From 8f08fd360154abdbedd579e5e0cf1e7c5c5a3028 Mon Sep 17 00:00:00 2001
From: A Wokaty <awokaty@users.noreply.github.com>
Date: Tue, 6 May 2025 16:23:29 -0400
Subject: [PATCH 1/3] Make meta dbs

---
 propagation/3.21/updateReposPkgs-bioc.sh | 11 ++++++++
 propagation/3.22/updateReposPkgs-bioc.sh | 11 ++++++++
 utils/makeMetaDbs.R                      | 33 ++++++++++++++++++++++++
 3 files changed, 55 insertions(+)
 create mode 100644 utils/makeMetaDbs.R

diff --git a/propagation/3.21/updateReposPkgs-bioc.sh b/propagation/3.21/updateReposPkgs-bioc.sh
index 63648e99..5eae549c 100755
--- a/propagation/3.21/updateReposPkgs-bioc.sh
+++ b/propagation/3.21/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
diff --git a/propagation/3.22/updateReposPkgs-bioc.sh b/propagation/3.22/updateReposPkgs-bioc.sh
index ba4aeccd..60b65810 100755
--- a/propagation/3.22/updateReposPkgs-bioc.sh
+++ b/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
diff --git a/utils/makeMetaDbs.R b/utils/makeMetaDbs.R
new file mode 100644
index 00000000..ec0926a1
--- /dev/null
+++ b/utils/makeMetaDbs.R
@@ -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)
+}

From 92af6a72909a83a93402e915d76c9516e001ead3 Mon Sep 17 00:00:00 2001
From: A Wokaty <awokaty@users.noreply.github.com>
Date: Wed, 4 Jun 2025 09:54:45 -0400
Subject: [PATCH 2/3] Remove meta db creation for 3.21

---
 propagation/3.21/updateReposPkgs-bioc.sh | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/propagation/3.21/updateReposPkgs-bioc.sh b/propagation/3.21/updateReposPkgs-bioc.sh
index 5eae549c..63648e99 100755
--- a/propagation/3.21/updateReposPkgs-bioc.sh
+++ b/propagation/3.21/updateReposPkgs-bioc.sh
@@ -17,10 +17,6 @@ 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
@@ -76,13 +72,6 @@ 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

From 8322516a91c5bf73401182eb5c7726eaf769c3df Mon Sep 17 00:00:00 2001
From: A Wokaty <awokaty@users.noreply.github.com>
Date: Wed, 4 Jun 2025 09:55:07 -0400
Subject: [PATCH 3/3] Add meta db creation for experiments, annotations

---
 propagation/3.22/updateReposPkgs-data-annotation.sh | 11 +++++++++++
 propagation/3.22/updateReposPkgs-data-experiment.sh | 11 +++++++++++
 2 files changed, 22 insertions(+)

diff --git a/propagation/3.22/updateReposPkgs-data-annotation.sh b/propagation/3.22/updateReposPkgs-data-annotation.sh
index da8d1316..01bd5b6a 100755
--- a/propagation/3.22/updateReposPkgs-data-annotation.sh
+++ b/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
diff --git a/propagation/3.22/updateReposPkgs-data-experiment.sh b/propagation/3.22/updateReposPkgs-data-experiment.sh
index ffaa53ab..35ba19e6 100755
--- a/propagation/3.22/updateReposPkgs-data-experiment.sh
+++ b/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