From 0f95ce9bfba8032e91df593538d8e508189db650 Mon Sep 17 00:00:00 2001 From: schuemie Date: Wed, 27 Mar 2024 08:54:34 +0100 Subject: [PATCH] Updating release scripts --- .github/workflows/R_CMD_check_Hades.yaml | 20 +++++++--- compare_versions | 47 ++---------------------- deploy.sh | 12 +++--- 3 files changed, 25 insertions(+), 54 deletions(-) diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml index fe6bcdf..21b362b 100644 --- a/.github/workflows/R_CMD_check_Hades.yaml +++ b/.github/workflows/R_CMD_check_Hades.yaml @@ -28,29 +28,40 @@ jobs: GITHUB_PAT: ${{ secrets.GH_TOKEN }} R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} - CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }} + 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_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }} + 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_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }} + 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_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }} + 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 @@ -169,4 +180,3 @@ jobs: 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/ - diff --git a/compare_versions b/compare_versions index 0d451b2..54e5fea 100644 --- a/compare_versions +++ b/compare_versions @@ -9,8 +9,6 @@ $r_major = $1; $r_minor = $2; $r_mod = $3; -print "New R version: $r_major-$r_minor-$r_mod\n"; - open(GIT_VERSION, "git describe --tags |"); $git = ; close(GIT_VERSION); @@ -20,49 +18,10 @@ $git_major = $1; $git_minor = $2; $git_mod = $3; -print "Current git version: $git_major-$git_minor-$git_mod\n"; - if ($r_major > $git_major || $r_minor > $git_minor || $r_mod > $git_mod) { - $monotonic = 0; + $new_version = "v$r_major.$r_minor.$r_mod"; } else { - $monotonic = -1; -} - -if ($monotonic != 0) { - print "Non-monotonically increasing versions numbers\n"; -} - -if ($monotonic == 0 & $ARGV[0] eq "--tag") { - - open(GIT_TAG, "git tag v$r_major.$r_minor.$r_mod |"); - - $fail = 0; - while ($line = ) { - if ($line =~ /fatal/) { - $fail = 1; - } - print "tag: $line"; - } # TODO Check for errors - close(GIT_TAG); - print "tag: END\n\n"; - - if ($fail eq 1) { - exit(-1); - } - - $cmd = "git config user.name \"Marc A. Suchard\"; " . - "git config user.email \"msuchard@ucla.edu\"; " . - "git tag v$r_major.$r_minor.$r_mod ; " . - "git push -q https://\$GH_TOKEN\@github.com/OHDSI/\$PKG_NAME.git --tags"; - - print "cmd: $cmd\n"; - - open(GIT_PUSH, "$cmd |"); - while ($line = ) { - print "push: $line"; - } # TODO Check for errors - close(GIT_PUSH); - print "push: END\n\n"; + $new_version = ""; } -exit($monotonic); +print($new_version); diff --git a/deploy.sh b/deploy.sh index d453ed0..b056f27 100644 --- a/deploy.sh +++ b/deploy.sh @@ -3,12 +3,15 @@ set -o errexit -o nounset addToDrat(){ PKG_REPO=$PWD + ## Build package tar ball + export PKG_TARBALL=$(ls *.tar.gz) + cd ..; mkdir drat; cd drat ## Set up Repo parameters git init - git config user.name "Marc A. Suchard" - git config user.email "msuchard@ucla.edu" + git config user.name "Martijn Schuemie" + git config user.email "schuemie@ohdsi.org" git config --global push.default simple ## Get drat repo @@ -16,13 +19,12 @@ addToDrat(){ git fetch upstream 2>err.txt git checkout gh-pages - ## Install drat - mkdir -p ~/Rlib + ## Link to local R packages echo 'R_LIBS=~/Rlib' > .Renviron Rscript -e "drat::insertPackage('$PKG_REPO/$PKG_TARBALL', \ repodir = '.', \ - commit='Travis update: $PKG_TARBALL build $TRAVIS_BUILD_NUMBER commit $TRAVIS_REPO_SLUG@$TRAVIS_COMMIT')" + commit='GitHub Actions release: $PKG_TARBALL run $GITHUB_RUN_ID')" git push }