Sync: BioPortal v6.8.0 release

.github/workflows/deploy.yml

@@ -14,25 +14,22 @@
 #
 # DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/deploy_id_rsa_enc (see miloserdow/capistrano-deploy)
 # this SSH key is used for accessing jump host, UI nodes, and private github repo.
-
 name: Capistrano Deployment
-# Controls when the action will run.
+
+permissions:
+  contents: read
+
 on:
-  push:
-    branches:
-      - master
-      - develop
   # Trigger deployment to staging after unit test action completes
   workflow_run:
     workflows: ["Ruby Unit Tests"]
     types:
       - completed
-    branches: [master, develop]
+    branches: [develop]  # trigger auto deployment to staging from develop branch
   # Allows running this workflow manually from the Actions tab
   workflow_dispatch:
-    branches: [master, develop]
     inputs:
-      BRANCH:
+      branch:
         description: 'Branch/tag to deploy'
         default: develop
         required: true
@@ -46,36 +43,62 @@ on:
 
 jobs:
   deploy:
+    concurrency:
+      group: deploy
     runs-on: ubuntu-latest
-    # run deployment only if "Ruby Unit Tests" workflow completes sucessefully or when manually triggered
-    if: ${{ (github.event.workflow_run.conclusion == 'success') || (github.event_name == 'workflow_dispatch') }}
+    # run deployment only if "Ruby Unit Tests" workflow completes sucessefully
+    # or when manually triggered
+    if: >
+      (github.event_name == 'workflow_run' &&
+       github.event.workflow_run.conclusion == 'success') ||
+      (github.event_name == 'workflow_dispatch')
     env:
-      BUNDLE_WITHOUT: default #install gems required primarily for the deployment in order to speed this workflow
+      BUNDLE_WITHOUT: default:test:development #install gems required primarily for the deployment in order to speed this workflow
       PRIVATE_CONFIG_REPO: ${{ format('git@github.com:{0}.git', secrets.CONFIG_REPO) }}
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
     - name: set branch/tag and environment to deploy from inputs
       run: |
-        # workflow_dispatch default input doesn't get set on push so we need to set defaults
-        # via shell parameter expansion
-        # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g
-        USER_INPUT_BRANCH=${{ inputs.branch }}
-        echo "BRANCH=${USER_INPUT_BRANCH:-develop}" >> $GITHUB_ENV
-        USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
-        echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV
+        if [ "${{ github.event_name }}" = "workflow_run" ]; then
+          # Auto: always deploy develop to staging
+          echo "BRANCH=develop" >> "$GITHUB_ENV"
+          # echo "BRANCH=${{ github.event.workflow_run.head_branch }}" >> "$GITHUB_ENV"  # auto deploy from branch if needed
+          echo "TARGET=staging" >> "$GITHUB_ENV"
+        else
+          # Manual: use inputs, with defaulting via parameter expansion
+          USER_INPUT_BRANCH=${{ inputs.branch }}
+          USER_INPUT_ENVIRONMENT=${{ inputs.environment }}
+
+          echo "BRANCH=${USER_INPUT_BRANCH:-develop}" >> "$GITHUB_ENV"
+          echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> "$GITHUB_ENV"
+        fi
+    - name: Provide deployment info
+      run: |
+        echo "=== Deployment Details ======================================"
+        echo "Time:        $(date -u +"%Y-%m-%d %H:%M:%S UTC")"
+        echo "Branch/Tag:  ${BRANCH}"
+        echo "Environment: ${TARGET}"
+        echo "Commit:      ${GITHUB_SHA}"
+        echo "Triggered by: ${GITHUB_ACTOR}"
+        echo "Event:       ${GITHUB_EVENT_NAME}"
+        if [ "${GITHUB_EVENT_NAME}" = "workflow_run" ]; then
+          echo "Mode:        auto-deploy from develop"
+        else
+          echo "Mode:        manual deployment"
+        fi
+        echo "=============================================================="
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - uses: ruby/setup-ruby@v1
       with:
         bundler-cache: true # runs 'bundle install' and caches installed gems automatically
     - name: get-deployment-config
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings
         token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
-        path:  deploy_config
+        path: deploy_config
     - name: copy-deployment-config
-      run:  cp -r deploy_config/ontologies_api/* .
+      run: cp -r deploy_config/ontologies_api/* .
     # add ssh hostkey so that capistrano doesn't complain
     - name: Add jumphost's hostkey to Known Hosts
       run: |

.github/workflows/testkit-unit-tests.yml

@@ -0,0 +1,87 @@
+name: Docker Unit Tests
+
+on:
+  push:
+    branches:
+      - '**'
+    tags-ignore:
+      - '**'
+  pull_request:
+
+env:
+  # CI execution mode for backend tests:
+  # - container: run `test:docker:<backend>:container` (default)
+  # - native: run `test:docker:<backend>` on host Ruby
+  OPTK_CI_RUN_MODE: ${{ vars.OPTK_CI_RUN_MODE || 'container' }}
+  # Example override to force native mode in this workflow file:
+  # OPTK_CI_RUN_MODE: native
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      backends: ${{ steps.cfg.outputs.backends }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - id: cfg
+        name: Read backend matrix from .ontoportal-testkit.yml
+        run: |
+          BACKENDS=$(ruby -ryaml -rjson -e 'c=YAML.safe_load_file(".ontoportal-testkit.yml") || {}; b=c["backends"] || %w[fs ag vo gd]; puts JSON.generate(b)')
+          echo "backends=$BACKENDS" >> "$GITHUB_OUTPUT"
+
+  test:
+    needs: prepare
+    runs-on: ubuntu-latest
+    timeout-minutes: 45
+    strategy:
+      fail-fast: false
+      matrix:
+        backend: ${{ fromJson(needs.prepare.outputs.backends) }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Ruby from .ruby-version
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: .ruby-version
+          bundler-cache: true
+
+      - name: Set up Java 11 (native mode)
+        if: env.OPTK_CI_RUN_MODE == 'native'
+        uses: actions/setup-java@v5
+        with:
+          distribution: temurin
+          java-version: '11'
+
+      - name: Install native system dependencies
+        if: env.OPTK_CI_RUN_MODE == 'native'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y raptor2-utils
+
+      - name: Run unit tests
+        env:
+          CI: "true"
+          TESTOPTS: "--verbose"
+          BACKEND: ${{ matrix.backend }}
+        run: |
+          MODE="${OPTK_CI_RUN_MODE:-container}"
+          TASK="test:docker:${BACKEND}"
+          if [ "$MODE" = "container" ]; then
+            TASK="${TASK}:container"
+          elif [ "$MODE" != "native" ]; then
+            echo "Invalid OPTK_CI_RUN_MODE=$MODE (expected container or native)"
+            exit 1
+          fi
+
+          bundle exec rake "$TASK"
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          flags: unittests,${{ matrix.backend }}
+          verbose: true
+          fail_ci_if_error: false

.gitignore

@@ -56,6 +56,12 @@ test/data/ontology_files/repo/**/*
 .classpath
 .project
 
+# Claude Code
+.claude/
+
+# Serena
+.serena/
+
 *.swp
 
 config/environments/console.rb

.ontoportal-testkit.yml

@@ -0,0 +1,9 @@
+component_name: ontologies_api
+app_service: test-container
+backends:
+  - fs
+  - ag
+  - vo
+  - gd
+dependency_services:
+  - mgrep

.ruby-version

@@ -1 +1 @@
-3.1.6
+3.2.10

Capfile

@@ -22,6 +22,6 @@ require 'capistrano/bundler'
 # require 'capistrano/rails/assets'
 # require 'capistrano/rails/migrations'
 require 'capistrano/locally'
-require 'new_relic/recipes' # announce deployments in NewRelic
+
 # Loads custom tasks from `lib/capistrano/tasks' if you have any defined.
 Dir.glob('lib/capistrano/tasks/*.cap').each { |r| import r }

Dockerfile

@@ -1,24 +1,20 @@
-ARG RUBY_VERSION=3.1
-ARG DISTRO_NAME=bullseye
+ARG RUBY_VERSION=3.2
+ARG DISTRO=bullseye
+ARG TESTKIT_BASE_IMAGE=ontoportal/testkit-base:ruby${RUBY_VERSION}-${DISTRO}
+FROM ${TESTKIT_BASE_IMAGE}
 
-FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+WORKDIR /app
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
-  openjdk-11-jre-headless \
-  raptor2-utils \
-  && rm -rf /var/lib/apt/lists/*
+COPY Gemfile* *.gemspec ./
 
-RUN mkdir -p /srv/ontoportal/ontologies_api
-RUN mkdir -p /srv/ontoportal/bundle
-COPY Gemfile* /srv/ontoportal/ontologies_api/
+# Respect the project's Bundler lock when present.
+RUN if [ -f Gemfile.lock ]; then \
+      BUNDLER_VERSION=$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1 | tr -d ' '); \
+      gem install bundler -v "$BUNDLER_VERSION"; \
+    fi
 
-WORKDIR /srv/ontoportal/ontologies_api
+RUN bundle install --jobs 4 --retry 3
 
-ENV BUNDLE_PATH=/srv/ontoportal/bundle
-RUN bundle install
+COPY . ./
 
-COPY . /srv/ontoportal/ontologies_api
-RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb
-
-EXPOSE 9393
 CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"]