From 8a9f216d2bd387b56f78aa06f5a4c0c0f6568753 Mon Sep 17 00:00:00 2001
From: Ameen Eetemadi <ameenetemady@github.com>
Date: Fri, 9 Jul 2021 13:35:58 -0700
Subject: [PATCH] source from script's directory

---
 R/convert_to_friendlyname_OMMs.R | 10 ++++++++--
 R/generate_OMMs.R                |  9 ++++++++-
 R/select_OMMs.R                  | 12 ++++++++++--
 R/visualize_OMMs.R               | 12 ++++++++++--
 4 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/R/convert_to_friendlyname_OMMs.R b/R/convert_to_friendlyname_OMMs.R
index 7f162db..ac6880c 100755
--- 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
index 123d6fc..1447896 100755
--- 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
index a16f0d0..b27a5f4 100755
--- 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
index e70b6ab..1becbc6 100755
--- 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