Added docker image and build pipeline

.github/workflows/build.yml

@@ -0,0 +1,94 @@
+name: Build Docker image
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  workflow_dispatch: # Allow manual run
+  push:
+    branches: [ "main" ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "main" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: masterzydra/bio-manager
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@v3
+        with:
+          cosign-release: 'v2.1.1'
+
+      # Set up BuildKit Docker container builder to be able to build
+      # multi-platform images and export cache
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Set tag
+      - name: Set tag
+        if: ${{ github.ref_type == 'tag' }}
+        run: echo "TAGS=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.ref_name }}" >> "$GITHUB_ENV"
+      - name: Set tag
+        if: ${{ github.ref_type != 'tag' }}
+        run: echo "TAGS=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest" >> "$GITHUB_ENV"
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ env.TAGS }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ env.TAGS }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

CHANGELOG.md

@@ -48,6 +48,7 @@ Types of changes: `Added`, `Changed`, `Deprecate`, `Removed`, `Fixed`, `Secruity
 - Added migration to call seeder and create a default user
 - Added namespace starting with `Resources` to autoloader
 - Added checkboxes for each role to the user create and edit form and added logic to controller
+- Added docker image and build pipeline
 
 ### Changed
 - Improved the autoloader to work for the new folder structure of version 2

Dockerfile

@@ -0,0 +1,22 @@
+FROM serversideup/php:8.2-fpm-apache
+
+WORKDIR /var/www/html
+
+COPY . .
+
+    # Rename env.example so that .env exists
+RUN cp .env.example .env; \
+    # Fix permissions
+    chown -R webuser:webgroup /var/www/html ; \
+    # Add bioman-automations to startup
+    mv ./bioman-automations /etc/s6-overlay/scripts ; \
+    sed -i 's/\r$//' /etc/s6-overlay/scripts/bioman-automations ; \
+    chown root:root /etc/s6-overlay/scripts/bioman-automations ; \
+    chmod ugo+x /etc/s6-overlay/scripts/bioman-automations ; \
+    mkdir /etc/s6-overlay/s6-rc.d/bioman-automations ; \
+    echo "/etc/s6-overlay/scripts/bioman-automations" > /etc/s6-overlay/s6-rc.d/bioman-automations/up ; \
+    echo "oneshot" > /etc/s6-overlay/s6-rc.d/bioman-automations/type ; \
+    echo "runas-user" > /etc/s6-overlay/s6-rc.d/bioman-automations/dependencies ; \
+    touch /etc/s6-overlay/s6-rc.d/user/contents.d/bioman-automations
+
+EXPOSE 80

bioman-automations

@@ -0,0 +1,30 @@
+#!/command/with-contenv bash
+
+# Exit on error
+set -e
+
+# Check to see if the bioman CLI exists and assume it means bioman is configured
+if [ -f $WEBUSER_HOME/bioman ] && [ ${AUTORUN_ENABLED:="true"} == "true" ]; then
+        echo "🏃‍♂️ Checking for automations..."
+
+        ############################################################################
+        # Automated file ownership fix
+        ############################################################################
+        if [ ${AUTORUN_BIOMAN_FILE_OWNERSHIP:="true"} == "true" ]; then
+            echo "🔐 Fixing file ownership..."
+            chown -R webuser:webgroup $WEBUSER_HOME
+        fi
+
+        ############################################################################
+        # Automated database upgrade
+        ############################################################################
+        if [ ${AUTORUN_BIOMAN_DATABASE_UPGRADE:="true"} == "true" ]; then
+            echo "🚀 Running database upgrade..."
+            s6-setuidgid webuser php $WEBUSER_HOME/bioman migrate
+        fi
+
+else
+    echo "👉 Skipping automations because we could not detect a bioman install or it was specifically disabled..."
+fi
+
+exit 0