Export Data #10
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| name: Export Data | |
| on: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| OPENBIS_V3: https://localhost:8128/openbis/openbis/rmi-application-server-v3.json | |
| 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: ${{ github.event.pull_request.head.ref }} | |
| submodules: recursive | |
| - name: run app | |
| run: | | |
| touch .env | |
| echo ADMIN_PASS=example >> .env | |
| echo OBSERVER_PASS=example >> .env | |
| echo HOST_NAME=127.0.0.1 >> .env | |
| echo OPENBIS_PORT=8127 >> .env | |
| echo OPENBIS_SSL_PORT=8128 >> .env | |
| echo POSTGRES_PASSWORD=example >> .env | |
| echo GROUP_NAME=openbis >> .env | |
| echo GROUP_ID=1000 >> .env | |
| echo OPENBISMANTIC_URL=https://openbis.matolab.orf >> .env | |
| docker compose up -d | |
| docker compose logs -f init_database | |
| docker compose exec -t init_database sleep 10000 | |
| - name: Update exported data | |
| run: | | |
| rm -rf exported_data | |
| mkdir -p exported_data | |
| token=$(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 -d "{\"method\": \"executeCustomASService\", \"params\": [\"${token}\", {\"@id\": 0, \"permId\": \"openbismantic-api\", \"@type\": \"as.dto.service.id.CustomASServiceCode\"}, {\"@id\": 0, \"parameters\": {\"method\": \"recursiveExport\", \"permID\": \"${permId}\"}, \"@type\": \"as.dto.service.CustomASServiceExecutionOptions\"}], \"id\": \"1\", \"jsonrpc\": \"2.0\"}" ${{env.OPENBIS_V3}} | jq -r '.result') | |
| filename=$(echo $result | jq -r ".[\"${permId}\"].identifier.identifier" | sed 's|^/||;s|/|_|g') | |
| echo $result >> "exported_data/${filename}.json" | |
| done | |
| - name: commit results | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| message: 'update exported data' | |
| add: '*.* --force' | |
| cwd: './exported_data/' |