NearForm pull request

.eslintignore

@@ -0,0 +1,3 @@
+assets/js/search.js
+assets/js/bioconductor.js
+assets/js/bioc_views.js

.eslintrc.json

@@ -0,0 +1,14 @@
+{
+ "env": {
+ "browser": true,
+ "es2021": true,
+ "es6": true,
+ "node": true
+ },
+ "extends": "eslint:recommended",
+ "parserOptions": {
+ "ecmaVersion": "latest",
+ "sourceType": "module"
+ },
+ "rules": {}
+}

.github/workflows/linter.yaml

@@ -0,0 +1,35 @@
+name: Run Linters
+on:
+ pull_request:
+ types: [opened, reopened, synchronize]
+
+jobs:
+ build:
+ if: github.event.pull_request.draft == false
+ name: Run Linters
+ runs-on: ubuntu-latest
+ permissions:
+ contents: read
+ packages: read
+ statuses: write
+ steps:
+ - name: Checkout Code
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+ - name: Lint Code Base
+ uses: super-linter/super-linter/slim@v5
+ env:
+ LINTER_RULES_PATH: /
+ VALIDATE_ALL_CODEBASE: false
+ VALIDATE_GITHUB_ACTIONS: false
+ VALIDATE_MARKDOWN: false
+ VALIDATE_NATURAL_LANGUAGE: false
+ VALIDATE_JSCPD: false
+ VALIDATE_JSON: false
+ VALIDATE_R: false
+ VALIDATE_RUBY: false
+ VALIDATE_JAVASCRIPT_STANDARD: false
+ JAVASCRIPT_ES_CONFIG_FILE: .eslintrc.json
+ DEFAULT_BRANCH: redesign2023
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pr_close.yaml

@@ -0,0 +1,32 @@
+name: PR - Closed
+on:
+ pull_request:
+ types: [closed]
+
+jobs:
+ dev-pr-close-s3:
+ runs-on: ubuntu-latest
+ environment: dev
+ steps:
+ - name: Empty Website Bucket
+ run: |
+ if aws s3api head-bucket --bucket pr-preview-bioconductor-pr${{github.event.number}} 2>/dev/null; then
+ aws s3 rm s3://pr-preview-bioconductor-pr${{github.event.number}} --recursive
+ echo "BUCKET_EXISTS=true" >> "$GITHUB_ENV"
+ else
+ echo "Bucket does not exist"
+ echo "BUCKET_EXISTS=false" >> "$GITHUB_ENV"
+ fi
+ env:
+ AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+ AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+ AWS_REGION: "us-east-1"
+ - name: Delete Website Bucket
+ if: ${{env.BUCKET_EXISTS == 'true'}}
+ uses: danburtenshaw/[email protected]
+ with:
+ bucket-prefix: "pr-preview-bioconductor"
+ env:
+ AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+ AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pr_deploy.yaml

@@ -0,0 +1,107 @@
+name: Pr - Preview
+on:
+ pull_request:
+ types: [opened, reopened, synchronize]
+jobs:
+ dev-pr-create-s3:
+ if: github.event.pull_request.draft == false
+
+ runs-on: ubuntu-latest
+ environment: dev
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+
+ - name: Restore Nanoc Cache
+ id: cache-nanoc-tmp
+ uses: actions/cache/restore@v3
+ with:
+ path: tmp
+ key: ${{ runner.os }}-nanoc-tmp
+
+ - name: Restore Site Output Cache
+ id: cache-site-output
+ uses: actions/cache/restore@v3
+ with:
+ path: output
+ key: ${{ runner.os }}-site-output
+
+ - name: Set up ruby
+ uses: ruby/setup-ruby@ec02537da5712d66d4d50a0f33b7eb52773b5ed1
+ with:
+ ruby-version: "2.6.5"
+
+ - name: Install dependencies
+ run: bundle install --jobs 4 --retry 3
+
+ - name: build website
+ run: rake
+
+ - name: Create Bucket
+ run: |
+ if aws s3api head-bucket --bucket pr-preview-bioconductor-pr${{github.event.number}} 2>/dev/null; then
+ echo "Bucket already exists"
+ else
+ aws s3 mb s3://pr-preview-bioconductor-pr${{github.event.number}}
+ aws s3api delete-public-access-block --bucket pr-preview-bioconductor-pr${{github.event.number}}
+ aws s3api delete-bucket-ownership-controls --bucket pr-preview-bioconductor-pr${{github.event.number}}
+ aws s3api put-bucket-website --bucket pr-preview-bioconductor-pr${{github.event.number}} \
+ --website-configuration '{"IndexDocument":{"Suffix":"index.html"},"ErrorDocument":{"Key":"404.html"}}'
+ fi
+ env:
+ AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+ AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+ AWS_REGION: "us-east-1"
+ - name: Deploy S3 Website
+ uses: danburtenshaw/[email protected]
+ with:
+ bucket-prefix: "pr-preview-bioconductor"
+ folder-to-copy: "./output"
+ env:
+ AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+ AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ kpi_metrics:
+ needs: dev-pr-create-s3
+ permissions:
+ pull-requests: write
+ name: All KPI metrics
+ runs-on: ubuntu-latest
+ steps:
+ - name: checkout
+ uses: actions/checkout@v3
+ - name: Setup Node.js environment
+ uses: actions/[email protected]
+ with:
+ node-version: 18
+ - name: install psi and axe
+ run: |
+ npm install psi
+ npm install @axe-core/cli
+ - name: run desktop psi
+ run: |
+ echo "DESKTOP_PSI_RESULTS<<EOF" >> $GITHUB_ENV
+ echo "$(node PageSpeed.js url=http://pr-preview-bioconductor-pr${{github.event.number}}.s3-website-us-east-1.amazonaws.com,strategy=desktop,threshold=50,apiKey=none)" >> $GITHUB_ENV
+ echo "EOF" >> $GITHUB_ENV
+ - name: run mobile psi
+ run: |
+ echo "MOBILE_PSI_RESULTS<<EOF" >> $GITHUB_ENV
+ echo "$(node PageSpeed.js url=http://pr-preview-bioconductor-pr${{github.event.number}}.s3-website-us-east-1.amazonaws.com,strategy=mobile,threshold=50,apiKey=none)" >> $GITHUB_ENV
+ echo "EOF" >> $GITHUB_ENV
+ - name: add_comment_pageSpeed
+ uses: mshick/add-pr-comment@v2
+ with:
+ message: |
+ ${{env.DESKTOP_PSI_RESULTS}}
+ ${{env.MOBILE_PSI_RESULTS}}
+ message-id: psi
+ - name: run axe accesibility test
+ run: |
+ echo "AXE_RESULTS<<EOF" >> $GITHUB_ENV
+ echo "$(npx axe http://pr-preview-bioconductor-pr${{github.event.number}}.s3-website-us-east-1.amazonaws.com)" >> $GITHUB_ENV
+ echo "EOF" >> $GITHUB_ENV
+ - name: add_comment_axe
+ uses: mshick/add-pr-comment@v2
+ with:
+ message: ${{env.AXE_RESULTS}}
+ message-id: axe

.github/workflows/staging.yaml

@@ -0,0 +1,99 @@
+name: Deploy To staging
+
+on:
+ push:
+ branches:
+ - redesign2023
+jobs:
+ staging-deploy:
+ concurrency: ci-${{ github.ref }}
+ runs-on: ubuntu-latest
+ environment: staging
+
+ steps:
+ - name: checkout
+ uses: actions/checkout@v3
+
+ - name: Use Nanoc Cache
+ id: cache-nanoc-tmp
+ uses: actions/cache@v3
+ with:
+ path: tmp
+ key: ${{ runner.os }}-nanoc-tmp
+
+ - name: Use Site Output Cache
+ id: cache-site-output
+ uses: actions/cache@v3
+ with:
+ path: output
+ key: ${{ runner.os }}-site-output
+
+ - name: Set up ruby
+ uses: ruby/setup-ruby@ec02537da5712d66d4d50a0f33b7eb52773b5ed1
+ with:
+ ruby-version: "2.6.5"
+
+ - name: Install dependencies
+ run: bundle install --jobs 4 --retry 3
+
+ - name: Build website
+ run: rake
+
+ - name: Deploy website to staging s3
+ uses: Reggionick/[email protected]
+ with:
+ folder: output
+ bucket: ${{secrets.S3_BUCKET}}
+ bucket-region: us-east-1
+ delete-removed: true
+ env:
+ AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+ AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+ kpi_metrics:
+ needs: staging-deploy
+ permissions:
+ pull-requests: write
+ name: All KPI metrics
+ runs-on: ubuntu-latest
+ steps:
+ - name: checkout
+ uses: actions/checkout@v3
+ - name: Setup Node.js environment
+ uses: actions/[email protected]
+ with:
+ node-version: 18
+ - name: install psi and axe
+ run: |
+ npm install psi
+ npm install @axe-core/cli
+ - name: run desktop psi
+ run: |
+ echo "DESKTOP_PSI_RESULTS<<EOF" >> $GITHUB_ENV
+ echo "$(node PageSpeed.js url=${{vars.STAGING_URL}},strategy=desktop,threshold=50,apiKey=none)" >> $GITHUB_ENV
+ echo "EOF" >> $GITHUB_ENV
+ - name: run mobile psi
+ run: |
+ echo "MOBILE_PSI_RESULTS<<EOF" >> $GITHUB_ENV
+ echo "$(node PageSpeed.js url=${{vars.STAGING_URL}},strategy=mobile,threshold=50,apiKey=none)" >> $GITHUB_ENV
+ echo "EOF" >> $GITHUB_ENV
+ - name: run axe accesibility test
+ run: |
+ echo "AXE_RESULTS<<EOF" >> $GITHUB_ENV
+ echo "$(npx axe ${{vars.STAGING_URL}})" >> $GITHUB_ENV
+ echo "EOF" >> $GITHUB_ENV
+ - name: send notification psi
+ if: ${{ github.ref == 'refs/heads/redesign2023' }}
+ uses: 8398a7/action-slack@v2
+ with:
+ status: ${{ job.status }}
+ text: "${{env.DESKTOP_PSI_RESULTS}} \n ${{env.MOBILE_PSI_RESULTS}}"
+ env:
+ SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}}
+ - name: send notification axe
+ if: ${{ github.ref == 'refs/heads/redesign2023' }}
+ uses: 8398a7/action-slack@v2
+ with:
+ status: ${{ job.status }}
+ text: "${{env.AXE_RESULTS}}"
+ env:
+ SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}}

.gitignore

@@ -23,4 +23,6 @@ assets/help/workflows/*
 workflows_tmp/
 content/help/workflows/*
 postgresql_password
-manifest/*
+manifest/*
+node_modules/
+package

.htmlhintrc

@@ -0,0 +1,21 @@
+{
+ "doctype-first": false,
+ "spec-char-escape": false,
+ "head-script-disabled": true,
+ "style-disabled": true,
+ "attr-lowercase": true,
+ "attr-no-duplications": true,
+ "attr-no-unnecessary-whitespace": true,
+ "attr-value-single-quotes": false,
+ "attr-value-double-quotes": true,
+ "attr-whitespace": true,
+ "alt-require": true,
+ "input-requires-lable": true,
+ "tag-pair": false,
+ "tagname-lowercase": true,
+ "tagname-specialchars": true,
+ "src-not-empty": true,
+ "id-class-value": "dash",
+ "inline-script-disabled": true,
+ "inline-style-disabled": true
+}

.stylelintrc.json

@@ -0,0 +1,3 @@
+{
+ "extends": ["stylelint-config-standard"]
+}

Dockerfile

@@ -1,31 +1,34 @@
 FROM ruby:2.6.5
 
 ## System dependencies
-
-RUN apt-get update && apt install -y \
- rsync \
- && apt-get clean \
- && rm -rf /var/lib/apt/lists/*
+RUN apt-get update && apt-get install -y \
+ rsync \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
 
 ## Install gems
+COPY Gemfile /opt
+COPY Gemfile.lock /opt
+
+## Set the working directory to /opt/bioconductor.org
+WORKDIR /opt/bioconductor.org
+
+## Copy the remaining files from bioconductor.org/ to /opt/bioconductor.org
+COPY . .
 
-COPY Gemfile /tmp
-COPY Gemfile.lock /tmp
-WORKDIR /tmp
-## RUN bundle lock
+## Install bundle and dependencies
+RUN gem install bundler
 RUN bundle install --jobs=4 && bundle clean --force
 
 ## Set up web server
-
 EXPOSE 3000
 
 ## Create startup script
-
-RUN echo '#! /bin/bash \n\
- cd /bioconductor.org \n\
- rake \n\
- cd output \n\
- adsf\n' > .startup.sh \\
+RUN echo '#! /bin/bash' > .startup.sh \
+ && echo 'cd /opt/bioconductor.org' >> .startup.sh \
+ && echo 'rake' >> .startup.sh \
+ && echo 'cd output' >> .startup.sh \
+ && echo 'adsf' >> .startup.sh \
  && chmod +x .startup.sh
 
-CMD ["./.startup.sh"]
+CMD ["/opt/bioconductor.org/.startup.sh"]

Gemfile

@@ -1,6 +1,6 @@
 raise 'Ruby version must be 2.3 or greater' unless RUBY_VERSION.to_f >= 2.3
 source 'http://rubygems.org'
-gem "nanoc", "~> 4.0"
+gem "nanoc", "~> 4.9.5"
 gem "pry"
 gem "pry-byebug"
 gem "rdiscount"