Merge branch 'main' into snapshots

.dockerignore

@@ -1,6 +1,7 @@
 .git/
 Dockerfile
 filestore*
+hooks/
 coverage/
 docker/solr/
 db/*.sqlite3

.github/workflows/ansible-install.yml

@@ -0,0 +1,92 @@
+name: ansible-install
+run-name: "Testing Ansible install after commit \"${{ github.event.head_commit.message }}\""
+on:
+  push:
+    branches:
+      - ansible
+      - full-test-suite
+  workflow_dispatch:
+
+jobs:
+  install-seek-from-ansible:
+    runs-on: ${{matrix.os}}
+    continue-on-error: true
+    strategy:
+      matrix:
+        os: [ubuntu-20.04,ubuntu-22.04]
+
+    services:
+      mysql:
+          image: mysql:8.0.21
+          env:
+              MYSQL_ALLOW_EMPTY_PASSWORD: yes
+              MYSQL_ROOT_PASSWORD: ''
+              MYSQL_DATABASE: test
+          ports:
+            - 3306:3306
+          options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 --restart=always
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Configure ansible for local install
+        working-directory: /home/runner/work/seek/seek/script/ansible/
+        run: |
+          sed -i '/vault_password_file/d' ansible.cfg
+          sed -i '/ssh_connection/d' ansible.cfg
+          sed -i '/pipelining/d' ansible.cfg
+          sed -i 's/\- hosts\: \[servers\]/\- hosts\: localhost/g' Deploy-SEEK.yml
+          sed -i '/\- hosts\: localhost/a \ \ connection\: local' Deploy-SEEK.yml
+          sed -i 's/user_var\: username/user_var\: runner/' group_vars/vars.yml
+          sed -i 's/git_dest\: \/home\/username/git_dest\: \/home\/runner\/work/' group_vars/vars.yml
+          sed -i 's|git_version: main|git_version: '"${GITHUB_REF_NAME}"'|' group_vars/vars.yml
+          sed -i '/sql_user\: sql_username/a sql_password: mysqlpassword' group_vars/vars.yml
+
+      - name: Prepares system for ansible install
+        run: |
+          sudo apt install acl -y
+
+      - name: Install SEEK through ansible
+        working-directory: /home/runner/work/seek/seek/script/ansible/
+        run: |
+          ansible-playbook Deploy-SEEK.yml --skip-tags database
+
+      - name: Configures database
+        working-directory: /home/runner/work/SEEK
+        run: |
+          cp config/database.default.yml config/database.yml
+          sed -i '/password\: mysqlpassword/a \ \ port\: 3306' config/database.yml
+          sed -i '/password\: mysqlpassword/a \ \ host\: 127.0.0.1' config/database.yml
+          sed -i 's/mysqluser/root/g' config/database.yml
+          sed -i 's/mysqlpassword//g' config/database.yml
+          bash -lc 'bundle exec rake db:setup'
+
+      - name: Runs seek unit tests
+        working-directory: /home/runner/work/SEEK
+        run: |
+          bash -lc 'bundle exec rails test test/unit'
+
+      - name: Runs seek integration tests
+        working-directory: /home/runner/work/SEEK
+        run: |
+          bash -lc 'bundle exec rails test test/integration'
+
+      - name: Runs seek functional tests
+        working-directory: /home/runner/work/SEEK
+        run: |
+          bash -lc 'bundle exec rails test test/functional'
+
+
+  fail-on-any-os:
+    # Without this step workflow remains "green" regardles of fails above.
+    name: Workflow Status
+    needs:
+      - install-seek-from-ansible
+    runs-on: ubuntu-latest
+    if: always()
+    steps:
+      - uses: technote-space/[email protected]
+      - name: Check Job Status status and fail if they are red
+        if: env.WORKFLOW_CONCLUSION == 'failure'
+        run: exit 1

.github/workflows/docker-image.yml

@@ -3,13 +3,14 @@ name: Test Docker Image Build
 on:
   push:
     branches:
-      - master
+      - main
       - workflow
       - workflowhub
       - seek-1.11
       - seek-1.12
       - seek-1.13
       - master-ibisba-demonstrator
+      - ruby-3
   pull_request:
 
 jobs:

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
       TERM: dumb-color
     services:
       postgres:
-        image: postgres:11
+        image: postgres:14
         env:
           POSTGRES_USER: seek
           POSTGRES_DB: seek_test
@@ -59,25 +59,23 @@ jobs:
             suite: rails test test/unit
     steps:
       - name: Install system dependencies
-        run: sudo apt update && sudo apt install -y graphicsmagick graphviz libcurl4-gnutls-dev libreoffice poppler-utils
-        # build-essential git imagemagick libgmp-dev \
-        #    libmagick++-dev libmysqlclient-dev libpq-dev libreadline-dev libreoffice libssl-dev \
-        #    libxml++2.6-dev libxslt1-dev nodejs openjdk-8-jdk openssh-server poppler-utils zip
+        run: |
+          sudo apt install -y software-properties-common
+          sudo add-apt-repository ppa:deadsnakes/ppa
+          sudo apt update
+          sudo apt install -y graphicsmagick graphviz libcurl4-gnutls-dev libreoffice poppler-utils build-essential \
+            git imagemagick libgmp-dev python3.9-dev python3.9-distutils python3-pip
       - name: Checkout code
         uses: actions/checkout@v3
       - name: Setup Java
         uses: actions/setup-java@v3
         with:
-          distribution: 'temurin'      
+          distribution: 'temurin'
           java-version: '11' # The JDK version to make available on the path.
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.7'
       - name: Cache pip
         uses: actions/cache@v3
         with:
@@ -89,7 +87,9 @@ jobs:
             ${{ runner.os }}-pip-
             ${{ runner.os }}-
       - name: Install Python dependencies
-        run: pip install -r requirements.txt
+        run: |
+          python3.9 -m pip install setuptools==58
+          python3.9 -m pip install -r requirements.txt
       - name: Create test database
         run: |
           cp test/config/database.github.${{ matrix.database }}.yml config/database.yml

.gitignore

@@ -91,3 +91,4 @@ docker-compose.override.yml
 .env.*.local
 .env.local
 
+*.ignore

.ruby-version

@@ -1 +1 @@
-ruby-2.7.6
+ruby-3.1.4

Dockerfile

@@ -1,19 +1,19 @@
-FROM ruby:2.7-buster
+FROM ruby:3.1-slim-bullseye
 
 LABEL maintainer="Stuart Owen <orcid.org/0000-0003-2130-0865>, Finn Bacall"
-
+ARG SOURCE_COMMIT
 ENV APP_DIR /seek
 ENV RAILS_ENV=production
 
 # need to set the locale, otherwise some gems file to install
 ENV LANG="en_US.UTF-8" LANGUAGE="en_US:UTF-8" LC_ALL="C.UTF-8"
 
 RUN apt-get update -qq && \
-    apt-get install -y --no-install-recommends build-essential cmake gettext graphviz git \
-		libcurl4-gnutls-dev libmagick++-dev libpq-dev libreadline-dev \
+    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 default-mysql-client nginx nodejs openjdk-11-jdk-headless \
-		python3.7-dev python3.7-distutils python3-pip \
+		libxslt1-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 && \
     rm -rf /var/lib/apt/lists/* && \
@@ -29,22 +29,25 @@ WORKDIR $APP_DIR
 # Bundle install throw errors if Gemfile has been modified since Gemfile.lock
 COPY Gemfile* ./
 RUN bundle config --local frozen 1 && \
-    bundle install --deployment --without development test
+    bundle config set deployment 'true' && \
+    bundle config set without 'development test' && \
+    bundle install
 
 # App code
 COPY . .
 RUN mkdir log tmp
 COPY docker/virtuoso_settings.docker.yml config/virtuoso_settings.yml
 
 USER root
+RUN if [ -n "$SOURCE_COMMIT" ] ; then echo $SOURCE_COMMIT > config/.git-revision ; fi
 RUN chown -R www-data solr config docker public /var/www db/schema.rb
 USER www-data
 RUN touch config/using-docker #allows us to see within SEEK we are running in a container
 
 # Python dependencies from requirements.txt
 ENV PATH="/var/www/.local/bin:$PATH"
-RUN python3.7 -m pip install setuptools==58
-RUN python3.7 -m pip install -r requirements.txt
+RUN python3.9 -m pip install setuptools==58
+RUN python3.9 -m pip install -r requirements.txt
 
 # SQLite Database (for asset compilation)
 RUN mkdir sqlite3-db && \

Gemfile

@@ -9,17 +9,18 @@ gem 'mysql2'
 gem 'pg'
 gem 'sqlite3', '~> 1.4'
 
-gem 'feedjira', '~>1'
+gem 'feedjira'
 gem 'google-analytics-rails'
 gem 'hpricot', '~>0.8.2'
 gem 'libxml-ruby', '~>2.9.0', require: 'libxml'
 gem 'uuid', '~>2.3'
 gem 'RedCloth', '>=4.3.0'
-gem 'simple-spreadsheet-extractor', '~>0.16.0'
-gem 'sample-template-generator', '~>0.5'
-gem 'rmagick', '2.15.2'
+gem 'simple-spreadsheet-extractor', '~> 0.18.0'
+gem 'open4'
+gem 'sample-template-generator', '~>0.7'
+gem 'rmagick', '4.2.5'
 gem 'rest-client', '~>2.0'
-gem 'factory_girl', '2.6.4'
+gem 'factory_bot', '~> 6.2.1'
 gem 'bio', '~> 1.5.1'
 gem 'sunspot_rails'
 gem 'progress_bar'
@@ -38,7 +39,8 @@ gem 'active_model_serializers', '~> 0.10.13'
 gem 'rubyzip'
 
 gem 'equivalent-xml'
-gem 'docsplit'
+# 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'
@@ -50,14 +52,14 @@ gem 'will_paginate', '~> 3.1'
 gem 'yaml_db'
 gem 'rails_autolink'
 gem 'rfc-822'
-gem 'nokogiri', '~> 1.13.9'
+gem 'nokogiri', '~> 1.14.3'
 #necessary for newer hashie dependency, original api_smith is no longer active
 gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b'
 gem 'rdf-virtuoso', '>= 0.2.0'
 gem 'terrapin'
 gem 'lograge'
 gem 'psych'
-gem 'stringio', '0.1.0' #locked to the default version for ruby 2.7
+gem 'stringio', '3.0.1' #locked to the default version for ruby 3.1
 gem 'validate_url'
 gem "attr_encrypted", "~> 3.0.0"
 gem 'libreconv'
@@ -69,9 +71,9 @@ gem 'bives', "~> 2.0"
 gem 'my_responds_to_parent', git: 'https://github.com/SysMO-DB/my_responds_to_parent.git'
 gem 'bioportal', '>=3.0', git: 'https://github.com/SysMO-DB/bioportal.git'
 gem 'doi_query_tool', git: 'https://github.com/seek4science/DOI-query-tool.git'
-gem 'fleximage', git: 'https://github.com/SysMO-DB/fleximage.git', ref: 'bb1182f2716a9bf1b5d85e186d8bb7eec436797b'
+gem 'fleximage', git: 'https://github.com/SysMO-DB/fleximage.git', ref: 'de03bf816a911dc4f69573fd300d4ff90225cca7'
 
-gem 'jquery-rails', '~> 4.2.2'
+gem 'jquery-rails', '~> 4.4.0'
 gem 'jquery-ui-rails'
 gem 'recaptcha', '~> 4.1.0'
 gem 'metainspector'
@@ -131,7 +133,7 @@ gem 'request_store'
 
 gem 'bundler', '>= 1.8.4'
 
-gem 'ro-crate', '~> 0.4.17'
+gem 'ro-crate', '~> 0.5.1'
 
 gem 'rugged'
 gem 'i18n-js'
@@ -147,6 +149,17 @@ gem 'json-schema'
 
 gem 'cff', '~> 0.9.0'
 
+gem 'remotipart', '~> 1.4.4' # Allows file upload in AJAX forms
+
+gem 'rails-static-router'
+
+gem 'caxlsx', '>= 3.0' # Write content to an xlsx file
+gem 'caxlsx_rails', '~> 0.6.2'
+
+gem 'net-ftp'
+
+gem 'licensee'
+
 group :production do
   gem 'passenger'
 end