From 651cf4a0a9452b582118c731ce7d1ba4326d0b13 Mon Sep 17 00:00:00 2001
From: Ameen Eetemadi <ameenetemady@github.com>
Date: Fri, 9 Jul 2021 14:58:18 -0700
Subject: [PATCH] source_from_here DEV_MODE

---
 R/convert_to_friendlyname_OMMs.R | 10 +++++++---
 R/generate_OMMs.R                | 10 +++++++---
 R/select_OMMs.R                  | 12 ++++++++----
 R/visualize_OMMs.R               | 10 +++++++---
 4 files changed, 29 insertions(+), 13 deletions(-)

diff --git a/R/convert_to_friendlyname_OMMs.R b/R/convert_to_friendlyname_OMMs.R
index ac6880c..390f317 100755
--- a/R/convert_to_friendlyname_OMMs.R
+++ b/R/convert_to_friendlyname_OMMs.R
@@ -20,9 +20,13 @@ get_args <- function() {
 
 # 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))
+  if (DEV_MODE){
+    source(file.path("R", filename))
+  } else {
+    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")
 
diff --git a/R/generate_OMMs.R b/R/generate_OMMs.R
index 1447896..ed3f8fc 100755
--- a/R/generate_OMMs.R
+++ b/R/generate_OMMs.R
@@ -77,9 +77,13 @@ get_proportions <- function(df_food_glycans, target_glycans){
 
 # 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))
+  if (DEV_MODE){
+    source(file.path("R", filename))
+  } else {
+    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")
 
diff --git a/R/select_OMMs.R b/R/select_OMMs.R
index b27a5f4..eea37ef 100755
--- a/R/select_OMMs.R
+++ b/R/select_OMMs.R
@@ -45,9 +45,13 @@ get_args <- function() {
 
 # 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))
+  if (DEV_MODE){
+    source(file.path("R", filename))
+  } else {
+    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")
@@ -94,4 +98,4 @@ selected_MMs <- cand_MMs[idx_selected_meals,]
 
 # 6) Save the selected mixed meals
 save_MMs(selected_MMs, args$output)
-print("Completed Successfully!")
\ No newline at end of file
+print("Completed Successfully!")
diff --git a/R/visualize_OMMs.R b/R/visualize_OMMs.R
index 1becbc6..7126168 100755
--- a/R/visualize_OMMs.R
+++ b/R/visualize_OMMs.R
@@ -35,9 +35,13 @@ get_args <- function() {
 
 # 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))
+  if (DEV_MODE){
+    source(file.path("R", filename))
+  } else {
+    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")