Export Data #6
Workflow file for this run
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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: ${{ github.event.pull_request.head.ref }} | |
submodules: recursive | |
- name: run app | |
run: | | |
touch .env | |
echo ADMIN_PASS=example >> .env | |
echo HOST_NAME=127.0.0.1 >> .env | |
echo OPENBIS_PORT=8127 >> .env | |
echo POSTGRES_PASSWORD=example >> .env | |
echo GROUP_NAME=openbis >> .env | |
echo GROUP_ID=1000 >> .env | |
echo OPENBIS_SSL_PORT=8128 >> .env | |
docker-compose up -d | |
docker-compose logs -f init_database | |
docker-compose exec -t init_database sleep 10000 | |
- name: Update exported data | |
run: | | |
rm -rf exported_data | |
mkdir -p exported_data | |
token=$(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/' |