add arachne folder #44
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| on: | |
| push: | |
| branches: main | |
| pull_request: | |
| branches: main | |
| name: Test CDMConnector cdm_from_environment | |
| jobs: | |
| CDMConnector: | |
| if: github.repository == 'darwin-eu-dev/AnalysisLibrary' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Cache Docker image layers | |
| id: cache-docker | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| /var/lib/docker | |
| key: ${{ runner.os }}-executionengine.azurecr.io/darwin-base:v0.1 | |
| - name: check cach hit | |
| run: echo ${{ steps.cache-docker.outputs.cache-hit }} | |
| - if: ${{ steps.cache-docker.outputs.cache-hit != 'true' }} | |
| name: pull docker image | |
| run: docker pull executionengine.azurecr.io/darwin-base:v0.1 | |
| - name: Run postgres test | |
| run: | | |
| docker run --rm \ | |
| -e DBMS_TYPE=postgresql \ | |
| -e DATA_SOURCE_NAME=synpuf \ | |
| -e CDM_VERSION=5.3 \ | |
| -e DBMS_SERVER=${{ secrets.POSTGRESQL_SERVER }} \ | |
| -e DBMS_PORT=${{ secrets.POSTGRESQL_PORT }} \ | |
| -e DBMS_NAME=${{ secrets.POSTGRESQL_DBNAME }} \ | |
| -e DBMS_USER=${{ secrets.POSTGRESQL_USER }} \ | |
| -e DBMS_PASSWORD=${{ secrets.POSTGRESQL_PASSWORD }} \ | |
| -e CDM_SCHEMA=${{ secrets.POSTGRESQL_CDM_SCHEMA }} \ | |
| -e WRITE_SCHEMA=${{ secrets.POSTGRESQL_SCRATCH_SCHEMA }} \ | |
| -v $(pwd)/TestCDMConnector:/tmp/TestCDMConnector \ | |
| executionengine.azurecr.io/darwin-base:v0.1 \ | |
| R -e 'setwd("/tmp/TestCDMConnector"); source("main.R")' | |
| - name: Run snowflake test | |
| run: | | |
| docker run --rm \ | |
| -e DBMS_TYPE=snowflake \ | |
| -e DATA_SOURCE_NAME=synpuf \ | |
| -e CDM_VERSION=5.3 \ | |
| -e DBMS_SERVER=${{ secrets.SNOWFLAKE_SERVER }} \ | |
| -e DBMS_PORT=443 \ | |
| -e DBMS_NAME=OMOP_SYNTHETIC_DATASET \ | |
| -e DBMS_USER=${{ secrets.SNOWFLAKE_USER }} \ | |
| -e DBMS_PASSWORD=${{ secrets.SNOWFLAKE_PASSWORD }} \ | |
| -e DBMS_CATALOG=${{ secrets.SNOWFLAKE_WAREHOUSE }} \ | |
| -e CDM_SCHEMA=${{ secrets.SNOWFLAKE_CDM_SCHEMA }} \ | |
| -e WRITE_SCHEMA=${{ secrets.SNOWFLAKE_SCRATCH_SCHEMA }} \ | |
| -v $(pwd)/TestCDMConnector:/tmp/TestCDMConnector \ | |
| executionengine.azurecr.io/darwin-base:v0.1 \ | |
| R -e 'setwd("/tmp/TestCDMConnector"); source("main.R")' | |
| # -e DBMS_NAME=${{ secrets.SNOWFLAKE_DBNAME }} \ | |