Commit 3da1c424 authored by Todor Kondic's avatar Todor Kondic
Browse files

Merge branch 'ccsbase-integration' into 'master'

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

See merge request !12
parents 13422631 6e43f94b
......@@ -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$ccs_src_path)
fn_mf_csv <- args[[2]]
fn_mf_res_csv <- args[[3]]
message("Input CCS file: ",fn_ccs)
......
declare -gx INPUTDIR
declare -agx ALL_STAGES=( "cleanup" "prepare" "fetch_scripts_sources" "build" "sanity_postbuild" "eval4pub" "quotes" "epilog")
declare -agx ALL_STAGES=( "cleanup" "prepare" "fetch_scripts_sources" "build" "quotes" "buildccs" "sanity_postbuild" "eval4pub" "epilog")
declare -a STAGES
STAGES=() # Which stages should be run.
......@@ -54,6 +54,10 @@ function finputdir() {
declare -gx OUTMFFILE=$(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
;;
......
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