commit

.github/workflows/docker_runner-r.yml → .github/workflows/docker_runner-conda.yml

@@ -1,43 +1,45 @@
-name: R Runner, main branch
+name: Conda Runner, main branch
 
 on:
   workflow_dispatch:
   push:
     branches:
       - main
     paths:
-      - 'runners/r-dockerfile'
+      - 'runners/conda-dockerfile'
+      - 'runners/r-environment.yml'
+      - 'runners/.condarc'
 
 jobs:
-  runner-r:
+  runner-conda:
     runs-on: ubuntu-latest
     steps:
     - name: Check out the repo
       uses: actions/checkout@v3
-    
+
     - name: Log in to Docker Hub
       uses: docker/login-action@v2
       with:
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
-    
+
     - name: Extract metadata (tags, labels) for Docker
       id: meta
       uses: docker/metadata-action@v4
       with:
         images: geobon/bon-in-a-box
         tags: |
           # Image used in compose file
-          type=raw,value=runner-r
+          type=raw,value=runner-conda
           # In case we want to replicate a specific legacy setup
-          type=sha,prefix=runner-r-
-    
+          type=sha,prefix=runner-conda-
+
     - name: Build and push Docker image
       uses: docker/build-push-action@v3
       with:
         context: runners
-        file: runners/r-dockerfile
+        file: runners/conda-dockerfile
         push: true
         tags: ${{ steps.meta.outputs.tags }}
         labels: ${{ steps.meta.outputs.labels }}
-  
+

.github/workflows/onPush.yml

@@ -1,59 +1,31 @@
 name: On push, any branch
 
 on: [push]
-
+# TODO change pipeline-repo-actions to main
 jobs:
-  run-script-server-test:
+  run-yml-validation:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up JDK 11
-      uses: actions/setup-java@v3
+    - uses: actions/checkout@v4
+    - uses: actions/checkout@v4
       with:
-        java-version: '11'
-        distribution: 'adopt'
+        # Repository name with owner. For example, actions/checkout
+        # Default: ${{ github.repository }}
+        repository: 'GEO-BON/bon-in-a-box-pipeline-engine.git'
 
-    - name: Validate Gradle wrapper
-      uses: gradle/wrapper-validation-action@v1
+        # The branch, tag or SHA to checkout. When checking out the repository that
+        # triggered a workflow, this defaults to the reference or SHA for that event.
+        # Otherwise, uses the default branch.
+        ref: 'main'
 
-    - name: Gradle build & test
-      uses: gradle/gradle-build-action@v2
-      with:
-        arguments: build --info
-        build-root-directory: script-server
-
-    - name: Save test results
-      uses: actions/upload-artifact@v3
-      if: always()
-      with:
-        name: Test results
-        path: script-server/build/reports/tests/test/
+        # Relative path under $GITHUB_WORKSPACE to place the repository
+        path: '.server'
 
-
-  run-yml-validation:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - name: YML file syntax validation
-      uses: navikt/yaml-validator@v4
-      with:
-        schema_path: scripts/cerberusValidationSchema
-        document_path: scripts
-        validate_file_extension: no
-        filter_extensions: .yml
-    - name: YML test files syntax validation
-      uses: navikt/yaml-validator@v4
-      with:
-        schema_path: scripts/cerberusValidationSchema
-        document_path: script-server/src/test/resources/scripts/
-        validate_file_extension: no
-        filter_extensions: .yml
-    - name: Find duplicate lines inside same step YML file
-      working-directory: ./scripts
-      run: ../.github/findDuplicateDescriptions.sh
+    - name: Creating empty runner.env
+      working-directory: .
+      run: touch runner.env
       shell: bash
-    - name: Find duplicate lines inside same pipeline JSON file
-      working-directory: ./pipelines
-      run: ../.github/findDuplicateIds.sh
+    - name: Script and pipelines basic validation
+      working-directory: .
+      run: .server/prod-server.sh validate
       shell: bash

.gitignore

@@ -1,6 +1,7 @@
-.env
+runner.env
 .Rproj.user
 .Rhistory
 .vscode
 **/.cache
 **/.config
+.server