source from script's directory

IBPA · Jul 9, 2021 · 8a9f216 · 8a9f216
1 parent 5d0d461
commit 8a9f216
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Showing 4 changed files with 36 additions and 7 deletions.
diff --git a/R/convert_to_friendlyname_OMMs.R b/R/convert_to_friendlyname_OMMs.R
@@ -4,8 +4,6 @@
 suppressPackageStartupMessages(library("argparse"))
 library(stringr)
 
-source("common_OMMs.R")
-
 get_args <- function() {
   parser <- ArgumentParser(description = "Use friendly food names instead of uids for the OMMs.")
   parser$add_argument("--glycanDB", required=TRUE,
@@ -20,6 +18,14 @@ get_args <- function() {
   return(args)
 }
 
+# source the filename from this script's directory
+source_from_here <- function(filename) {
+  initial.options <- commandArgs(trailingOnly = FALSE)
+  script.name <- sub("--file=", "", initial.options[grep("--file=", initial.options)])
+  source(file.path(dirname(script.name), filename))
+}
+source_from_here("common_OMMs.R")
+
 args <- get_args()
 
 # 1) Load mixed-meals

diff --git a/R/generate_OMMs.R b/R/generate_OMMs.R
@@ -7,7 +7,6 @@ library(readxl)
 library(stringr)
 library(gurobi)
 
-source("common_OMMs.R")
 DEV_MODE <- FALSE
 
 # Parse and return command line arguments of this script (return defaults if DEV_MODE is TRUE).
@@ -76,6 +75,14 @@ get_proportions <- function(df_food_glycans, target_glycans){
   return(result$x[1:n])
 }
 
+# source the filename from this script's directory
+source_from_here <- function(filename) {
+  initial.options <- commandArgs(trailingOnly = FALSE)
+  script.name <- sub("--file=", "", initial.options[grep("--file=", initial.options)])
+  source(file.path(dirname(script.name), filename))
+}
+source_from_here("common_OMMs.R")
+
 args <- get_args()
 
 # 1) Load food data

diff --git a/R/select_OMMs.R b/R/select_OMMs.R
@@ -9,8 +9,6 @@ library(ggplot2)
 library(reshape2)
 library(scales)
 
-source("common_OMMs.R")
-source("theme_util_OMMs.R")
 DEV_MODE <- FALSE
 
 # Parse and return command line arguments of this script (return defaults if DEV_MODE is TRUE).
@@ -45,6 +43,16 @@ get_args <- function() {
   return(parser$parse_args())
 }
 
+# source the filename from this script's directory
+source_from_here <- function(filename) {
+  initial.options <- commandArgs(trailingOnly = FALSE)
+  script.name <- sub("--file=", "", initial.options[grep("--file=", initial.options)])
+  source(file.path(dirname(script.name), filename))
+}
+source_from_here("common_OMMs.R")
+source_from_here("theme_util_OMMs.R")
+
+
 args <- get_args()
 
 # 1) Load data

diff --git a/R/visualize_OMMs.R b/R/visualize_OMMs.R
@@ -9,8 +9,6 @@ library(ggplot2)
 library(reshape2)
 library(scales)
 
-source("common.R")
-source("theme_util.R")
 DEV_MODE <- FALSE
 
 # Parse and return command line arguments of this script (return defaults if DEV_MODE is TRUE).
@@ -35,6 +33,16 @@ get_args <- function() {
   return(parser$parse_args())
 }
 
+# source the filename from this script's directory
+source_from_here <- function(filename) {
+  initial.options <- commandArgs(trailingOnly = FALSE)
+  script.name <- sub("--file=", "", initial.options[grep("--file=", initial.options)])
+  source(file.path(dirname(script.name), filename))
+}
+source_from_here("common_OMMs.R")
+source_from_here("theme_util_OMMs.R")
+
+
 args <- get_args()
 
 # 1) Load data