Merge branch 'redesign2023' of https://github.com/nearform/bioconduct…

…or.org into nearform-redesign2023
Bioconductor · Aug 24, 2023 · a61bbe9 · a61bbe9
2 parents 229b8e9 + 05b39bb
commit a61bbe9
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diff --git a/.eslintignore b/.eslintignore
@@ -0,0 +1,3 @@
+assets/js/search.js
+assets/js/bioconductor.js
+assets/js/bioc_views.js
diff --git a/.eslintrc.json b/.eslintrc.json
@@ -0,0 +1,14 @@
+{
+  "env": {
+    "browser": true,
+    "es2021": true,
+    "es6": true,
+    "node": true
+  },
+  "extends": "eslint:recommended",
+  "parserOptions": {
+    "ecmaVersion": "latest",
+    "sourceType": "module"
+  },
+  "rules": {}
+}
diff --git a/.github/workflows/linter.yaml b/.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: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/pr_close.yaml b/.github/workflows/pr_close.yaml
@@ -0,0 +1,32 @@
+name: PR - Closed
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  dev-pr-close-s3:
+    runs-on: ubuntu-latest
+    environment: dev
+    steps:
+      - name: Empty Website Bucket
+        run: |
+          if aws s3api head-bucket --bucket pr-preview-bioconductor-pr${{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 }}
diff --git a/.github/workflows/pr_deploy.yaml b/.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: ${{env.AXE_RESULTS}}
+          message-id: axe
diff --git a/.github/workflows/staging.yaml b/.github/workflows/staging.yaml
@@ -0,0 +1,99 @@
+name: Deploy To staging
+
+on:
+  push:
+    branches:
+      - redesign2023
+jobs:
+  staging-deploy:
+    concurrency: ci-${{ 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}}
diff --git a/.gitignore b/.gitignore
@@ -23,4 +23,6 @@ assets/help/workflows/*
 workflows_tmp/
 content/help/workflows/*
 postgresql_password
-manifest/*
+manifest/*
+node_modules/
+package
diff --git a/.htmlhintrc b/.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
+}
diff --git a/.stylelintrc.json b/.stylelintrc.json
@@ -0,0 +1,3 @@
+{
+  "extends": ["stylelint-config-standard"]
+}
diff --git a/Dockerfile b/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"]
diff --git a/Gemfile b/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"