.3.5)
     ruby-ole (1.2.12.2)
-    ruby2_keywords (0.0.4)
+    ruby2_keywords (0.0.5)
     rubyvis (0.6.1)
-    simplecov (0.16.1)
+    simplecov (0.22.0)
       docile (~> 1.1)
-      json (>= 1.8, < 3)
-      simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.2)
-    sinatra (2.1.0)
-      mustermann (~> 1.0)
+      simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
+    simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.4)
+    sinatra (2.2.4)
+      mustermann (~> 2.0)
       rack (~> 2.2)
-      rack-protection (= 2.1.0)
+      rack-protection (= 2.2.4)
       tilt (~> 2.0)
     sinatra-cross_origin (0.4.0)
+    singleton (0.1.1)
     slim (3.0.9)
       temple (>= 0.7.6, < 0.9)
       tilt (>= 1.3.3, < 2.1)
-    spreadsheet (1.2.9)
+    spreadsheet (1.3.1)
+      bigdecimal
       ruby-ole
     statsample (2.1.0)
       awesome_print (~> 1.6)
@@ -96,18 +115,22 @@ GEM
       spreadsheet (~> 1.1)
     temple (0.8.2)
     text-table (1.2.4)
-    tilt (2.0.10)
-    yard (0.9.16)
+    tilt (2.0.11)
+    time (0.3.0)
+      date
+    timeout (0.4.1)
+    webrick (1.8.1)
+    yard (0.9.34)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
   genevalidator!
   minitest (~> 5.10)
-  rake (~> 10.3, >= 10.3.2)
+  rake (~> 13.0)
   simplecov
   yard (~> 0.9.11)
 
 BUNDLED WITH
-   1.17.3
+   2.5.5

Rakefile

@@ -59,36 +59,42 @@ require 'bundler/setup'
 
 TMP_DIR = "#{Rake.original_dir}/tmp".freeze
 APP_NAME = "#{GEMSPEC.name}-#{GEMSPEC.version}".freeze
-PLATFORMS = %w[linux-x86_64 osx].freeze
-TRAVELING_RUBY_VERSION = 'traveling-ruby-20210206-2.4.10'.freeze
-TRAVELING_RUBYGEMS_VERSION = 'traveling-ruby-gems-20210206-2.4.10'.freeze
-NOKOGIRI_VERSION = 'nokogiri-1.10.10'.freeze
+PLATFORMS = %w[linux-x86_64 osx-x86_64 osx-arm64].freeze
+TR_RUBY_VERSION = '3.2'.freeze
+TRAVELING_RUBY_BASE_URL = "https://github.com/YOU54F/traveling-ruby/releases/download/rel-20230803"
+TRAVELING_RUBY_VERSION = "traveling-ruby-20230803-3.2.2".freeze
+TRAVELING_RUBYGEMS_VERSION = "traveling-ruby-gems-20230803-3.2.2".freeze
+NOKOGIRI_VERSION = 'nokogiri-1.15.3'.freeze
 MAFFT = {
-  version: '7.475',
-  'linux-x86_64': 'https://mafft.cbrc.jp/alignment/software/mafft-7.475-linux.tgz',
-  osx: 'https://mafft.cbrc.jp/alignment/software/mafft-7.475-mac.zip'
+  version: '7.490',
+  'linux-x86_64': 'https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz',
+  'osx-x86_64': 'https://mafft.cbrc.jp/alignment/software/mafft-7.490-mac.zip',
+  'osx-arm64': 'https://mafft.cbrc.jp/alignment/software/mafft-7.490-mac.zip'
 }.freeze
 BLAST = {
-  version: '2.11.0+',
-  'linux-x86_64': 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.11.0/ncbi-blast-2.11.0+-x64-linux.tar.gz',
-  osx: 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.11.0/ncbi-blast-2.11.0+-x64-macosx.tar.gz'
+  version: '2.15.0+',
+  'linux-x86_64': 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-linux.tar.gz',
+  'osx-x86_64': 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-macosx.tar.gz',
+  'osx-arm64': 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-macosx.tar.gz'
 }.freeze
 JQ = {
-  version: '1.6',
-  'linux-x86_64': 'https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64',
-  osx: 'https://github.com/stedolan/jq/releases/download/jq-1.6/jq-osx-amd64'
+  version: '1.7.1',
+  'linux-x86_64': 'https://github.com/jqlang/jq/releases/download/jq-1.7.1/jq-linux-amd64',
+  'osx-x86_64': 'https://github.com/jqlang/jq/releases/download/jq-1.7.1/jq-macos-amd64',
+  'osx-arm64': 'https://github.com/jqlang/jq/releases/download/jq-1.7.1/jq-macos-arm64'
 }.freeze
 CSVTK = {
-  version: '0.21.0',
-  'linux-x86_64': 'https://github.com/shenwei356/csvtk/releases/download/v0.21.0/csvtk_linux_amd64.tar.gz',
-  osx: 'https://github.com/shenwei356/csvtk/releases/download/v0.21.0/csvtk_darwin_amd64.tar.gz'
+  version: '0.29.0',
+  'linux-x86_64': 'https://github.com/shenwei356/csvtk/releases/download/v0.29.0/csvtk_linux_amd64.tar.gz',
+  'osx-x86_64': 'https://github.com/shenwei356/csvtk/releases/download/v0.29.0/csvtk_darwin_amd64.tar.gz',
+  'osx-arm64': 'https://github.com/shenwei356/csvtk/releases/download/v0.29.0/csvtk_darwin_arm64.tar.gz'
 }.freeze
 
 desc 'Create standalone GeneValidator packages'
 task :package do
   rm_rf TMP_DIR
   mkdir TMP_DIR
-  task('package:build' => ['package:linux-x86_64', 'package:osx']).invoke
+  task('package:build' => ['package:linux-x86_64', 'package:osx-x86_64', 'package:osx-arm64']).invoke
   rm_rf TMP_DIR
 end
 
@@ -101,12 +107,12 @@ end
 # ## TO RUN with DOCKER
 # Start docker, mounting an empty folder called `output`:
 #
-# `docker run --rm -it -v $PWD/output:/gv ruby:2.4.10 /bin/bash`
+# `docker run --rm -it -v $PWD/output:/gv ruby:3.2.2 /bin/bash`
 #
 # Then inside the shell:
 #
 # ```
-# apt update && apt install unzip && gem install bundler -v 1.17.3
+# apt update && apt install unzip && gem install bundler
 # cd /gv
 # git clone https://github.com/wurmlab/genevalidator
 # cd genevalidator
@@ -202,8 +208,9 @@ namespace :package do
 
   desc 'Install gems to local directory'
   task :bundle_install do
-    if RUBY_VERSION !~ /^2\.4\./
-      abort "You can only 'bundle install' using Ruby 2.4, because that's " \
+    puts "Using Ruby #{TR_RUBY_VERSION}"
+    if RUBY_VERSION !~ /^3\.2\./
+      abort "You can only 'bundle install' using Ruby #{TR_RUBY_VERSION}, because that's " \
             'what Traveling Ruby uses.'
     end
 
@@ -213,12 +220,12 @@ namespace :package do
     end
 
     cd TMP_DIR do
-      Bundler.with_clean_env do
-        sh "env BUNDLE_IGNORE_CONFIG=1 BUNDLE_GEMFILE=#{TMP_DIR}/Gemfile" \
+      Bundler.with_unbundled_env do
+        sh "env BUNDLE_IGNORE_CONFIG=1 BUNDLE_GEMFILE=#{TMP_DIR}/Gemfile BUNDLE_FORCE_RUBY_PLATFORM=1" \
            ' bundle install --path vendor --without development test'
       end
 
-      cd 'vendor/ruby/2.4.0' do
+      cd "vendor/ruby/#{TR_RUBY_VERSION}.0" do
         cd 'gems' do
           mkdir APP_NAME
           %w[aux lib].each { |d| cp_r "#{Rake.original_dir}/#{d}", APP_NAME }
@@ -253,9 +260,9 @@ namespace :package do
     cd "#{TMP_DIR}/vendor" do
       sh 'rm -f */*/cache/*'
       sh 'rm -rf ruby/*/extensions'
-      sh "find ruby/2.4.0/gems -name '*.so' | xargs rm -f"
-      sh "find ruby/2.4.0/gems -name '*.bundle' | xargs rm -f"
-      sh "find ruby/2.4.0/gems -name '*.o' | xargs rm -f"
+      sh "find ruby/#{TR_RUBY_VERSION}.0/gems -name '*.bundle' | xargs rm -f"
+      sh "find ruby/#{TR_RUBY_VERSION}.0/gems -name '*.so' | xargs rm -f"
+      sh "find ruby/#{TR_RUBY_VERSION}.0/gems -name '*.o' | xargs rm -f"
 
       # Remove tests
       %w[test tests spec features benchmark].each do |dir|
@@ -284,9 +291,9 @@ namespace :package do
       sh "find ruby -name '*.h' | xargs rm -f"
       sh "find ruby -name '*.rl' | xargs rm -f"
       sh "find ruby -name 'extconf.rb' | xargs rm -f"
-      sh "find ruby/2.4.0/gems -name '*.o' | xargs rm -f"
-      sh "find ruby/2.4.0/gems -name '*.so' | xargs rm -f"
-      sh "find ruby/2.4.0/gems -name '*.bundle' | xargs rm -f"
+      sh "find ruby/#{TR_RUBY_VERSION}.0/gems -name '*.o' | xargs rm -f"
+      sh "find ruby/#{TR_RUBY_VERSION}.0/gems -name '*.so' | xargs rm -f"
+      sh "find ruby/#{TR_RUBY_VERSION}.0/gems -name '*.bundle' | xargs rm -f"
 
       # Remove Java files. They're only used for JRuby support
       sh "find ruby -name '*.java' | xargs rm -f"
@@ -306,12 +313,12 @@ end
 
 def download_runtime(platform)
   sh "curl -L --fail -o #{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz " \
-     "https://d6r77u77i8pq3.cloudfront.net/releases/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz"
+     "#{TRAVELING_RUBY_BASE_URL}/#{TRAVELING_RUBY_VERSION}-#{platform}.tar.gz"
 end
 
 def download_native_extension(platform, gem_name_and_version)
   sh "curl -L --fail -o #{TMP_DIR}/#{TRAVELING_RUBY_VERSION}-#{platform}-#{gem_name_and_version}.tar.gz " \
-     "https://d6r77u77i8pq3.cloudfront.net/releases/#{TRAVELING_RUBYGEMS_VERSION}-#{platform}/#{gem_name_and_version}.tar.gz"
+     "#{TRAVELING_RUBY_BASE_URL}/#{TRAVELING_RUBYGEMS_VERSION}-#{platform}-#{gem_name_and_version}.tar.gz"
 end
 
 def process_package(url, package_name)
@@ -335,7 +342,7 @@ def edited_gemspec_content
     next if index < 4 # skip first four lines
     l = "s.version = '#{GEMSPEC.version}'\n" if l =~ /^\s+s.version/
     l = "s.files = ['#{file_list.join("','")}']\n" if l =~ /^\s+s.files/
-    l = "s.add_dependency 'nokogiri', '1.10.10'\nend" if l =~ /^end/
+    l = "s.add_dependency 'nokogiri', '#{NOKOGIRI_VERSION.split('-').last}'\nend" if l =~ /^end/
     edited_gemspec << l
   end
   edited_gemspec.join
@@ -347,7 +354,7 @@ source 'http://rubygems.org'
 gem 'bio', '~> 1.4'
 gem 'bio-blastxmlparser', '~> 2.0'
 gem '#{GEMSPEC.name}', '#{GEMSPEC.version}'
-gem 'nokogiri', '1.10.10'
+gem 'nokogiri', '#{NOKOGIRI_VERSION.split('-').last}'
 gem 'statsample', '2.1.0'
 GEMFILE
 

bin/genevalidator

@@ -464,9 +464,15 @@ elsif command == 'serve'
   }
 elsif command == 'ncbi-blast-dbs'
   require 'rake'
-  load 'ncbi-blast-dbs.rake'
 
-  Rake.application.init 'ncbi-blast-dbs'
+  if ARGV.include? "http"
+    load "genevalidator/ncbi-blast-dbs/http-ncbi-blast-dbs.rake"
+    Rake.application.init 'http-ncbi-blast-dbs'
+  else
+    load "genevalidator/ncbi-blast-dbs/ncbi-blast-dbs.rake"
+    Rake.application.init 'ncbi-blast-dbs'
+  end
+
   Rake.application.load_imports
   Rake.application.top_level
 

genevalidator.gemspec

@@ -18,16 +18,20 @@ Gem::Specification.new do |s|
   s.required_ruby_version = '>= 2.2.0'
 
   s.add_development_dependency 'minitest', '~> 5.10'
-  s.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
+  s.add_development_dependency 'rake', '~> 13.0'
   s.add_development_dependency 'yard', '~> 0.9.11'
 
   s.add_dependency 'bio', '~> 1.4'
   s.add_dependency 'bio-blastxmlparser', '~> 2.0'
   s.add_dependency 'genevalidatorapp', '~> 2.1.8'
-  s.add_dependency 'ncbi-blast-dbs', '0.0.6'
+  s.add_dependency 'matrix', '~> 0.4.2' # required by statsample
+  s.add_dependency 'net-ftp', '~> 0.1.3' # required by ncbi-blast-dbs
+  s.add_dependency 'prime', '~> 0.1.2' # required by distribution (statsample)
   s.add_dependency 'rack', '~> 2.0'
   s.add_dependency 'slim', '~>3.0'
   s.add_dependency 'statsample', '2.1.0'
+  s.add_dependency 'rexml', '~> 3.2', '>= 3.2.6' # required by prawn (statsample)
+  s.add_dependency 'webrick', '~> 1.8'
 
   s.files         = `git ls-files -z`.split("\x0")
   s.executables   = s.files.grep(%r{^bin/}) { |f| File.basename(f) }

lib/genevalidator/ext/file.rb

@@ -0,0 +1,6 @@
+# Needed for Prawn (from Statsample)
+class File
+  class << self
+    alias_method :exists?, :exist? unless respond_to?(:exists?)
+  end
+end