Merge pull request #3 from IBPA/master

updates
IBPA · Jul 9, 2021 · ad43a6e · ad43a6e
2 parents f571e29 + 651cf4a
commit ad43a6e
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Showing 4 changed files with 53 additions and 8 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 +18,18 @@ get_args <- function() {
   return(args)
 }
 
+# source the filename from this script's directory
+source_from_here <- function(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")
+
 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 +75,18 @@ 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) {
+  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")
+
 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 +43,20 @@ get_args <- function() {
   return(parser$parse_args())
 }
 
+# source the filename from this script's directory
+source_from_here <- function(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")
+
+
 args <- get_args()
 
 # 1) Load data
@@ -86,4 +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
@@ -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 +33,20 @@ get_args <- function() {
   return(parser$parse_args())
 }
 
+# source the filename from this script's directory
+source_from_here <- function(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")
+
+
 args <- get_args()
 
 # 1) Load data