Move rds creation to propagation step

Author: jwokaty

3.20/bioc/bbscentral2/postrun.sh

@@ -32,7 +32,6 @@ if [ -n "$BBS_OUTGOING_MAP" ]; then
     find OUTGOING -type d -exec chmod 755 {} \;
     $BBS_PYTHON_CMD $BBS_HOME/BBS-make-PROPAGATION_STATUS_DB.py
     chmod -R +r .
-    $BBS_PYTHON_CMD $BBS_HOME/BBS-make-meta-dbs.py
 fi
 
 # Generate the HTML report

3.21/bioc/bbscentral1/postrun.sh

@@ -32,7 +32,6 @@ if [ -n "$BBS_OUTGOING_MAP" ]; then
     find OUTGOING -type d -exec chmod 755 {} \;
     $BBS_PYTHON_CMD $BBS_HOME/BBS-make-PROPAGATION_STATUS_DB.py
     chmod -R +r .
-    $BBS_PYTHON_CMD $BBS_HOME/BBS-make-meta-dbs.py
 fi
 
 # Generate the HTML report

BBS-make-meta-dbs.py

@@ -58,6 +58,16 @@ update_repo "$MAC_BIG_SUR_arm64_CONTRIB" "mac.binary.big-sur-arm64" "tgz"
 
 echo ""
 
+echo ""
+echo "========================================================================"
+/bin/date
+echo "------------------------------------------------------------------------"
+
+$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$REPOS_ROOT', '$META_SRC'))"
+
+echo ""
+
+
 ## FIXME: Why aren't manuals propagated based on the same criteria as source
 ## packages? Looks like the former are propagated based on their timestamps
 ## only (see below) while for source packages we use the more refined
@@ -68,13 +78,12 @@ MANUALS_DEST="$REPOS_ROOT/manuals"
 MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
 echo "Updating $BIOC_VERSION/bioc repo with reference manuals..."
 for i in `ls $MANUALS_SRC`; do
-	pkg=`echo $i| awk '{split($0,a,".pdf"); print(a[1])}'`
+	pkg=`echo $i| awk '{split($0,a,".(html|pdf)"); print(a[1])}'`
 	mkdir -p $MANUALS_DEST/$pkg/man
 	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
 done
 
 echo "Updating $SRC_CONTRIB with aliases and cross references dbs ..."
-META_SRC="$BBS_OUTGOING_DIR/Meta"
 cp --recursive --update --verbose $META_SRC $SRC_CONTRIB
 
 echo "DONE."

propagation/3.20/updateReposPkgs-bioc.sh

@@ -17,6 +17,9 @@ WIN_CONTRIB="$REPOS_ROOT/bin/windows/contrib/$R_VERSION"
 MAC_BIG_SUR_x86_64_CONTRIB="$REPOS_ROOT/bin/macosx/big-sur-x86_64/contrib/$R_VERSION"
 MAC_BIG_SUR_arm64_CONTRIB="$REPOS_ROOT/bin/macosx/big-sur-arm64/contrib/$R_VERSION"
 
+META_SRC="$SRC_CONTRIB/Meta"
+META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')"
+
 if [ ! -f "$PROPAGATION_DB_FILE" ]; then
         echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?"
         exit 1
@@ -58,6 +61,16 @@ update_repo "$MAC_BIG_SUR_arm64_CONTRIB" "mac.binary.big-sur-arm64" "tgz"
 
 echo ""
 
+echo ""
+echo "========================================================================"
+/bin/date
+echo "------------------------------------------------------------------------"
+
+$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$REPOS_ROOT', '$META_SRC'))"
+
+echo ""
+
+
 ## FIXME: Why aren't manuals propagated based on the same criteria as source
 ## packages? Looks like the former are propagated based on their timestamps
 ## only (see below) while for source packages we use the more refined
@@ -74,7 +87,6 @@ for i in `ls $MANUALS_SRC`; do
 done
 
 echo "Updating $SRC_CONTRIB with aliases and cross references dbs ..."
-META_SRC="$BBS_OUTGOING_DIR/Meta"
 cp --recursive --update --verbose $META_SRC $SRC_CONTRIB
 
 echo "DONE."

propagation/3.21/updateReposPkgs-bioc.sh

@@ -1,8 +1,7 @@
-makeMetaDbs <- function(outgoing_path, db_filepath) {
+makeMetaDbs <- function(db_filepath, repos_root, meta_path) {
 
   meat_dir <- Sys.getenv("BBS_MEAT_PATH")
-  bbs_central_rdir <- Sys.getenv("BBS_CENTRAL_RDIR")
-  prop_status <- read.dcf(file.path(bbs_central_rdir, db_filepath))
+  prop_status <- read.dcf(db_filepath)
 
   pkgs <- c()
   for (i in 1:dim(prop_status)[2]) {
@@ -13,26 +12,22 @@ makeMetaDbs <- function(outgoing_path, db_filepath) {
     }
   }
 
-  # Because the location is always recreated, we always create the Meta
-  # directory and always create all the databases
-  web_dir <- file.path(bbs_central_rdir, "web", "packages")
-  meta_dir <- file.path(bbs_central_rdir, "OUTGOING", "Meta")
+  web_dir <- file.path(repos_root "web", "packages")
+  meta_dir <- file.path(meta_path)
   if (!dir.exists(meta_dir)) {
     dir.create(meta_dir, recursive = TRUE)
   }
 
   pkg_paths <- file.path(meat_dir, pkgs)
   for (pkg_path in pkg_paths) {
-    biocViews::build_db_from_source(pkg_path, bbs_central_rdir)
+    biocViews::build_db_from_source(pkg_path, repos_root)
   }
 
   aliases_db_file <- file.path(meta_dir, "aliases.rds")
-  meta_aliases_db <- biocViews::build_meta_aliases_db(web_dir, aliases_db_file,
-                                                      TRUE)
+  meta_aliases_db <- biocViews::build_meta_aliases_db(web_dir, aliases_db_file)
   saveRDS(meta_aliases_db, aliases_db_file, version = 2)
 
   rdxrefs_db_file <- file.path(meta_dir, "rdxrefs.rds")
-  meta_rdxrefs_db <- biocViews::build_meta_rdxrefs_db(web_dir, rdxrefs_db_file,
-                                                      TRUE)
+  meta_rdxrefs_db <- biocViews::build_meta_rdxrefs_db(web_dir, rdxrefs_db_file)
   saveRDS(meta_rdxrefs_db, rdxrefs_db_file, version = 2)
 }