Add makeMetaDbs with fixes (#452)

Author: jwokaty

propagation/3.22/updateReposPkgs-bioc.sh

@@ -17,6 +17,10 @@ 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="$SRC_CONTRIB/Meta"
+META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')"
+MEAT_PATH="/home/biocbuild/bbs-$BIOC_VERSION-bioc/meat"
+
 if [ ! -f "$PROPAGATION_DB_FILE" ]; then
         echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?"
         exit 1
@@ -72,6 +76,13 @@ for i in `ls $MANUALS_SRC`; do
 	mkdir -p $MANUALS_DEST/$pkg/man
 	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
 done
+echo ""
+echo "========================================================================"
+/bin/date
+echo "------------------------------------------------------------------------"
+
+echo "Updating $META_SRC with aliases and cross refences dbs..."
+$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$MEAT_PATH', '$REPOS_ROOT', '$META_SRC'))"
 
 echo "DONE."
 exit 0

propagation/3.22/updateReposPkgs-data-annotation.sh

@@ -14,6 +14,10 @@ PROPAGATION_DB_FILE="$BBS_OUTGOING_DIR/../PROPAGATION_STATUS_DB.txt"
 REPOS_ROOT="$HOME/PACKAGES/$BIOC_VERSION/data/annotation"
 SRC_CONTRIB="$REPOS_ROOT/src/contrib"
 
+META_SRC="$SRC_CONTRIB/Meta"
+META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')"
+MEAT_PATH="/home/biocbuild/bbs-$BIOC_VERSION-data-annotation/meat"
+
 if [ ! -f "$PROPAGATION_DB_FILE" ]; then
         echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?"
         exit 1
@@ -58,6 +62,13 @@ for i in `ls $MANUALS_SRC`; do
 	mkdir -p $MANUALS_DEST/$pkg/man
 	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
 done
+echo ""
+echo "========================================================================"
+/bin/date
+echo "------------------------------------------------------------------------"
+
+echo "Updating $META_SRC with aliases and cross refences dbs..."
+$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$MEAT_PATH', '$REPOS_ROOT', '$META_SRC'))"
 
 echo "DONE."
 exit 0

propagation/3.22/updateReposPkgs-data-experiment.sh

@@ -14,6 +14,10 @@ PROPAGATION_DB_FILE="$BBS_OUTGOING_DIR/../PROPAGATION_STATUS_DB.txt"
 REPOS_ROOT="$HOME/PACKAGES/$BIOC_VERSION/data/experiment"
 SRC_CONTRIB="$REPOS_ROOT/src/contrib"
 
+META_SRC="$SRC_CONTRIB/Meta"
+META_R_EXPR="source('/home/biocbuild/BBS/utils/makeMetaDbs.R')"
+MEAT_PATH="/home/biocbuild/bbs-$BIOC_VERSION-data-experiment/meat"
+
 if [ ! -f "$PROPAGATION_DB_FILE" ]; then
         echo "ERROR: $PROPAGATION_DB_FILE not found. Did postrun.sh run?"
         exit 1
@@ -58,6 +62,13 @@ for i in `ls $MANUALS_SRC`; do
 	mkdir -p $MANUALS_DEST/$pkg/man
 	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
 done
+echo ""
+echo "========================================================================"
+/bin/date
+echo "------------------------------------------------------------------------"
+
+echo "Updating $META_SRC with aliases and cross refences dbs..."
+$Rscript -e "$META_R_EXPR; try(makeMetaDbs('$PROPAGATION_DB_FILE', '$MEAT_PATH', '$REPOS_ROOT', '$META_SRC'))"
 
 echo "DONE."
 exit 0

utils/makeMetaDbs.R

@@ -0,0 +1,37 @@
+makeMetaDbs <- function(db_filepath, meat_path, repos_root, meta_path) {
+
+  prop_status <- read.dcf(db_filepath)
+
+  pkgs <- c()
+  for (i in 1:dim(prop_status)[2]) {
+    pkg_type_stage <- strsplit(colnames(prop_status)[i], "#")[[1]]
+    if ("source" %in% pkg_type_stage &&
+        strsplit(prop_status[i], ",")[[1]][1] %in% c("YES", "UNNEEDED")) {
+        pkgs <- c(pkgs, pkg_type_stage[1])
+    }
+  }
+
+  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_path, pkgs)
+  for (pkg_path in pkg_paths) {
+    tryCatch(
+      biocViews::build_db_from_source(pkg_path, repos_root),
+      error = function(e) {
+        print(paste('Failed to build db for', pkg, '-', e))
+      }
+    )
+  }
+
+  aliases_db_file <- file.path(meta_dir, "aliases.rds")
+  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)
+  saveRDS(meta_rdxrefs_db, rdxrefs_db_file, version = 2)
+}