source_from_here DEV_MODE

IBPA · Jul 9, 2021 · 651cf4a · 651cf4a
1 parent 8a9f216
commit 651cf4a
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Showing 4 changed files with 29 additions and 13 deletions.
diff --git 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
@@ -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
@@ -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!")
+print("Completed Successfully!")
diff --git 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")