migration.yaml

name: migration-with-java-action
on: workflow_dispatch
# wget or curl?! which is noisier
# combine run statements?
# could run some jobs in parallel
jobs:
  migration-with-java-job:
    runs-on: ubuntu-latest
    steps:
      - name: Install Poetry
        uses: snok/install-poetry@v1.3
      - uses: actions/checkout@v3
      - name: Install dependencies
        run: poetry install --no-interaction --no-root
      - name: Install library
        run: poetry install --no-interaction
      - uses: actions/setup-java@v3
        with:
          distribution: 'corretto'
          java-version: '17'
      - run: wget https://github.com/ontodev/robot/releases/download/v1.9.5/robot.jar
      - run: wget https://raw.githubusercontent.com/ontodev/robot/master/bin/robot
      - run: sudo chmod u+x robot
      #      - run: ./robot convert --input project/owl/nmdc.owl.ttl --output project/owl/nmdc.ofn
      #      - run: ls -l project/owl/nmdc.ofn
      - uses: foooomio/setup-jena@v2
      - run: make squeaky-clean all test validate-filtered-request-all
      - run: touch local/.env # create empty .env file
      - run: make make-rdf
      #      - run: make validate-Gs0114663-study-biosample-ids
      - run: tdb2.tdbloader --loc=tdbcontent --graph=https://w3id.org/nmdc/nmdc project/owl/nmdc.owl.ttl
      - run: tdb2.tdbloader --loc=tdbcontent --graph=mongodb://mongo-loadbalancer.nmdc.production.svc.spin.nersc.gov:27017 local/mongo_as_nmdc_database_cuire_repaired.ttl
      - run: tdb2.tdbquery  --loc=tdbcontent --query=assets/sparql/tdb-test.rq
      - run: tdb2.tdbquery  --loc=tdbcontent --query=assets/sparql/tdb-graph-list.rq
      - uses: actions/upload-artifact@v3
        with:
          path: local/mongo_as_nmdc_database_cuire_repaired.ttl