Merge branch 'main' into add-ror-support

.github/workflows/docker-image.yml

@@ -5,7 +5,9 @@ on:
     branches:
       - main
       - workflowhub
+      - rails-7-hacking-rebased
       - full-test-suite
+      - seek-1.16
 
   pull_request:
 

.github/workflows/tests.yml

@@ -29,7 +29,7 @@ jobs:
           - 33306:3306
         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
       virtuoso:
-        image: tenforce/virtuoso
+        image: openlink/virtuoso-opensource-7
         env:
           DBA_PASSWORD: tester
           SPARQL_UPDATE: true
@@ -86,6 +86,7 @@ jobs:
             ${{ runner.os }}-
       - name: Install Python dependencies
         run: |
+          python3.9 -m pip install --upgrade pip
           python3.9 -m pip install setuptools==58
           python3.9 -m pip install -r requirements.txt
       - name: Create test database

.gitignore

@@ -8,6 +8,8 @@ rails_best_practices_output.html
 
 db/*.sqlite3
 db/*.sqlite3-journal
+db/*.sqlite3-shm
+db/*.sqlite3-wal
 config/database.yml
 config/initializers/seek_local.rb
 config/environment_local.rb
@@ -93,3 +95,4 @@ docker-compose.override.yml
 .env.local
 
 *.ignore
+/tmp/local_secret.txt

.ruby-version

@@ -1 +1 @@
-ruby-3.1.4
+ruby-3.3.6

Dockerfile

@@ -1,4 +1,4 @@
-FROM ruby:3.1-slim-bullseye
+FROM ruby:3.3-slim-bullseye
 
 LABEL maintainer="Stuart Owen <orcid.org/0000-0003-2130-0865>, Finn Bacall"
 ARG SOURCE_COMMIT
@@ -12,7 +12,7 @@ RUN apt-get update -qq && \
     apt-get install -y --no-install-recommends build-essential cmake curl default-mysql-client gettext graphviz git \
 		libcurl4-gnutls-dev libmagick++-dev libmariadb-dev libpq-dev libreadline-dev \
 		libreoffice libsqlite3-dev libssl-dev libxml++2.6-dev \
-		libxslt1-dev locales nginx nodejs openjdk-11-jdk-headless \
+		libxslt1-dev libyaml-dev locales nginx nodejs openjdk-11-jdk-headless \
 		python3.9-dev python3.9-distutils python3-pip \
 		poppler-utils postgresql-client shared-mime-info sqlite3 links telnet vim-tiny zip && \
     apt-get clean && \
@@ -46,6 +46,7 @@ RUN touch config/using-docker #allows us to see within SEEK we are running in a
 
 # Python dependencies from requirements.txt
 ENV PATH="/var/www/.local/bin:$PATH"
+RUN python3.9 -m pip install --upgrade pip
 RUN python3.9 -m pip install setuptools==58
 RUN python3.9 -m pip install -r requirements.txt
 

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 
-gem 'rails', '~> 6.1.7'
+gem 'rails', '~> 7.2.2'
 gem 'rdoc'
 
 #database adaptors
@@ -11,11 +11,10 @@ gem 'sqlite3', '~> 1.4'
 
 gem 'feedjira'
 gem 'google-analytics-rails'
-gem 'hpricot', '~>0.8.2'
-gem 'libxml-ruby', '~>2.9.0', require: 'libxml'
+gem 'libxml-ruby', '~>5.0', require: 'libxml'
 gem 'uuid', '~>2.3'
 gem 'RedCloth', '>=4.3.0'
-gem 'simple-spreadsheet-extractor', '0.18.1'
+gem 'simple-spreadsheet-extractor', '0.18.2'
 gem 'open4'
 gem 'sample-template-generator', '~>0.7'
 gem 'rmagick', '5.3.0'
@@ -41,7 +40,6 @@ gem 'rubyzip'
 gem 'equivalent-xml'
 # FIXME: Change back to "official" docsplit if this PR is ever merged: https://github.com/documentcloud/docsplit/pull/159
 gem 'docsplit', git: 'https://github.com/tuttiq/docsplit.git', ref: '6127e3912b8db94ed84dca6be5622d3d5ec0d879'
-gem 'pothoven-attachment_fu'
 gem 'exception_notification'
 gem 'fssm'
 gem 'acts-as-taggable-on'
@@ -59,9 +57,8 @@ gem 'rdf-virtuoso', '>= 0.2.0'
 gem 'terrapin'
 gem 'lograge'
 gem 'psych'
-gem 'stringio', '3.0.1.1' #locked to the default version for ruby 3.1
 gem 'validate_url'
-gem "attr_encrypted", "~> 3.0.0"
+gem "attr_encrypted"
 gem 'libreconv'
 
 # gem for BiVeS and BudHat
@@ -92,11 +89,11 @@ gem 'zenodo-client', git: 'https://github.com/seek4science/zenodo-client.git'
 gem 'unicorn-rails'
 gem 'seedbank'
 
-gem 'rspec-rails','~> 5.1'
+gem 'rspec-rails'
 
 gem 'citeproc-ruby', '~> 2.0.0'
 gem 'csl-styles', '~> 2.0.0'
-gem 'bibtex-ruby', '~> 5.1.0'
+gem 'bibtex-ruby', '~> 6.1.0'
 
 gem 'omniauth', '~> 2.1.0'
 gem 'gitlab_omniauth-ldap', '~> 2.2.0'
@@ -105,8 +102,6 @@ gem 'openid_connect','1.3.0'
 gem 'omniauth-rails_csrf_protection'
 gem 'omniauth-github'
 
-gem 'ransack'
-
 gem 'terser', '~> 1.1', '>= 1.1.1'
 
 
@@ -163,6 +158,13 @@ gem 'licensee'
 
 gem "sitemap_generator", "~> 6.3"
 
+# removed from Standard in Ruby 3.4
+gem 'observer'
+gem 'abbrev'
+gem 'csv'
+gem 'nkf'
+gem 'mutex_m'
+
 group :production do
   gem 'passenger'
 end