From 0ecb54aaf7917abe952b207b7921adb8770421a0 Mon Sep 17 00:00:00 2001
From: hollorol <hollorol@gmail.com>
Date: Sat, 2 Sep 2017 00:55:30 +0200
Subject: [PATCH] Creating an extended file path concatenator function

---
 RBBGCMuso/NAMESPACE                 |  1 +
 RBBGCMuso/R/cleanup.R               | 51 +++++++++--------------------
 RBBGCMuso/R/otherUsefullFunctions.R | 20 +++++++++++
 RBBGCMuso/man/file.path2.Rd         | 23 +++++++++++++
 4 files changed, 60 insertions(+), 35 deletions(-)
 create mode 100644 RBBGCMuso/man/file.path2.Rd

diff --git a/RBBGCMuso/NAMESPACE b/RBBGCMuso/NAMESPACE
index c10acaf..0d4df57 100644
--- a/RBBGCMuso/NAMESPACE
+++ b/RBBGCMuso/NAMESPACE
@@ -3,6 +3,7 @@
 export(calibMuso)
 export(cleanupMuso)
 export(corrigMuso)
+export(file.path2)
 export(getyearlycum)
 export(getyearlymax)
 export(musoDate)
diff --git a/RBBGCMuso/R/cleanup.R b/RBBGCMuso/R/cleanup.R
index 05c88df..c566690 100644
--- a/RBBGCMuso/R/cleanup.R
+++ b/RBBGCMuso/R/cleanup.R
@@ -11,59 +11,40 @@
 
 
 cleanupMuso <- function(location=NULL, simplicity=TRUE,deep=FALSE){
-    areThereAnyFolders <- FALSE
+    
+    
     whereAmI <- getwd()
     if(!is.null(location)){
         setwd(location)
     }
 
     if(deep){
-        if(dir.exists("LOG")){
-            setwd("LOG")
+
+
+        
+        if(dir.exists(paste(location,"/LOG",sep=""))){
             file.remove(
-                grep("(out$)|(endpoint$)|(log$)",
-                     list.files(), value = T))
-            areThereAnyFolders <- TRUE
+                list.files("LOG/",pattern="(out$)|(endpoint$)|(log$)", full.names=TRUE)
+         )
         }
         
-        
-        if(dir.exists("../ERROR")){
-            setwd("../ERROR")
-
+        if(dir.exists("ERROR")){
             file.remove(
-                grep("(out$)|(endpoint$)|(log$)",
-                     list.files(), value = T))
-            areThereAnyFolders <- TRUE
+                list.files("ERROR/",pattern="(out$)|(endpoint$)|(log$)", full.names=TRUE))
         }
 
-
-        if(dir.exists("../EPCS")){
-            setwd("../EPCS")
-
+        if(dir.exists("EPCS")){
             file.remove(
-                grep("(out$)|(endpoint$)|(log$)|(epc$)",
-                     list.files(), value = T))
-            areThereAnyFolder <- TRUE
+                list.files("EPCS/",pattern="(out$)|(endpoint$)|(log$)", full.names=TRUE))
         }
 
-        if(dir.exists("../WRONGEPC")){
-            setwd("../WRONGEPC")
+        if(dir.exists("WRONGEPC")){
             file.remove(
-                grep("(out$)|(endpoint$)|(log$)|(epc$)",
-                     list.files(), value = T))
-            areThereAnyFolders <- TRUE
+                list.files("WRONGEPC/",pattern="(out$)|(endpoint$)|(log$)", full.names=TRUE))
         }
 
-        if(areThereAnyFolders){
-            setwd("..")    
-            file.remove(
-                grep("(out$)|(endpoint$)|(log$)",
-                     list.files(), value = T))
-        } else {
-            file.remove(
-                grep("(out$)|(endpoint$)|(log$)",
-                     list.files(), value = T))}
-    }
+       file.remove(list.files(pattern="(out$)|(endpoint$)|(log$)",full.names=TRUE))}
+    
     
     if(!simplicity){    
         file.remove(
diff --git a/RBBGCMuso/R/otherUsefullFunctions.R b/RBBGCMuso/R/otherUsefullFunctions.R
index ddbe61f..b15f8dc 100644
--- a/RBBGCMuso/R/otherUsefullFunctions.R
+++ b/RBBGCMuso/R/otherUsefullFunctions.R
@@ -113,3 +113,23 @@ corrigMuso <- function(settings, data){
     }
     return(data)
 }
+
+#' file.path2
+#'
+#' It is an extended file.path function, it can concatenate path where the first ends and the second begins with "/", so
+#' there wont be two  slash nearby eachother
+#' @author Roland Hollos
+#' @param str1 This is the first path string
+#' @param str2 This is the second path string
+#' @return A concatenated path
+#' @export
+#' @usage file.path2(str1, str2)
+
+file.path2<-function(str1, str2){
+    str1<-file.path(dirname(str1),basename(str1))
+    if(substring(str2,1,1)=="/"){
+        return(paste(str1,str2,sep=""))
+    } else{
+        return(file.path(str1,str2))
+    }
+} 
diff --git a/RBBGCMuso/man/file.path2.Rd b/RBBGCMuso/man/file.path2.Rd
new file mode 100644
index 0000000..f243191
--- /dev/null
+++ b/RBBGCMuso/man/file.path2.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/otherUsefullFunctions.R
+\name{file.path2}
+\alias{file.path2}
+\title{file.path2}
+\usage{
+file.path2(str1, str2)
+}
+\arguments{
+\item{str1}{This is the first path string}
+
+\item{str2}{This is the second path string}
+}
+\value{
+A concatenated path
+}
+\description{
+It is an extended file.path function, it can concatenate path where the first ends and the second begins with "/", so
+there wont be two  slash nearby eachother
+}
+\author{
+Roland Hollos
+}