Merge pull request #884 from NFDI4Chem/development

Development

.github/workflows/deploy-docs.yml

@@ -0,0 +1,33 @@
+name: Docs Deployment - GitHub pages
+on:
+  workflow_dispatch: {}
+  push:
+    branches:
+      - development
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-node@v3
+        with:
+          node-version: 16
+          cache: npm
+      - run: npm ci
+      - name: Build
+        run: npm run docs:build
+      - uses: actions/configure-pages@v2
+      - uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/.vitepress/dist
+      - name: Deploy
+        id: deployment
+        uses: actions/deploy-pages@v2.0.2

.github/workflows/build.yml → .github/workflows/dev-build.yml

@@ -1,4 +1,4 @@
-name : Deploy to Dev
+name : Setup, Build and Publish to Dev
 
 on:
   push:
@@ -11,11 +11,16 @@ env:
   DEPLOYMENT_NAME: nmrxiv-nmrxiv-app
   SCHEDULER_DEPLOYMENT_NAME: nmrxiv-scheduler
   WORKER_DEPLOYMENT_NAME: nmrxiv-worker
-  REPOSITORY_NAME: nmrxiv-dev
-  APP_IMAGE: nmrxiv-app
-  NGINX_IMAGE: nmrxiv-nginx
+  DOCKER_HUB_USERNAME : ${{ secrets.DOCKER_HUB_USERNAME  }}
+  DOCKER_HUB_PASSWORD : ${{ secrets.DOCKER_HUB_PASSWORD  }}
+  REPOSITORY_NAME: nmrxiv
+  REPOSITORY_NAMESPACE: nfdi4chem
+  DEV_URL: https://dev.nmrxiv.org
 
 jobs:
+  # php-unit-test:
+  #   uses: NFDI4Chem/nmrxiv/.github/workflows/test.yml@development
+
   php-unit-test:
     name: Run test
     runs-on: ubuntu-latest
@@ -43,7 +48,7 @@ jobs:
         composer install --ignore-platform-reqs
     - name: Prepare Laravel Application
       run: |
-        php -r "file_exists('.env') || copy('.env.ci.dev', '.env');"
+        php -r "file_exists('.env') || copy('.env.ci.test', '.env');"
 
         echo AWS_ACCESS_KEY_ID=${{ secrets.AWS_ACCESS_KEY_ID_DEV }} >> .env
         echo AWS_SECRET_ACCESS_KEY=${{ secrets.AWS_SECRET_ACCESS_KEY_DEV }} >> .env
@@ -63,12 +68,13 @@ jobs:
     - name: Run Test
       run: php artisan test --parallel
 
-
   setup-build-publish-deploy:
     name: Build & deploy to development
-    if: github.ref == 'refs/heads/development'
     runs-on: ubuntu-latest
     needs: php-unit-test
+    environment:
+      name: Dev
+      url: ${{ env.DEV_URL }}
     steps:
     - name: Checkout
       uses: actions/checkout@v2
@@ -79,40 +85,47 @@ jobs:
         service_account_key: ${{ secrets.GKE_SA_KEY }}
         project_id: ${{ secrets.GKE_PROJECT }}
 
-    # Configure docker to use the gcloud command-line tool as a credential helper
-    - run: |-
-        gcloud auth configure-docker europe-west3-docker.pkg.dev
-    # Get the GKE credentials so we can deploy to the cluster
+    # Get the GKE credentials
     - uses: google-github-actions/get-gke-credentials@v0.3.0
       with:
         cluster_name: ${{ env.GKE_CLUSTER }}
         location: ${{ env.GKE_ZONE }}
         credentials: ${{ secrets.GKE_SA_KEY }}
 
-    # Build the Docker image
-    - name: Build App Image
-      run: |-
-        docker build -f ./resources/ops/docker/app/app.dockerfile \
-          --tag "europe-west3-docker.pkg.dev/$PROJECT_ID/$REPOSITORY_NAME/$APP_IMAGE:latest" \
-          --build-arg GITHUB_SHA="$GITHUB_SHA" \
-          --build-arg GITHUB_REF="$GITHUB_REF" \
-          .
-    - name: Build Nginx Image
-      run: |-
-        docker build -f ./resources/ops/docker/nginx/nginx.dockerfile \
-          --tag "europe-west3-docker.pkg.dev/$PROJECT_ID/$REPOSITORY_NAME/$NGINX_IMAGE:latest" \
-          --build-arg GITHUB_SHA="$GITHUB_SHA" \
-          --build-arg GITHUB_REF="$GITHUB_REF" \
-          .
-    # Push the Docker image to Google Container Registry
-    - name: Publish App Image to GCR
-      run: |-
-        docker push "europe-west3-docker.pkg.dev/$PROJECT_ID/$REPOSITORY_NAME/$APP_IMAGE:latest"
+    # Login to Docker
+    - name: Log in to Docker Hub
+      uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+      with:
+        username: ${{ env.DOCKER_HUB_USERNAME  }}
+        password: ${{ env.DOCKER_HUB_PASSWORD  }}
 
-    - name: Publish Nginx Image to GCR
-      run: |-
-        docker push "europe-west3-docker.pkg.dev/$PROJECT_ID/$REPOSITORY_NAME/$NGINX_IMAGE:latest"
+    # Build and push the app Docker image
+    - name: Build and push App Docker image
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        file: ./resources/ops/docker/app/app.dockerfile
+        push: true
+        build-args: |
+          RELEASE_VERSION=dev-app-latest
+        tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:dev-app-latest
+        username: ${{ env.DOCKER_HUB_USERNAME  }}
+        password: ${{ env.DOCKER_HUB_PASSWORD  }}
+
+    # Build and push the nginx Docker image
+    - name: Build and push Nginx Docker image
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        file: ./resources/ops/docker/nginx/nginx.dockerfile
+        push: true
+        build-args: |
+          RELEASE_VERSION=dev-nginx-latest
+        tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:dev-nginx-latest
+        username: ${{ env.DOCKER_HUB_USERNAME  }}
+        password: ${{ env.DOCKER_HUB_PASSWORD  }}
 
+    # Deploy the latest Docker image to the GKE cluster
     - name: Deploy
       run: |-
         kubectl rollout restart deployment/$DEPLOYMENT_NAME

.github/workflows/test.yml

@@ -0,0 +1,52 @@
+name : Test
+
+on:
+  workflow_call:
+
+jobs:
+  php-unit-test:
+    name: Run test
+    runs-on: ubuntu-latest
+    container:
+      image: kirschbaumdevelopment/laravel-test-runner:8.2
+
+    services:
+      postgres:
+        image: postgres:13
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: nmrxiv
+        ports:
+        - 5432:5432
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        fetch-depth: 1
+
+    - name: Install composer dependencies
+      run: |
+        composer install --ignore-platform-reqs
+    - name: Prepare Laravel Application
+      run: |
+        php -r "file_exists('.env') || copy('.env.ci.test', '.env');"
+
+        echo AWS_ACCESS_KEY_ID=${{ secrets.AWS_ACCESS_KEY_ID_DEV }} >> .env
+        echo AWS_SECRET_ACCESS_KEY=${{ secrets.AWS_SECRET_ACCESS_KEY_DEV }} >> .env
+        echo MEILISEARCH_KEY=${{ secrets.MEILISEARCH_KEY_DEV }} >> .env
+        echo MEILISEARCH_PUBLICKEY=${{ secrets.MEILISEARCH_PUBLICKEY_DEV }} >> .env
+        echo TWITTER_CLIENT_ID=${{ secrets.TWITTER_CLIENT_ID_DEV }} >> .env
+        echo TWITTER_CLIENT_SECRET=${{ secrets.TWITTER_CLIENT_SECRET_DEV }} >> .env
+        echo GITHUB_CLIENT_ID=${{ secrets.CLIENT_ID_GITHUB_DEV }} >> .env
+        echo GITHUB_CLIENT_SECRET=${{ secrets.CLIENT_SECRET_GITHUB_DEV }} >> .env
+
+        php artisan key:generate
+        php artisan migrate --seed
+    - name: Install front-end dependencies
+      run: |
+        npm install
+        npm run build
+    - name: Run Test
+      run: php artisan test --parallel

app/Actions/Project/AssignIdentifier.php

@@ -3,8 +3,10 @@
 namespace App\Actions\Project;
 
 use App\Models\Project;
+use App\Models\Study;
 use App\Models\Ticker;
 use App\Services\DOI\DOIService;
+use Illuminate\Support\Collection;
 
 class AssignIdentifier
 {
@@ -21,83 +23,97 @@ public function __construct(DOIService $doiService)
     }
 
     /**
-     * Archive the given project.
+     * Archive the given model.
      *
-     * @param  mixed  $project
+     * @param  mixed  $model
      * @return void
      */
-    public function assign($project)
+    public function assign($model)
     {
-        $projectIdentifier = $project->identifier ? $project->identifier : null;
-
-        if ($projectIdentifier == null) {
-            $projectTicker = Ticker::whereType('project')->first();
-            $projectIdentifier = $projectTicker->index + 1;
-            $projectTicker->index = $projectIdentifier;
-            $projectTicker->save();
-
-            $project->identifier = $projectIdentifier;
-            $project->save();
-            $project->fresh()->generateDOI($this->doiService);
+        $project = null;
+        $studies = null;
+        if ($model instanceof Project) {
+            $project = $model;
+        } elseif ($model instanceof Collection) {
+            $studies = $model;
         }
 
-        $studies = $project->studies;
-        foreach ($studies as $study) {
-            $studyIdentifier = $study->identifier ? $study->identifier : null;
-
-            if ($studyIdentifier == null) {
-                $studyTicker = Ticker::whereType('study')->first();
-                $studyIdentifier = $studyTicker->index + 1;
-                $study->identifier = $studyIdentifier;
-                $studyTicker->index = $studyIdentifier;
-                $studyTicker->save();
-            }
-            $study->save();
-            $study->generateDOI($this->doiService);
+        if ($project) {
+            $projectIdentifier = $project->identifier ? $project->identifier : null;
 
-            $sample = $study->sample;
-            $sampleIdentifier = $sample->identifier ? $sample->identifier : null;
+            if ($projectIdentifier == null) {
+                $projectTicker = Ticker::whereType('project')->first();
+                $projectIdentifier = $projectTicker->index + 1;
+                $projectTicker->index = $projectIdentifier;
+                $projectTicker->save();
 
-            if ($sampleIdentifier == null) {
-                $sampleTicker = Ticker::whereType('sample')->first();
-                $sampleIdentifier = $sampleTicker->index + 1;
-                $sample->identifier = $sampleIdentifier;
-                $sample->save();
-
-                $sampleTicker->index = $sampleIdentifier;
-                $sampleTicker->save();
+                $project->identifier = $projectIdentifier;
+                $project->save();
+                $project->fresh()->generateDOI($this->doiService);
             }
 
-            $molecules = $sample->molecules;
-
-            foreach ($molecules as $molecule) {
-                $moleculeIdentifier = $molecule->identifier ? $molecule->identifier : null;
-                if ($moleculeIdentifier == null) {
-                    $moleculeTicker = Ticker::whereType('molecule')->first();
-                    $moleculeIdentifier = $moleculeTicker->index + 1;
-                    $molecule->identifier = $moleculeIdentifier;
-                    $molecule->save();
-
-                    $moleculeTicker->index = $moleculeIdentifier;
-                    $moleculeTicker->save();
-                }
-            }
-
-            $datasets = $study->datasets;
-            foreach ($datasets as $dataset) {
-                $dsIdentifier = $dataset->identifier ? $dataset->identifier : null;
-
-                if ($dsIdentifier == null) {
-                    $dsTicker = Ticker::whereType('dataset')->first();
-                    $dsIdentifier = $dsTicker->index + 1;
-                    $dataset->identifier = $dsIdentifier;
+            $studies = $project->studies;
+        }
 
-                    $dsTicker->index = $dsIdentifier;
-                    $dsTicker->save();
+        if ($studies) {
+            foreach ($studies as $study) {
+                if ($study instanceof Study) {
+                    $studyIdentifier = $study->identifier ? $study->identifier : null;
+                    if ($studyIdentifier == null) {
+                        $studyTicker = Ticker::whereType('study')->first();
+                        $studyIdentifier = $studyTicker->index + 1;
+                        $study->identifier = $studyIdentifier;
+                        $studyTicker->index = $studyIdentifier;
+                        $studyTicker->save();
+                    }
+                    $study->save();
+                    $study->generateDOI($this->doiService);
+
+                    $sample = $study->sample;
+                    $sampleIdentifier = $sample->identifier ? $sample->identifier : null;
+
+                    if ($sampleIdentifier == null) {
+                        $sampleTicker = Ticker::whereType('sample')->first();
+                        $sampleIdentifier = $sampleTicker->index + 1;
+                        $sample->identifier = $sampleIdentifier;
+                        $sample->save();
+
+                        $sampleTicker->index = $sampleIdentifier;
+                        $sampleTicker->save();
+                    }
+
+                    $molecules = $sample->molecules;
+
+                    foreach ($molecules as $molecule) {
+                        $moleculeIdentifier = $molecule->identifier ? $molecule->identifier : null;
+                        if ($moleculeIdentifier == null) {
+                            $moleculeTicker = Ticker::whereType('molecule')->first();
+                            $moleculeIdentifier = $moleculeTicker->index + 1;
+                            $molecule->identifier = $moleculeIdentifier;
+                            $molecule->save();
+
+                            $moleculeTicker->index = $moleculeIdentifier;
+                            $moleculeTicker->save();
+                        }
+                    }
+
+                    $datasets = $study->datasets;
+                    foreach ($datasets as $dataset) {
+                        $dsIdentifier = $dataset->identifier ? $dataset->identifier : null;
+
+                        if ($dsIdentifier == null) {
+                            $dsTicker = Ticker::whereType('dataset')->first();
+                            $dsIdentifier = $dsTicker->index + 1;
+                            $dataset->identifier = $dsIdentifier;
+
+                            $dsTicker->index = $dsIdentifier;
+                            $dsTicker->save();
+                        }
+
+                        $dataset->save();
+                        $dataset->generateDOI($this->doiService);
+                    }
                 }
-
-                $dataset->save();
-                $dataset->generateDOI($this->doiService);
             }
         }
     }