Make Meta dbs

Author: jwokaty

Diff for: 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

Diff for: 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

Diff for: BBS-make-meta-dbs.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+
+import sys
+import os
+import time
+import subprocess
+
+import BBSutils
+import BBSvars
+import BBSbase
+
+def make_meta():
+    ## Prepare Rexpr (must be a single string with no spaces).
+    Rscript_path = os.path.join(BBSvars.BBS_home,
+                                'utils',
+                                'generateMetaDbs.R')
+    Rfun = 'generateMetaDbs'
+    OUTGOING_dir = 'OUTGOING'
+    db_filepath = 'PROPAGATION_STATUS_DB.txt'
+    Rfuncall = f"{Rfun}('{OUTGOING_dir}','{db_filepath}')"
+    Rexpr = f"source('{Rscript_path}');{Rfuncall}"
+
+    ## Turn Rexpr into a system command.
+    cmd = BBSbase.Rexpr2syscmd(Rexpr)
+
+    try:
+        ## Nasty things (that I don't really understand) can happen with
+        ## subprocess.run() if this code is runned by the Task Scheduler
+        ## on Windows (the child process tends to almost always return an
+        ## error). Apparently using 'stderr=subprocess.STDOUT' fixes this pb.
+        subprocess.run(cmd, stdout=None, stderr=subprocess.STDOUT, shell=True,
+                       check=True)
+    except subprocess.CalledProcessError as e:
+        print(f'BBS> [generateMetaDbs] Failed at {time.asctime()} . . .')
+        print(f'BBS> [generateMetaDbs] Error: {e} . . .')
+    return
+
+
+##############################################################################
+### MAIN SECTION
+##############################################################################
+
+if __name__ == "__main__":
+    if not os.path.isfile('PROPAGATION_STATUS_DB.txt'):
+        msg = (
+            f'Make sure to be in {BBSvars.Central_rdir.path} and run '
+            f'BBS-make-PROPAGATION_STATUS_DB.py before BBS-make-meta.py.'
+        )
+        sys.exit('=> EXIT.')
+    print('BBS> ==============================================================')
+    print(f'BBS> [generateMetaDbs] STARTING on {time.asctime()} ...')
+    sys.stdout.flush()
+    generate_meta_dbs()
+    print(f'BBS> [generateMetaDbs] DONE on {time.asctime()} ...')
+

Diff for: 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)
+}