ExportData.yml

name: Export Data

on:
  release:
    types: [published]
  workflow_dispatch:
env:
  OPENBIS_V3: https://localhost:8128/openbis/openbis/rmi-application-server-v3.json
  OPENBISMANTIC_API: https://localhost:8128/openbismantic
  SAMPLE_TYPE: EXPERIMENTAL_STEP_EMODUL

jobs:
  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          repository: ${{ github.event.pull_request.head.repo.full_name }}
          ref: ${{ github.event.pull_request.head.ref }}
          submodules: recursive
      - name: run app
        run: |
          touch .env
          echo ADMIN_PASS=example >> .env
          echo OBSERVER_PASS=example >> .env
          echo HOST_NAME=127.0.0.1 >> .env
          echo OPENBIS_PORT=8127 >> .env
          echo OPENBIS_SSL_PORT=8128 >> .env
          echo POSTGRES_PASSWORD=example >> .env
          echo GROUP_NAME=openbis >> .env
          echo GROUP_ID=1000 >> .env
          echo OPENBISMANTIC_URL=https://openbis.matolab.org >> .env
          docker compose up -d
          docker compose logs -f init_database
      - name: Update exported data
        run: |
          rm -rf exported_data
          mkdir -p exported_data
          token=$(curl -sk -d "{\"method\": \"login\", \"params\": [\"admin\", \"example\"], \"id\": \"1\", \"jsonrpc\": \"2.0\"}" ${{env.OPENBIS_V3}} | jq -r '.result')
          if [[ $token == "null" ]]
          then
            echo "failed to log in"
            exit 1
          fi
          echo "logged in successfully"
          permIds=$(curl -sk -d "{\"method\":\"searchSamples\",\"params\":[\"${token}\",{\"@id\":0,\"criteria\":[{\"@id\":1,\"criteria\":[{\"@id\":2,\"fieldName\":\"code\",\"fieldType\":\"ATTRIBUTE\",\"fieldValue\":{\"@id\":3,\"value\":\"${{env.SAMPLE_TYPE}}\",\"@type\":\"as.dto.common.search.StringEqualToValue\"},\"useWildcards\":false,\"@type\":\"as.dto.common.search.CodeSearchCriteria\"}],\"@type\":\"as.dto.sample.search.SampleTypeSearchCriteria\",\"operator\":\"AND\"}],\"relation\":\"SAMPLE\",\"operator\":\"AND\",\"negated\":false,\"@type\":\"as.dto.sample.search.SampleSearchCriteria\"},{\"type\": {\"@type\": \"as.dto.sample.fetchoptions.SampleTypeFetchOptions\"}}],\"id\":\"1\",\"jsonrpc\":\"2.0\"}" ${{env.OPENBIS_V3}} | jq -r '[.result.objects[].permId.permId]|join(" ")')
          echo "found samples ${permIds}"
          for permId in $permIds
          do
            result=$(curl -sk -H "Cookie: openbis=${token}" "${{env.OPENBISMANTIC_API}}/object/${permId}")
            echo $result >> "exported_data/${permId}.json"
          done
      - name: commit results
        uses: EndBug/add-and-commit@v9
        with:
          message: 'update exported data'
          add: '*.* --force'
          cwd: './exported_data/'