Update Worklfows

.github/workflows/Build_and_deploy_website.yml

@@ -1,24 +1,15 @@
-name: Build and deploy OpenData-Website
-
+name: Manually build and deploy OpenData-Website
 on:
   workflow_dispatch:
-  workflow_run:
-    workflows: ["Create release on tag push"]
-    types:
-      - completed
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # This workflow contains a single job called "build"
   build:
-    # The type of runner that the job will run on
-    name: Bulid and deploy OpenData Website
-    if: ${{ github.event.workflow_run.conclusion == 'success' }}
-    runs-on: ubuntu-latest
-
     # Steps represent a sequence of tasks that will be executed as part of the job
+    runs-on: ubuntu-latest
     steps:  
-    - name: Bulid and deploy OpenData Website
-      uses: robert-koch-institut/OpenData-Website@main
-      with:
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}   
+      - name: Bulid and deploy OpenData Website
+        uses: robert-koch-institut/OpenData-Website@main
+        with:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}   

.github/workflows/Create_release_with_latest_tag.yml

@@ -0,0 +1,27 @@
+name: Manually create relese with latest tag
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  create_release:
+    name: Create reslese 
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get latest tag and set env
+        run: |
+          echo "LATEST_TAG=$(git describe --tags `git rev-list --tags --max-count=1`)" >> $GITHUB_ENV
+
+      - name: Create Release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: robert-koch-institut/OpenData-Workflows/Create_release_on_tag_push@main
+        with:
+          REF_NAME: ${{ env.LATEST_TAG }}

.github/workflows/OpenData_Workfow.yml

@@ -0,0 +1,40 @@
+name: OpenData Workfow for FAIR Data
+on:
+  push:
+    tags:
+      - '[0-9][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9]'
+  #workflow_dispatch:
+
+jobs:
+  build:
+    uses: robert-koch-institut/OpenData-Workflows/.github/workflows/OpenData_Workflows.yml@main
+    with:
+      # Push to OpenCoDE
+      OPENCODE_ACTIVE: true
+      OPENCODE_GROUPID: 2781
+      OPENCODE_ACCESS_USER: RKIOpenData
+      OPENCODE_ZENODOJSON_PATH: Metadaten/zenodo.json
+
+      # Push to GovData Repositoy
+      GOVDATA_ACTIVE: true
+      GOVDATA_DESTINATION_REPO: robert-koch-institut/Metadaten_fuer_GovData
+
+      # Push to NFDI4Health
+      NFDI4HEALTH_ACTIVE: true
+
+      #Build Open Data Website
+      WEBSITE_ACTIVE: true
+
+    secrets:
+      # Token from GovData Repository
+      GOVDATA_GITHUB_TOKEN: ${{secrets.GOVDATA_TOKEN}}
+
+      # Token from OpenCoDE Account
+      OPENCODE_TOKEN: ${{secrets.OPENCODE_TOKEN}}
+
+      # NFDI4Health Credentials
+      NFDI4HEALTH_CLIENT_ID: CSH_RKI_CLIENT
+      NFDI4HEALTH_CLIENT_SECRET: ${{secrets.NFDI4HEALTH_SECRET}}
+
+      # Github Token
+      GH_TOKEN: ${{secrets.GITHUB_TOKEN}}

.github/workflows/Send_metadata_to_Govdata.yml

@@ -1,44 +1,17 @@
-name: Send metadata to Govdata
+name: Manually send metadata to GovData
 on:
   workflow_dispatch:
-  push:
-    paths:
-      - 'Metadaten/**.ttl'
+
+permissions:
+  contents: write
+
 jobs:
-  Push_Govdata_ttl:
-    name: Push metadata to Govdata-Repository
+  push_govdata:
+    name: Push ttl to GovData repository
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-
-      - name: Rename ttl with reponame
-        run: cp Metadaten/govdata.ttl Metadaten/${{ github.event.repository.name }}.ttl
-
-      - name: Push dataset ttl to Govdata repository
-        id: pushStep1
-        continue-on-error: true
-        uses: dmnemec/copy_file_to_another_repo_action@main
-        env:
-          API_TOKEN_GITHUB: ${{ secrets.GOVDATA_TOKEN }}
+      - name: run GovData Action
+        uses: robert-koch-institut/OpenData-Workflows/Send_metadata_to_Govdata@main
         with:
-          source_file: 'Metadaten/${{ github.event.repository.name }}.ttl'
-          destination_repo: 'robert-koch-institut/Metadaten_fuer_GovData'
-          destination_folder: 'Datensaetze'
-          commit_message: 'adding ${{ github.event.repository.name }}.ttl'
-          user_email: '[email protected]'
-          user_name: 'RKIOpenData'
-
-      - name: Retry push dataset ttl to Govdata repository
-        id: pushStep2
-        if: steps.pushStep1.outcome == 'failure'
-        uses: dmnemec/copy_file_to_another_repo_action@main
-        env:
-          API_TOKEN_GITHUB: ${{ secrets.GOVDATA_TOKEN }}
-        with:
-          source_file: 'Metadaten/${{ github.event.repository.name }}.ttl'
-          destination_repo: 'robert-koch-institut/Metadaten_fuer_GovData'
-          destination_folder: 'Datensaetze'
-          commit_message: 'adding ${{ github.event.repository.name }}.ttl'
-          user_email: '[email protected]'
-          user_name: 'RKIOpenData'
+          govdata_github_token: ${{secrets.GOVDATA_TOKEN}}
+          destination_repo: robert-koch-institut/Metadaten_fuer_GovData

.github/workflows/Send_metadata_to_nfdi4health.yml

@@ -0,0 +1,18 @@
+name: Manually send metadata to NFDI4Health
+on:
+  workflow_dispatch:
+
+jobs:
+  sync_opencode:
+    name: Send metadata to NFDI4Health
+    runs-on: ubuntu-latest
+    steps:
+      - name: Sync Github Open Data repository
+        uses: robert-koch-institut/OpenData-Workflows/Send_metadata_to_NFDI4Health@main
+        with:
+          nfdi4health_client_id: CSH_RKI_CLIENT
+          nfdi4health_client_secret: ${{secrets.NFDI4HEALTH_SECRET}}
+          nfdi4health_metadata_path: Metadaten/nfdi4health.json
+          nfdi4health_authorization_endpoint: "https://sso.studyhub.nfdi4health.de/realms/nfdi4health/protocol/openid-connect/token"
+          github_token: ${{secrets.GITHUB_TOKEN}}
+          nfdi4health_base_url: "https://csh.nfdi4health.de/api/"

.github/workflows/Sync_OpenData_repo_to_OpenCoDE.yml

@@ -1,92 +1,19 @@
-name: Sync Github Open Data repository and its metadata to OpenCoDE.de
+name: Manually sync Github Open Data repository and its metadata to OpenCoDE.de
 
 on:
   workflow_dispatch:
-  workflow_run:
-    workflows: ["Create release on tag push"]
-    types:
-      - completed
-
-env:    
-  # OpenCoDE Metadata 
-  GROUP_ID: 2781
-  ACCESS_USER: RKIOpenData
-
-  # The repository name must not start or end with a special character and must not contain consecutive special characters
-  REPO_PATH: ${{ github.event.repository.name }} 
-  ZENODOJSON_PATH: Metadaten/zenodo.json
 
 jobs:
-  sync_metadata_to_opencode:
-    name: Sync Open Data metadata to OpenCoDE
+  sync_opencode:
+    name: Sync Github Open Data repository and its metadata to OpenCoDE.de
     runs-on: ubuntu-latest
-    outputs:
-      GROUP_PATH: ${{ steps.group_path.outputs.GROUP_PATH }}
     steps:
-
-      # Get OpenCoDE group path from the OpenCoDE API
-      - name: Get OpencoDE group path
-        id: group_path
-        run: | 
-            GROUP_INFO=$(curl \
-              --request GET "https://gitlab.opencode.de/api/v4/groups/$GROUP_ID" \
-              --header "PRIVATE-TOKEN: ${{ secrets.OPENCODE_TOKEN }}")
-            
-            # Add metadata to enviroment 
-            echo "GROUP_PATH="$(echo $GROUP_INFO | jq -r '.path')"" >> $GITHUB_OUTPUT
-      
-      # Get metadata on name, description and keywords from the zenodo.json   
-      - name: Get zenodo.json metadata from Github Open Data repository
-        run: |          
-           ZENODOJSON_URL=$(curl \
-            --request GET https://api.github.com/repos/${{ github.repository }}/contents/${{ env.ZENODOJSON_PATH }} \
-            --header "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
-            --header "Accept: application/vnd.github.mercy-preview+json" \
-            | jq -r '.download_url')
-           
-           # Add Zenodo metadata to enviroment 
-           echo "REPO_NAME="$(curl $ZENODOJSON_URL | jq -r '.title')"" >> $GITHUB_ENV 
-           echo "DESCRIPTION="$(curl $ZENODOJSON_URL | jq -r '.description'| head -c 2000)"" >> $GITHUB_ENV
-           echo "TOPICS="$(curl $ZENODOJSON_URL| jq -r '.keywords | join(",")')"" >> $GITHUB_ENV
-     
-
-      - name: Create OpenCoDE repository and update repository metadata
-        run: |
-            # Create OpenCoDE repository
-            curl \
-              --request POST "https://gitlab.opencode.de/api/v4/projects" \
-              --header "PRIVATE-TOKEN: ${{ secrets.OPENCODE_TOKEN }}" \
-              --data-urlencode  "path=${{ env.REPO_PATH }}" \
-              --data-urlencode  "namespace_id=${{ env.GROUP_ID }}"
-              
-            # Update OpenCoDE repository metadata
-            response=$(curl \
-              --request PUT "https://gitlab.opencode.de/api/v4/projects/${{ steps.group_path.outputs.GROUP_PATH }}%2F${{ env.REPO_PATH }}" \
-              --header "PRIVATE-TOKEN: ${{ secrets.OPENCODE_TOKEN }}" \
-              --data "name=${{ env.REPO_NAME }}" \
-              --data "description=${{ env.DESCRIPTION }}" \
-              --data "topics='${{ env.TOPICS }}'" \
-              --data "visibility=public") 
-      
-  sync_data_to_opencode:
-    name: Sync Github Open Data repository data to OpenCoDE
-    needs: sync_metadata_to_opencode
-    runs-on: ubuntu-latest    
-    steps:
-
-      # Clone Github Open Data repository into the action enviroment
-      - name: Checkout Github repository
-        uses: actions/checkout@v3
+      - name: Sync Github Open Data repository
+        uses: robert-koch-institut/OpenData-Workflows/Sync_OpenData_repo_to_OpenCoDE@main
         with:
-          persist-credentials: false
-          lfs: 'true'
-          ref: 'main'
-          fetch-depth: '0'
-
-      # Force push latest Github Open Data repository status to OpenCoDE     
-      - name: Force push latest status to OpenCoDE 
-        run: |
-          git remote add opencode https://${{ env.ACCESS_USER  }}:${{ secrets.OPENCODE_TOKEN }}@gitlab.opencode.de/${{ needs.sync_metadata_to_opencode.outputs.GROUP_PATH }}/${{ env.REPO_PATH }}.git
-          git push opencode -f
-          
-          
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          OPENCODE_TOKEN: ${{ secrets.OPENCODE_TOKEN }}
+          GROUP_ID: 2781
+          ACCESS_USER: RKIOpenData
+          # REPO_PATH: The repository name must not start or end with a special character and must not contain consecutive special characters
+          ZENODOJSON_PATH: Metadaten/zenodo.json