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change getEunomiaConnectionDetails so that it only downloads datasets if they have not been previously downloaded. #176

change getEunomiaConnectionDetails so that it only downloads datasets if they have not been previously downloaded.

change getEunomiaConnectionDetails so that it only downloads datasets if they have not been previously downloaded. #176

# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
push:
branches:
- '**'
pull_request:
branches:
- '**'
name: R-CMD-check
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: windows-latest, r: 'release'}
- {os: macOS-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
env:
GITHUB_PAT: ${{ secrets.GH_TOKEN }}
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
CDM5_POSTGRESQL_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }}
CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
CDM5_SQL_SERVER_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }}
CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
CDM5_REDSHIFT_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }}
CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
CDM_SNOWFLAKE_CDM53_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_CDM53_SCHEMA }}
CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }}
CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }}
CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }}
CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}
CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }}
CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }}
CDM_BIG_QUERY_CONNECTION_STRING: ${{ secrets.CDM_BIG_QUERY_CONNECTION_STRING }}
CDM_BIG_QUERY_KEY_FILE: ${{ secrets.CDM_BIG_QUERY_KEY_FILE }}
CDM_BIG_QUERY_CDM_SCHEMA: ${{ secrets.CDM_BIG_QUERY_CDM_SCHEMA }}
CDM_BIG_QUERY_OHDSI_SCHEMA: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }}
steps:
- uses: actions/checkout@v3
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-tinytex@v2
- uses: r-lib/actions/setup-pandoc@v2
- name: Install system requirements
if: runner.os == 'Linux'
run: |
sudo apt-get install -y libssh-dev
Rscript -e 'install.packages("remotes")'
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check
- uses: r-lib/actions/check-r-package@v2
with:
args: 'c("--no-manual", "--as-cran")'
error-on: '"warning"'
check-dir: '"check"'
- name: Upload source package
if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
uses: actions/upload-artifact@v4
with:
name: package_tarball
path: check/*.tar.gz
- name: Install covr
if: runner.os == 'macOS'
run: |
install.packages("covr")
shell: Rscript {0}
- name: Test coverage
if: runner.os == 'macOS'
run: covr::codecov()
shell: Rscript {0}
Release:
needs: R-CMD-Check
runs-on: macOS-latest
env:
GH_TOKEN: ${{ secrets.GH_TOKEN }}
if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }}
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Check if version has increased
run: |
echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV
- name: Display new version number
if: ${{ env.new_version != '' }}
run: |
echo "${{ env.new_version }}"
- name: Create release
if: ${{ env.new_version != '' }}
uses: actions/create-release@v1
env:
GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
with:
tag_name: ${{ env.new_version }}
release_name: Release ${{ env.new_version }}
body: |
See NEWS.md for release notes.
draft: false
prerelease: false
- uses: r-lib/actions/setup-r@v2
if: ${{ env.new_version != '' }}
- name: Install drat
if: ${{ env.new_version != '' }}
run: |
install.packages('drat')
shell: Rscript {0}
- name: Remove any tarballs that already exists
if: ${{ env.new_version != '' }}
run: |
rm -f *.tar.gz
- name: Download package tarball
if: ${{ env.new_version != '' }}
uses: actions/download-artifact@v2
with:
name: package_tarball
- name: Push to drat
if: ${{ env.new_version != '' }}
run: |
bash deploy.sh
- name: Push to BroadSea
if: ${{ env.new_version != '' }}
run: |
curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/