Merge branch 'ccsbase-integration' into 'master'

pcl: pb-lite-driver: Add new phase buildccs

See merge request !12

pubchemlite/R/add_ccs2csv.R

@@ -7,37 +7,20 @@
 require(data.table)
 require(assertthat)
 require(yaml)
-USAGE_STRING <- "Rscript [--vanilla] add_ccs2csv.R <input ccs csv> <input metfrag csv> <output metfrag csv>"
+USAGE_STRING <- "Rscript [--vanilla] add_ccs2csv.R <pubchemlite input file> <input metfrag csv> <output metfrag csv>"
 
 SEL_ADDUCTS <- NULL # Change to adducts needed, if a subset of adducts
                     # desired. Otherwise, all shall be returned.
 
 
-## Alternative way of adding arguments, read from FN_CONFIG with these
-## contents.
-## 
-## config:
-##   - fn_ccs: ...
-##   - fn_mf_csv: ...
-##   - fn_mf_res_csv: ...
-
-FN_CONFIG <- "add_ccs2csv.yaml"
-
-
+dir_start <- Sys.getenv("STARTDIR")
 args <- commandArgs(trailingOnly = T)
-
-if (length(args) == 3) {
-    fn_ccs <- args[[1]]
-    fn_mf_csv <- args[[2]]
-    fn_mf_res_csv <- args[[3]]
-    
-} else {
-    x <- yaml::yaml.load_file(FN_CONFIG)
-    fn_ccs <- x$config$fn_ccs
-    fn_mf_csv <- x$config$fn_mf_csv
-    fn_mf_res_csv <- x$config$$fn_mf_res_csv
-
-}
+fn_config <- args[[1]]
+if (!file.exists(fn_config)) stop("Config file", fn_config," does not exist.")
+x <- yaml::yaml.load_file(fn_config)
+fn_ccs <- file.path(dir_start,x$ccs_src_path)
+fn_mf_csv <- args[[2]]
+fn_mf_res_csv <- args[[3]]
 
 
 message("Input CCS file: ",fn_ccs)

pubchemlite/pb-lite-driver.sh

 declare -gx INPUTDIR
-declare -agx ALL_STAGES=( "cleanup" "prepare" "fetch_scripts_sources" "build" "sanity_postbuild" "eval4pub" "quotes" "epilog")
+declare -agx ALL_STAGES=( "cleanup" "prepare" "fetch_scripts_sources" "build" "quotes" "buildccs" "sanity_postbuild" "eval4pub" "epilog")
 declare -a STAGES
 STAGES=() 			# Which stages should be run.
 
@@ -54,6 +54,10 @@ function finputdir() {
     declare -gx OUTMFFILE=$(basename "${MAPFILE%.map}_$(date +%Y%m%d).csv")
     declare -gx OUTMFCLONE=$(basename "${MAPFILE%.map}.csv")
 
+    # CCS filename.
+    declare -gx OUTMFCCSFILE=$(basename "${MAPFILE%.map}_CCSBase_$(date +%Y%m%d).csv")
+    declare -gx OUTMFCCCSCLONE=$(basename "${MAPFILE%.map}_CCSBase.csv")
+
 
     # Does manifest exist?
     [ ! -e "$MANIF" ] && fatal "(pb-lite-driver.sh): Manifest file $MANIF not found, or unreadable."
@@ -118,6 +122,13 @@ function build() {
     (cd "$WORKDIR"; source "${SCRIPTDIR}/generate" "$FILTERFILE" "$LEGENDFILE")
     footer BUILD
 }
+
+function buildccs() {
+    header BUILDCCS
+    (export STARTDIR="$PWD";cd "$WORKDIR"; Rscript --vanilla "${SCRIPTDIR}/R/add_ccs2csv.R" "$STARTDIR/$MANIF" "$WORKDIR/$OUTMFFILE" "$WORKDIR/$OUTMFCCSFILE")
+    footer BUILDCCS
+}
+
 function quotes() {
     header FIX TRIPLE QUOTES IN MZ
     (cd "WORKDIR"; ${SCRIPTDIR}/fix_mass_quotes.R "$WORKDIR/$OUTMFFILE")
@@ -204,6 +215,12 @@ for stage in "${STAGES[@]}";do
 	"build")
 	    build
 	    ;;
+	"quotes")
+	    quotes
+	    ;;
+	"buildccs")
+	    buildccs
+	    ;;
 	"sanity_postbuild")
 	    header POST-BUILD CHECK
 	    "${SCRIPTDIR}"/sanity_postbuild
@@ -214,9 +231,6 @@ for stage in "${STAGES[@]}";do
 	    (cd "$WORKDIR"; source "${SCRIPTDIR}/eval4pub.sh")
 	    footer EVAL4PUB CHECK
 	    ;;
-	"quotes")
-	    quotes
-	    ;;
 	"epilog")
 	    epilog
 	    ;;