Updating release scripts

.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/
-

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 = <GIT_VERSION>;
 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 = <GIT_TAG>) {
-		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 = <GIT_PUSH>) {
-		print "push: $line";
-	} # TODO Check for errors
-	close(GIT_PUSH);
-	print "push: END\n\n";
+	$new_version = "";
 }
 
-exit($monotonic);
+print($new_version);

deploy.sh

@@ -3,26 +3,28 @@ 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 "[email protected]"
+  git config user.name "Martijn Schuemie"
+  git config user.email "[email protected]"
   git config --global push.default simple
 
   ## Get drat repo
   git remote add upstream "https://$GH_TOKEN@github.com/OHDSI/drat.git"
   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
 
 }