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Merged
merged 3 commits into from
Jun 4, 2025
Merged

Make meta dbs #448

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8f08fd3
Make meta dbs
May 6, 2025
92af6a7
Remove meta db creation for 3.21
Jun 4, 2025
8322516
Add meta db creation for experiments, annotations
Jun 4, 2025
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11 changes: 11 additions & 0 deletions propagation/3.22/updateReposPkgs-bioc.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
11 changes: 11 additions & 0 deletions propagation/3.22/updateReposPkgs-data-annotation.sh
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Expand Up @@ -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
Expand Down Expand Up @@ -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
11 changes: 11 additions & 0 deletions propagation/3.22/updateReposPkgs-data-experiment.sh
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Expand Up @@ -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
Expand Down Expand Up @@ -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
33 changes: 33 additions & 0 deletions utils/makeMetaDbs.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
makeMetaDbs <- function(db_filepath, repos_root, meta_path) {

meat_dir <- Sys.getenv("BBS_MEAT_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_dir, pkgs)
for (pkg_path in pkg_paths) {
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)
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)
}