Make Meta dbs

Author: jwokaty

3.20/bioc/bbscentral2/postrun.sh

@@ -32,6 +32,7 @@ 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.py
 fi
 
 # Generate the HTML report

3.21/bioc/bbscentral1/postrun.sh

@@ -32,6 +32,7 @@ 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.py
 fi
 
 # Generate the HTML report

utils/makeMetaDbs.R

@@ -0,0 +1,29 @@
+generateMetaDbs <- function(outgoing_path, db_filepath) {
+
+  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))
+
+  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])
+    }
+  }
+
+  # 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")
+  dir.create(meta_dir, recursive = TRUE)
+
+  biocViews::build_db_from_source(file.path(meat_dir, pkgs), bbs_central_rdir)
+
+  aliases_db_file <- file.path(meta_dir, "aliases.rds")
+  biocViews::build_meta_aliases_db(web_dir, aliases_db_file, TRUE)
+
+  rdxrefs_db_file <- file.path(meta_dir, "rdxrefs.rds")
+  biocViews::build_meta_rdxrefs_db(web_dir, rdxrefs_db_file, TRUE)
+}